The Hebrew University of Jerusalem Edmond Safra Campus, Jerusalem 91904, Israel

THE FRITZ HABER CENTER for MOLECULAR DYNAMICS

http://www.fh.huji.ac.il

Annual Science and Activity Report January – December 2005

Presented to the Advisory Scientific Committee, the Beirat:

Professors W. Domcke (Chair), H. Grubmüller, G. Meijer, H. Bercovier, M. Asscher, N. Moiseyev, A. Nitzan

By the members of the Fritz Haber Center:

Professors A. Ben-Shaul (Director), N. Agmon, V. Buch, R.B. Gerber, R. Kosloff, R.D. Levine

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Jerusalem, January 2006 Contents:

I Annual Science Progress Report, 2005 3

1 Overview 3

2 Individual Research Progress Reports 6 2.1 Noam Agmon ...... 7 2.2 Avinoam Ben-Shaul ...... 12 2.3 Victoria Buch ...... 20 2.4 Robert B. Gerber ...... 26 2.5 Ronnie Kosloff ...... 28 2.6 Raphael D. Levine ...... 32

II Status Report 41

3 Background 42 3.1 Brief history of the center ...... 42 3.2 Scientific scope ...... 43 3.3 Academic activities ...... 44 3.4 Personnel ...... 45 3.5 Interaction with the Institute of Chemistry ...... 45 3.6 The computer unit ...... 45 3.7 The Beirat ...... 46

4 Update 47 4.1 Research and support staff ...... 47 4.2 Symposia supported by the Center ...... 48

III Appendices 51

5 List of visitors and seminars 52

6 Publications 67 6.1 Noam Agmon ...... 67 6.2 Avinoam Ben-Shaul ...... 71 6.3 Victoria Buch ...... 74 6.4 Robert B. Gerber ...... 77 6.5 Ronnie Kosloff ...... 83 6.6 Raphael D. Levine ...... 88

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Part I

Annual Science Progress Report, 2005

1. Overview

The Fritz Haber Center, which started its activities in 1981, is the first Minerva center at the Hebrew University. Currently, the center consists of six research groups, and in February 2006 will be joined by a new faculty member, Dr. Daniel Harries. Beginning next year it is likely that Professor R. Baer, who for all practical purposes is a very active member of the center, will join us officially. In addition to the faculty members, there are about 35 graduate students in the center (40 including Baer’s group whose members, like most other students and faculty, are located in the Aronberg wing of the Los Angeles building of chemistry). There are typically about 10 postdoctoral fellows in the center, as well as several short term visitors and many long term collaborators who come for short visits from other universities in Israel or abroad. The substantial computing activity is taken care of by one system manager, with part time “soft money” support. Similarly, the administrative activities are handled by one staff member with occasional part time help. Additional details about the history of the center, personnel, budget, etc. are given in Part II of this report.

During the nearly 25 years of its existence the Fritz Haber center scheduled its weekly seminars to run uninterruptedly, hosting world leading scientists, as well as young researchers and graduate students. The center has also organized and contributed to numerous scientific symposia. Notably, in March 2005, on the occasion of the last Beirat meeting, we organized a special symposium on Biophysical Dynamics where, in addition to several German and other foreign speakers, most lectures were given by young faculty members from different Israeli institutes. This has been a very successful and inspiring meeting.

Over the years, more than a hundred graduate students completed their doctoral theses in the center, and a comparable number of post-graduate students from many countries began here their training as independent researchers. Many of our former students and postdocs now hold academic positions at first rate academic institutions in various countries, including Israeli universities such as The Technion, The Weizmann Institute, Tel-Aviv University and at the Hebrew University. Others occupy leading positions in industrial and governmental institutions. Many of our visitors have arrived here from Germany, among them Minerva fellows who are now faculty members in various German academic institutes. The students, postdocs and our more senior collaborators in Germany and other countries have of course contributed to the numerous research articles (more than 1000), reviews, and books published by the members of the center, many of which have been frequently cited and used by other researchers around the world. It should be stressed that the affiliation 'Fritz Haber Research Center' appears as part of the authors’ address in all of these publications. The support of 4

Minerva is mentioned again in the Acknowledgement sections. Lists of publications during the last five years, as well as a list of vistors and seminars are given in Part II of this report.

The academic activities of the center are supervised by the scientific advisory committee, the Beirat. The Beirat generally consists of 6-7 members, typically three German and four Israeli scientists (including the vice-president for research of the HU). Professor Edward Schlag served as the first chairman of the Beirat since its inception until 1998, and contributed substantilally to its recognition as a leading center of theoretical chemical physics. Similar support and encouragement was given to the center by the second chairman of the Beirat, Professor George Comsa, who fulfilled this function from 1998 until the end of 2005. We take this opportunity to wholeheartedly thank Professor Comsa for his consistently strong support of the center and the encouragement of its members during his term of service. We also thank Professors Erich Sackmann, Jurgen Troe, Hanoch Gutfreund and Joshua Jortner who served as Beirat members for many years, and devoted their time to share their experience and contribute their advice to encourage the scientific activity of the center. On this occasion we thank Professor Wolfgang Domcke, who agreed to serve as the new chairman of the Beirat, and Professor Moiseyev who agreed to continue his membership. We welcome the new members of the Beirat, Professors Helmut Grubmüller, Gerard Meijer, Abraham Nitzan and Micha Asscher, and look forward to fruitful advice, constructive criticism and support in some of the eventual struggles ahead.

The scientific activities of the center have been extensively reviewed, twice, by international evaluation committees composed of world leading scientists. First in 1994 and then in 2002. The first Minerva review committee was headed by Professor H. Schwarz and the second by Professor H. –J. Werner. The members of the second evaluation committee were Professors E. J. Heller, W. H. Miller, M. Parrinello and K. Schulten. In both reviews, the reports have been extremely enthusiastic, and at the same time provided useful advice about possible ways to improve the center’s activities. Both committees have also recommended an increase of the Center’s endowment as well as granting a special equipment fund. In 1994 this has indeed lead to a substantial increase of the budget and upgrading of equipment. Owing to budgetary cuts the recommendations of the second committee could not be met. In this connection we should mention that the annual operation budget of the Fritz Haber center in recent years is ca. 80,000€, which constitutes just a modest fraction (about 15%) of the total operation budget of the groups in the center. While modest, this budget is essential, since this is the only source of support of our joint activities, such as the exchange of students and visitors with Germany, maintenance of computing equipment, seminars and symposia, as well as the salaries of our administrator and that of the part time assistant system manager.

The research carried out in the center encompasses a wide range of systems, phenomena and theoretical approaches. The topics include, for example, cold matter phenomena such as the production of ground state molecules in Bose-Einstein condensates and coherent control of ultra-cold collisions. Theoretical and computational studies of the chemistry and physics of molecular systems under extreme conditions, such as high density and high energy collisions of clusters with surfaces which represent a rather different limit of molecular interactions. Other examples of surface-molecule interactions include, for example, the energetics and spectroscopy of acid adsorption onto (and solvation into) hydrogen bonded solids, or charge 5 transfer from molecular adsorbates to metal surfaces. A very different type of molecule surface interaction is the interaction of charged flexible macromolecules (such as some natively unfolded proteins) on mixed fluid lipid membranes. This and various other topics represent the increasing tendency of researchers in the center to study systems and phenomena of biophysical interest. This includes, for instance, the study of proton kinetic pathways in the Green Fluorescence Protein (GFP), the vibrational spectra of biological molecules such as the G-C nucleotide pair, or larger scale phenomena such as actin polymerization, branching and phase behavior. Much effort has always been invested towards the development of new theoretical and computational methods. Thus, for example, this year’s report includes brief accounts pertaining to the development of a new Molecular Dynamics approach for the search of molecular crystal structures, the formulation of new force fields for calculating structure and spectra of biological molecules, or the application of a novel Monte Carlo simulation algorithm for annealed vs. quenched membrane-protein systems.

More details on the research in the center is provided in the Individual Reports in the next section, and the topics studied are also reflected by the lists of publications in Part III. It should be emphasized that each member is responsible for the style, extent, and format of his report. Part II of the report provides background material, describing briefly the history of the center, its budget, activities, personnel, relations with the Hebrew University and the Institute of Chemistry, as well as updated lists of people in the center. In Part III we list the seminar visitors and titles of their talks, and the recent publications by the research groups in the center.

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2. Individual Research Progress Reports

N. Agmon

A. Ben-Shaul

V. Buch

R. B. Gerber

R. Kosloff

R. D. Levine

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2.1 Noam Agmon

The Remarkable Dynamics of the Green Fluorescence Protein and its Chromophore

The Green Fluorescence Protein (GFP) has attracted much interest as a biological fluorescence marker and as one of the few examples of functionally important excited-state proton transfer (ESPT) in nature. Its chromophore is formed by a post-translational cyclization reaction involving three consecutive amino-acid residues. When isolated in solution, it does not fluoresce, but does so upon lowering of the temperature, T. Within the protein its excited anion shines with a bright green light, following an intra-protein reaction of ESPT.

Figure 1. p-hydroxybenzylidene- dimethylimidazolinone (p- HBDI), a model chromophore of the green fluorescence protein, in its ground and excited state, with model potential energy surfaces for the two exocyclic angles (calculated by Christiana Scharnagl from Munich).

In collaboration with Prof. Dan Huppert (TAU), we find that the isolated anionic chromophore in solution (no ESPT to consider here) shows a remarkably non- exponential excited-state decay over a wide range of temperatures. This contrasts with ES decay of common dye molecules, which is mono-exponential. We were able to explain this behavior quantitatively by inhomogeneous kinetics. The exocyclic angle φ is widely distributed in the glassy matrix before excitation (S0), whereas the approach to the conical intersection in the ES occurs along ψ. Each frozen conformation φ has a different excited-state decay rate due to the varying potential profile in ψ .

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Figure 2. Radiationless decay of an excited p-HBDI dye in a 0.5 mole fraction glycerol-water glass at various temperatures (indicated). The observed fluorescence signal was corrected for its radiative decay with a lifetime τf=3.2 ns. The sample was excited at 395 nm, and the fluorescence collected at 530 nm.

The mathematical expression which fits these decay curves involves a conformational-dependent rate constant. Each conformation, x, decays exponentially, and the overall kinetics is averaged over an equilibrium conformational distribution. At each x, the rate constant was found to conform to the Arrhenius equation in T, albeit with an activation energy varying as x2. The range of small-x corresponds to perpendicular configurations in Fig. 1, from which there is facile approach to the conical intersection of the two potential surfaces and thus fast internal conversion to the ground-state. The reason for the high fluorescence within the protein is thus that the protein maintains the chromophore in its planar conformation, which is the most remote from this conical intersection.

The study of the transient fluorescence of the intact wild-type (wt) protein (again, over a wide range of temperatures) provides additional surprises. Below a critical temperature (230 K), the decay of the acidic form is power-law rather than 9 exponential. The t-1/2 power indicates one-dimensional diffusion along pre-formed “proton-wires” within the protein. Indeed, we were able to fit the whole time dependence to the solution of a one-dimensional diffusion equation with a reversible boundary condition for the dissociated proton. A special computer code allows automated fits to the error-function solution of the partial differential equation in its simplest form. Thus one obtains a unique example where diffusion along “proton- wires” can be observed in real-time.

Figure 3. Transient fluorescence decay from the acidic form of wt-GFP due to ESPT, at the different indicated temperatures. Lines (shifted vertically for clarity) depict fits to one dimensional diffusion with a boundary condition accounting for a reversible reaction.

The dissociation rate constant obtained from these fits exhibits non-Arrhenius temperature dependence indicative of nuclear tunneling at low T:

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Figure 4. Temperature dependence of the dissociation rate constant for ESPT in wt-GFP. Note the leveling-off at low T due to nuclear tunneling.

Above the critical temperature (230 K) the time-resolved kinetics drop below the t-1/2 power-law, exhibiting a t-3/2 behavior near room-temperature. This is indicative of proton leakage out of the protein with diffusion in the (three-dimensional) bulk solution surrounding it:

Figure 5. Time resolved fluorescence from wt-GFP above 230 K showing break-down on the t-1/2 kinetics.

Careful analysis of the x-ray data of wt-GFP indeed reveals a long internal proton-wire on which the proton may be trapped at low T:

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Figure 6. A hydrogen-bonded “proton wire” in wt- GFP connects the bottom of the GFP barrel to the active site (Tyr-66) via Asp-82 and Glu-222.

At the higher temperatures, a threonine switch may rotate and open a short pathway leading to the surface of the protein, presumably allowing for proton escape to solution:

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Figure 7. The exit pathway (dashed blue) opens by a 1200 rotation of the Thr-203 side-chain into the shown position.

Curiously, then, the GFP protein (which is a solution-phase protein) shows characteristics resembling membranal proton-pumping proteins (cyt-c-oxidase, bacetriorhodopsin). Conceivably, excitation may open the exit pathway for the dissociating proton, whereas another proton could then enter after relaxation to the ground state, along the pathway depicted in Fig. 6.

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2.2. Avinoam Ben-Shaul

In last year’s report we have outlined our research on membrane-macromolecule interactions, emphasizing the coupling between lipid lateral mobility, membrane elasticity and electrostatic effects. The research during this period has focused on membranes containing charged lipids interacting with rigid oppositely charged macromolecules, such as DNA, amphipathic peptides and globular proteins. In 2005 we have continued research along these lines, but the major progress has been achieved with respect to the interaction between mixed fluid membranes and flexible polyelectrolytes. With the graduate student Assaf Zemal and in close collaboration with Dr. Sylvio May from Jena university, we have continued studying the mechanisms of membrane perforation induced by amphipathic (e.g., anti-microbial) peptides[1]. Also, with E. Mbamala and Sylvio May we have published a detailed study emphasizing the role of protein size, charge and shape in the phase behavior (especially the phase separation characteristics) of a protein-dressed lipid membrane [2]. These topics were mentioned in the previous report and will not be repeated here. On the other hand, we shall (briefly) describe our recent work on the interaction between mixed fluid membranes and flexible macromolecules. The membrane adsorption of such macromolecules, e.g., naturally unfolded proteins, involves qualitatively different characteristics in comparison to rigid macromolecules, owing to the additional, conformational, degrees of a flexible polymer. We have recently completed a comprehensive study of this system, which, in addition to providing new insights into the adsorption of polyelectrolytes onto fluid membranes, has provided some surprising general results, as well as novel computer modeling schemes. This work was done by the graduate student Shelly Tzlil, [3]. In 2005 we have continued our collaboration on viral assembly with the groups of W. M. Gelbart from UCLA and Diana Murray from Cornell medical school. Together with Barry Honig from Columbia university we took part in a new research direction, dealing with cadherin-mediated cell adhesion [4]. Another research topic on which we have briefly reported last year is concerned with Actin polymerization and cell locomotion. This topic is the subject of the PhD thesis of Yifat Brill-Karniely. We have recently completed a joint manuscript with the experimental group of Dr. Anne Bernheim-Groswasser [5]. (The paper, with T. Pollard from Yale as a coauthor, was submitted to (and essentially accepted by) PNAS.) Notably, this ongoing and fruitful collaboration began following the lecture given by Dr. Bernheim- Grosswasser last March in Jerusalem, during the symposium organized by the FH center as a part of the last Beirat meeting. Assaf Zemel, who closely collaborated with Sylvio May and spent time with him in Jena, has completed his PhD work in fall 2004 and is now doing his postdoctoral research. Shelly Tzlil will submit her PhD dissertation in summer 2006. Yifat Brill-Karniely continues her graduate research. A new graduate student, Orly Slavin, has recently joined our group. A postdoctoral fellow, Dr. Vladimir Teif from Minsk, came for a 3 month stay and may come again for a longer period next year. We continue our collaborations with colleagues in Israel and abroad, especially those mentioned above. Below we outline two of the projects completed in 2005, and briefly describe our research plans for the near future.

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Flexible Charged Macromolecules Interacting with Mixed Fluid Lipid Membranes: Theory and Monte-Carlo Simulations.

The lipid bilayer, constituting the central structural element of biological membranes, is a 2D fluid mixture, composed typically of many lipid species. Owing to the lateral mobility of lipids at physiological temperatures, the membrane can respond to interactions with integral and peripheral macromolecules by mobilizing those lipids interacting favorably with the macromolecule into the interaction zone. This process leads to local changes in lipid composition around the guest molecules which, under certain conditions, may evolve into larger scale reorganization of membrane components, resulting in “domain formation”. The molecular composition and phase characteristics of the domains, as in “lipid rafts”, are different from those of the surrounding membrane. The segregation of charged lipids induced by the peripheral macromolecule may involve a non-negligible entropic penalty. In previous works (e.g., [2]) we have carefully analyzed the energetic-entropic balance associated with electrostatic adsorption of rigid macromolecules (such as DNA or globular proteins) onto fluid membranes. It was shown, for instance, that the extent of lipid segregation, the corresponding entropy loss and the interaction free energy depends sensitively on the shape, charge and concentration of the adsorbing macromolecule. In the present work [3] we have focused on the energetic and structural characteristics of the interaction between flexible, electrically charged, macromolecules (polyelectrolytes), and mixed, oppositely charged, fluid membranes. We considered three-component membranes composed of one electrically neutral species and two differently charged lipids. Electrostatic adsorption on such membranes may involve significant changes in the spatial configuration of the adsorbing polyelectrolyte and, consequently, a substantial loss of conformational entropy. The two kinds of entropy losses, those associated with lipid segregation and those which lower the macromolecule’s conformational freedom, tend to offset the gain in electrostatic interaction energy between the oppositely charged molecules. It should be noted, however, that both degrees of freedom, namely, lipid mobility and macromolecule flexibility enable the interacting complex to select with higher probability those mutual membrane-macromolecule configurations of lowest free energy. We studied the energetic-entropic interplay based on Monte Carlo simulations and theory. Our model system consisted of a flexible cationic polyelectrolyte interacting, via Debye- Hückel and short-ranged repulsive potentials, with membranes containing neutral (“PC”) lipids, 1% tetravalent (“PIP2”) and 10% (or 1%) monovalent (“PS”) anionic lipids. We found, as expected, that adsorption onto a fluid membrane is invariably stronger than to equally charged frozen or uniform membrane. We also found that while monovalent lipids may suffice for binding rigid macromolecules, polyvalent counter-lipids (PIP2), whose entropy loss upon localization is negligible, are crucial for binding flexible macromolecules, which lose conformational entropy upon adsorption. Fig. 1 illustrates some typical membrane-polymer configurations.

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Fig. 1 Side and top views of two, rather arbitrary, simulation snapshots (left and right), of a polyelectrolyte interacting with a weakly charged fluid membrane (1% PIP2, and 1% PS). PIP2 and PS lipids are represented by blue and purple spheres, respectively. Note the localization of the charged lipids in the vicinity of the polymer.

In this work we have extended the Rosenbluth’s Monte-Carlo scheme to directly simulate polymer adsorption on fluid membranes. The idea here is to simultaneously generate polymer and membrane configurations, whereas the traditional Rosenbluth method applies to polymer conformations only. On the more theoretical side, we have shown that similar information on polymer-membrane statistics could be derived from a biased superposition of quenched membrane simulations. Furthermore using a simple cell model we could account for surface concentration effects, and showed that the average adsorption probabilities on annealed and quenched membranes coincide at vanishing surface concentrations. Our model is relevant, and in fact was inspired by the electrostatic-switch mechanism of, e.g., of the MARCKS protein (as described briefly below).

Lamellipodia to Filopodia Transition in a Membrane Free System

The cell cytoskeleton is a complex dynamical network that is constantly remodeling when cells divide and move. This reorganization process occurs not only at the cell membrane, but also in the cell interior (bulk). During locomotion, regulated actin assembly takes place at the plasma membrane. Therefore, most in vitro experiments explore phenomena taking place in the vicinity of a surface. Yet, in order to understand how the molecular-machinery of a cell self-organizes in a more general way, it is of great interest to study a "membrane free" model system which can explain reorganization processes generated not only in proximity of the cell membrane (i.e., lamellipodia and filopodia protrusions) but also those taking place in the cell interior, such as star formation.

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Fig. 2 Total internal reflection fluorescence images of aster formation. Conditions: 1 µM actin, 200 nM VCA and 10 nM Arp2/3 complex. (a) Images in the time-lapse series are spaced 30 seconds apart for a total time of 3.5 minutes. (b) An image of the aster part that is close to the cover slip surface clearly shows branches, three of them are marked in red. All the actin pointed (minus) ends are pointing towards the center. The growth direction is from the pointed (–) end to the barbed (+) end.

Fig. 3 (a-c): snapshots taken 10, 13 and 16 seconds after actin nucleation, respectively. The initial concentrations are similar to those used experimentally: 7.47 µM G-actin, 100 nM Arp2/3 complex; bar = 0.5 µm. (d) and (e) are magnified regions from (c) and (b). All filament tips are barbed ends and marked in red, (some are not seen because they point away from the figure plane). (f): The volume fraction, ρ, and the orientational order parameter (η) of 17 polymerized actin, as a function of the distance, r, from the nucleation center, after all G-actin has been consumed and cluster growth has been completed.

In a series of experiments performed by Lior Haviv and Anne Bernhein-Groswasser at Ben- Gurion university it was shown that bulk polymerization of actin in the presence of VCA and Arp2/3 complex results in spontaneous formation of diffuse aster-like structures. Furthermore, the addition of fascin induces their transition into stars, similar to star-like structures recently observed in vivo. Our theoretical work in Jerusalem, based mostly on Kinetic Monte Carlo simulation studies by Yifat Brill-Karniely, has nicely reproduced the experimental results and provided additional insights into the mechanisms governing actin polymerization. Figures 2 and 3 illustrate the experimental aster structures and theoretical predictions of our MC simulations, respectively. Our future plans regarding this topic are outlined below.

Additional Projects and Future plans

The electrostatic switch mechanism

Fig. 4 illustrates a charged and flexible biopolymer , e.g., the natively unfolded protein myristoylated alanine-rich C kinase substrate (MARCKS), interacting with an oppositely charged, mixed, fluid lipid membrane. This protein adsorbs onto the inner leaflet of the cell membrane through its 25-residue long basic effector domain (ED), which includes 13 basic amino acid groups .

Fig. 1: The effector domain of MARCKS sequesters and binds to ~3 (tetravalent) anionic PIP2 lipids.

Experiments show that MARCKS sequesters and binds electrostatically to about 3 phosphatidylinositol 4,5 bisphosphate (PIP2) lipids. The local concentration of these multivalent (here of valence z=-4) lipids in the interaction zone is dramatically enhanced as compared to their average membrane abundance of about 1%. On the other hand, the local concentration of monovalent lipids, primarily phosphatidylserine (PS, z=-1), appears similar to 18 that in the bare membrane (typically 15-30%). The MARCKS/ED charge is thus mainly neutraized by the multivalent PIP2 lipids. Upon phosphorylation by PKC (protein kinase C) the net charge of ED drops to about +7. As a result of the weakened electrostatic attraction MARCKS detaches from the membrane, thereby exposing PIP2 to cleavage by PLC (phospholipase C), initiating various possible signal transduction events. The electrostatic switch mechanism prevails in various other biological systems besides MARCKS. It clearly involves a subtle interplay between electrostatic and non-electrostatic interactions (e.g., the hydrophobic binding energy of the myristoyl anchor at the N-terminal of the protein) , as well as a delicate balance of conformational and lipid demixing entropies. While non-trivial computationally, the extension of our polymer-membrane studies to model the electrostatic switch is, in principle, straightforward. Work in this direction, involving both simulation studies and semi-analytical lattice-type model are in progress.

Viral Assembly

Complex and subtle interplay between energetic and entropic factors appears in various other biological processes. One of the most intricate examples is the assembly of animal viruses, as schematized in Fig. 5 for a C-type retrovirus, in which case the process takes place on the inner leaflet of the plasma membrane. The immature viral bud consists of three concentric spherical shells, composed of three types of biopolymers. The outermost shell lipid- protein envelope, whose lipid composition is distinct from the average composition of the cell membrane from which it derives. In fact, like membrane rafts, it is rich with PIP2, cholesterol and sphyngolipids. The middle layer consists of many (generally several thousands), tightly packed Gag polyproteins, and the innermost shell is the genomic RNA. The binding of Gag to the cell membrane is, most likely, due to electrostatic attraction between its basic matrix domain (MA) and anionic lipids, including PIP2, which are either present in raft-like patches prior to Gag adsorption or recruited by MA, resembling the case of MARCKS. Electrostatic attraction is also responsible for binding the RNA to the basic nucleo-capsid domain (NC) of Gag. In between MA and NC is the electrically neutral capsid domain (CA), which, in the mature virus, constitutes the viral capsid (of the well-known conical shape in HIV-1). The MA, CA and NC domains are connected by shorter flexible amino acid chains, which are cleaved in the mature infectious virus, after the bud pinches off from the membrane. The structural changes associated with the transition from immature to mature virus are quite dramatic. In particular, the viral capsid is generally non-spherical and typically consists of less than half of the CA proteins originally present in the immature virion. Our ultimate goal is to gain insight into the mechanisms governing the assembly of the premature bud. Based on the simulation methods that we have developed, and on our experience in modeling the coupling between electrostatic, bending and hydrophobic interactions, we hope to shed light on at least some of the relevant processes. In particular, we have recently begun modeling the interaction between RNA and a layer of NC protein domain, taking into account the distribution of charges on the proteins and the RNA, and the changes in energy and entropy upon RNA-induced NC aggregation. 19

We hope to report progress on this and additional aspects of viral assembly, such as RNA folding in the confined virus environment, in the next annual report. On these topics we closely collaborate with our colleagues Dina Murray [6] and Bill Gelbart [7].

Fig. 5: The basic MA domain of Gag adsorbs onto the inner leaflet of the plasma membrane, attracting anionic lipids. The genomic RNA adsorbs to the basic NC domains. These interactions, in addition to the nonpolar attraction between the CA domains, govern the assembly and structure of the premature virion. The figure displays an early stage in the budding process, at the end of which the membrane-Gag-RNA trilayer closes on itself into a nearly complete spherical shell. The pinching off from the membrane is mediated biochemically.

Actin Polymerization and Cell Locomotion

Our research plans on this topic are along two related directions. First we shall continue our collaboration with the group of Dr. Bernehim-Groswasser, on membrane free actin polymerization. In parallel, and close collaboration and correlation, to the experiments already performed and those that will be performed in BGU we intend to model the role of capping proteins and, especially, the role of the linker protein fascin in mediating the transition from an 20 aster to a star structure [5]. This would necessitate the introduction of actin filament bending into the model, in addition to polyemerization, branching, depolymerization and capping. Work along these lines is in progress, and both new experiments and calculations are underway. Another direction, which we have started studying a while ago is the mechanisms underlying the growth of lamellipodia and cell locomotion. We have already formulated a simulation model which takes into account, to the best of our knowledge for the first time, the role of excluded volume interactions between actin filaments. We believe, and actually know that these interaction play an important role in the time evolution of a growing actin cluster (see e.g., Fig. 3). Coupling with the lipid membrane is another component of our model. Partial results predicted by this model were described in the previous report. We hope to report considerably more progress on this front in the next annual report.

[1] A. Zemel, A. Ben-Shaul and S. May, Perturbation of a Lipid Membrane by Amphipathic Peptides and its Role in Pore Formation Eur. Biophys. J. 34, 230-242 (2005).

[2] E. Mbamala, A. Ben-Shaul and S. May Domain Formation Induced by the Adsorption of Charged Proteins on Mixed Fluid Membranes. Biophys. J. 88, 1702-1714 (2005)

[3] S. Tzlil and A. Ben-Shaul Flexible Charged Macromolecules On Mixed Fluid Lipid Membranes: Theory and Monte- Carlo Simulations. Biophys. J. 89, 2972-2987 (2005)

[4] C. P. Chen, S. Posy, A. Ben-Shaul, L. Shapiro and B. H. Honig Specificity of Cell-Cell Adhesion by Classical Cadherins: Critical Role for Low Affinity Dimerization through β-Strand. Proc. Nat’l Acad. Sci. USA 102, 8531-8536 (2005)

[5] L. Haviv, Y. Brill-Karniely, R. Mahaffy, F. Backouche, A. Ben-Shaul, T. D. Pollard and A. Bernheim-Groswasser Lamellipodia to Filopodia Transition in a Membrane Free System Proc. Nat’l Acad. Sci. USA (submitted)

[6] L. Rogers, A. Zemel, T. Lazaridis, A. Ben-Shaul and D. Murray Computational Analysis of the Membrane Adsorbed cPLA2 C2 Domain Biophys. J. 88 (1): 426A-426A Part 2 Suppl. S, Jan (2005)

[7] A. Yoffe, W. M. Gelbart and A. Ben-Shaul Secondary Structure Statistics of Random Vs. Viral RNA Biophys. J. 88 (1): 573A-573A Part 2 Suppl. S, Jan (2005)

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2.3 Victoria Buch

I. Solid phase solvation of acids: acid adsorption on hydrogen bonding solid surfaces; mixed acid solvent solids

The following work represents joint effort with our collaborators: the experimental group of J.P. Devlin (OSU, BSF partner), J. Sadlej (Warsaw University; ab initio specialist) and N. Uras (Suleiman Demirel University, Turkey; simulations). The major computational tool used was Quickstep, a new generation on the-fly-dynamics code developed by the Parrinello group; we enjoyed support of the members of this group, most notably F. Mohamed.

Synopsis: We initiated a series of studies on the general topic of solid-phase solvation of acids. Solvation of hydrohalic acids HX (X=Cl,Br) was studied for a series of solvents - water, methanol, and ethers. In contrast to the liquid phase, solid-phase solvent-acid crystals display discrete composition ratios, enabling observation of distinct acid solvation states in a semi-rigid environment (Fig. 1). This is in contrast to concentrated acid solutions which are characterized by broad nearly featureless IR continua (1000~3500 cm-1), that reflect a broad distribution of + protonated-water configurations, ranging from H3O to the Zundel ion (i.e., proton sharing by + two molecules, H2O..H ..OH2, [1]).On the other hand, spectra of crystalline acid hydrates enable observation of distinct protonated-water species; e.g., the spectrum of the isolated + - Zundel ion can be observed in the FTIR spectrum of crystal HX dihydrate (H2O..H ..OH2)(X ) – see Fig. 2. Note the intense ~1000 cm-1 band of the central proton vibration. The crystal phases of nH2O:HCl (1:1, 2:1, 3:1 and 6:1) have been studied in the past [2,3]. During the present funding period, the Devlin group discovered new families of solvent-acid crystals: nCH3OH:mHX, with alcohol:acid ratios ranging from 3:1 to 1:3, and n-ether:mHX (ether = di-methyl ether DME or tetrahydrofuran THF), with the ratios ranging from 2:1 to 1:6 [4]. Computational studies of acid-solvation states in these systems have already been initiated by V. Buch and N. Uras [5,6], in collaboration with the Parrinello group, the authors of “Quickstep” on-the-fly code [7]. The solids display a strikingly broad range of solvation states, ranging from molecular to ionic, with variable proton sharing depending on the composition ratios [5].

a) Interaction of H-bonded nanoparticles with acids and bases: Surface interactions at < 100K. The surface spectra with acid adsorbate are characterized by broad bands with underlying continua [23, 24], as exemplified in Fig. 3 for HCl on methanol. The interpretation was initiated, with the help of on-the-fly simulations of model methanol-acid cluster spectra such as the one shown in Fig. 3 [6]. This cluster includes one ionized HCl within a methanol ring, and another extra-ring adsorbate HCl solvating the Cl- anion (Since condensed-phase methanol favors chain and ring structures, this cluster constitutes an initial model for the methanol nanoparticle surface exposed to HCl.). The calculations indicate extremely anharmonic dynamics, well beyond the scope of the harmonic approximation. The cluster is a molecular wire, with proton delocalization over the entire ring on a time scale of several picoseconds. Transient proton states include localization on different methanol molecules in the form of + CH3OH2 , proton sharing between different pairs of methanol molecules, and proton sharing 22 between methanol and Cl-. The broad bands in the spectrum reflect the transient proton states, while the underlying continuum results from the fluxional nature of the proton. A related result was obtained in a 60K trajectory of an HCl molecule adsorbed on a water hexamer [8] (an initial model for molecular acid kinetically stabilized on the ice surface). There, full proton transfer to the cluster never occurred. However distinct solvation states, probed by a single HCl molecule during several ps (1- and 2-coordinated HCl, and proton sharing with neighboring H2O), yielded three overlapping bands spanning a broad frequency range(Fig. 4). b) Spectra, structure and proton dynamics within new mixed crystals of HX with methanol and small ethers: Acid solvation in crystalline nH2O:HX, nMeOH:mHX, nTHF:mHX and nDME:mHX. Another approach to gain insight to acid solvation is the investigation of mixed solvent-HX crystals. As noted above, the list of the known solvent:HCl solids was recently extended to include methanol-acid and ether-acid solids [4]. The ether:acid crystals were found for ether:acid ratios ranging from 2:1 to 1:6. The acid-rich phases are especially striking. Fig. [1] shows the measured spectra of nHCl:DME crystals, in conjunction with spectra from on-the-fly dynamics[5]. Acid ionization requires effective solvation of both the cations and the anions, and anion solvation cannot be supplied by the ether. Still, presence of intense low frequency features suggests extensive proton transfer. Model ether:acid solids were generated by replicating, in 3D, cluster structures of appropriate compositions. Resulting spectra were in semi-quantitative agreement with experiment as shown in Fig [1]. A full gamut of proton behavior was revealed. The 1:1 DME:HCl solid can be viewed as a 3D array of “asymmetric Zundel” units, with proton-sharing between the ether oxygen and the chloride; the partial proton transfer is driven by mutual solvation of these Zundel units. In the 1:2 solid, self-solvation of the chloride by an additional HCl molecule results in completion of acid ionization. Simulations indicate that the latter system is composed of protonated ether, Cl-, and molecular HCl solvating the anion. The 1:6 solid is fully molecular, with ether oxygen acting as a (weak) double acceptor towards acid chains. The composition range of nMeOH:mHCl solids is intermediate between that of water and ether mixed crystals, ranging from 1:3 to 3:1. As with water, all crystal phases appear to be ionic. + - - Acid-rich crystals include MeOH2 , Cl and (excess) molecular HCl solvating Cl . In the methanol-rich solids, the cation appears to be of the Zundel form, with proton sharing between two acceptor molecules as in the water dihydrate [4]. The spectra of the amorphous analogs are characterized by very intense underlying continua, suggesting presence of molecular wires, similarly to the adsorbate-surface systems[6]. The initial interpretation was carried out with the help of cluster models such as the one described above [6]. Isotopic and substitutional effects are other interesting aspects of the proton-rich solvent-acid solids. The solids include typically a number of distinct spectroscopically identifiable H/D- sites. In mixed H/D systems, preferred locations for either isotope are in evidence. For example, we have shown that in the isotopically mixed dihydrate, the central position of the + + Zundel ion is adopted preferentially by H , as in D2O.. H ..OD2 [9]. This is in contrast to the neutral water dimer for which central positions are adopted preferentially by D.

23

Figures:

Fig. 1 FTIR of crystals mDME:nHCl (m=1, n=1, 2, 6: going up from next to bottom); and (right) spectra from “Quickstep”[45] with red bands from molecular HCl components. Bottom is spectrum of deuterated 1:1. Models at bottom: unit cell structures used in the calculations.

Fig. 2 FTIR spectra of films of nH2O:HCl hydrates: amorphous (left) and crystalline (right).

Fig. 3 Top - surface spectrum of MeOH particles with ~50% HCl cover at 60K. Middle – calculated spectrum of the (HCl)2(MeOH)4 cluster. Bottom – snapshots of 4 ps trajectory of the calculation 24

Fig. 4 Spectrum for a single HCl on a water-cluste by “Quickstep” [45]. Three transient structures were accessed repetitively during the 7 picosecond trajectory.

Agmon, N. Chem. Phys. Lett. 1995, 244, 456-462; Ando, K.; Hynes, J.T. J. Phys. Chem. B 1997, 101, 10464; Tuckerman, M. E.; Laasonen; K., Sprik, M.; Parrinello, M. J. Phys. Chem.1995, 99, 5749; Lobaugh, J; Voth, G. A., J. Chem. Phys. 1996, 104, 2056; Vuilleumier, R.; Borgis, D. J. Mol. Struct. 1997, 437, 555. Yoon, Y.K; Carpenter, G. B.. Acta Cryst. 1959, 12, 17-20; Lundgren, J. O.; Olovsson, I. Acta Cryst. 1967, 23, 966-976. Taesler, I; Lundgren, J. O. Acta Cryst. 1978, B34, 2424. Delzeit, L; Rowland, B.; Devlin, J. P. J. Phys. Chem. 1993, 97, 10312. Devlin, J.P.; Sadlej, J.; Hollman, M.; Buch, V. J. Phys. Chem. A 2004, 108, 2030-2043. Buch, V.; Mohamed, F.; Krack, M.;, Sadlej , J.; Devlin, J.P.; Parrinello, M. J. Chem. Phys. 2004, 121 , 12135-12138. Aytemiz-Uras, N.,; Devlin, J.P.; Sadlej, J..; Buch, V. in preparation. Lippert, G.; Hutter, J. Parrinello, M. Mol. Phys. 1997, 92, 477-487; CP2K, http://cp2k.berlios.de/ (2000-2004); VandeVondele, J.; Krack, M.; Mohammed, F.; Parrinello, M.; Chassaing, T.; Hutter, J.; Comp. Phys. Comm. 2005, 167, 103-128. Devlin, J.P.,; Farnik, M.;, Suhm, M.A.; Buch, V. J. Phys. Chem. A 2005, 109, 955. Devlin, J.P.; Severson, M.W.; Mohamed, F.; Sadlej, J; Buch, V.; Parrinello, M. Chem. Phys. Lett. 2005, 408, 439

25

II. A new MD-based approach for molecular crystal structure search

This project was initiated during my summer sabbatical in the group of M. Parrinello in Lugano, Switzerland. The initial results were published as a rapid communication in the J. Chem. Phys. [10].

Overview: A new molecular-dynamics based approach was proposed to search for candidate crystal structures of molecular solids. The procedure is based on the observation of spontaneous transitions between ordered and disordered states in molecular-dynamics simulations of an artificial periodic system with a small unit cell. In such a way only the most stable structures are automatically selected. The method can be applied to the solution of crystal structures from low-quality or very complex diffraction data. Tests are presented for H2O-ice polymorphs.

Finding crystal structures of molecular solids from just molecular formulas has been a long- standing theoretical/computational quest of significance both in basic sciences, such as solid- state physics, geophysics, and planetary science, and in practical applications, e.g., in the pharmaceutical industry or materials science[11-13]. The problem itself can be formulated as an identification of the free-energy minima as a function of atomic coordinates and of unit-cell vectors. At zero temperature, the problem is simplified to the minimization of the enthalpy H=U+PV in M dimensions, where M=3N+3. (N is the number of atoms, 3N–3 is the number of independent coordinates after the elimination of the translation, and the number of independent unit-vector elements after the elimination of unit-cell rotations is 6.) Exploration of this M- dimensional space in search of minima has been pursued in the past by a variety of methods; for some recent reviews and articles see Refs. 13-15. Due to the inaccuracies of the available potentials, all such calculations produce candidate crystal structures, to be compared with experiment rather than structural predictions. Still, calculations of candidate structures for molecular crystals are of great theoretical and practical interest. A new molecular-dynamics based approach was proposed to search for candidate crystal structures of molecular solids. Suppose that an NVE simulation is run for a periodic system, such that the unit-cell dimensions and the number of molecules per unit cell match some stable crystal forms. The initial configuration is arbitrarily disordered. The ensuing dynamics depends on the total energy of the system. The potential-energy surface (PES) can be studied by means of an inherent structure analysis, i.e., by performing local minimizations which employ trajectory configurations as input. At low energies the system is confined to a neighborhood of the input structure because of limited mobility; the energy is insufficient to cross barriers between minima and thus to explore effectively the PES. At high energies, numerous minima are explored, however, preference is expected for the high-energy "liquidlike" configurations. The proposed method relies on the existence of an intermediate "optimal" energy regime in which the mobility is sufficient for effective exploration of the PES, however, the system still has a finite probability of visiting low-PE regions, whose corresponding inherent structures are crystalline. Observation of temporary crystallization in the course of the trajectory is likely to be facilitated (with respect to a realistic model with numerous molecules) by a reduced number of liquidlike structures and by the fact that the latter are energetically penalized in a small periodic system. The optimal energy range can be easily located by MD.

26

The method was tested successfully on ice polymorphs (see Fig. 5). We then proceeded to the more interesting case of a search for crystal structures with unknown unit-cell dimensions. The simplest approach is to perform a sequence of MD simulations at the optimal energy for a coarse grid of cell dimensions. For wrong dimensions, low-lying minima will not be found. But if the scheme works, freezing to a structure approximating a crystal should be observed for cell sizes close to some crystal cells. To obtain the final crystal structures, the minimization of the enthalpy should be carried out both with respect to the coordinates and the cell dimensions. The success of the approach depends on whether a coarse-grained search over the possible unit-cell dimensions is sufficient to produce first approximations for the crystal structures. If freezing to approximately correct structures requires unit-cell dimensions which are very close to the correct ones, the method may not be practical. Again, tests on the ice crystal forms were successfully carried out.

Fig. 5. Crystal structures of ice polymorphs located in the present study

[10] Buch, V.; Martonak, R., Parrinello, M. J. Chem. Phys. 123, 051108, 2005. [11] J. Maddox, Nature (London) 335, 201 (1988). [12] A. Gavezzotti, Acc. Chem. Res. 27, 309 (1994). [13] J. D. Dunitz, Chem. Commun. (Cambridge) 3, 545 (2003). [14] P. Verwer and F. J. J. Leusen, Rev. Comput. Chem. 12, 327 (1998). [15] T. Beyer, T. Lewis, and S. L. Price, CrystEngCommun 3, 178 (2001).

27

2.4 Robert B. Gerber

1. Vibrational Spectroscopy and New Force Field for Biological Molecules

In previous research reports, we described the development of a method of the calculation of anharmonic vibrational spectra of polyatomic (Vibrational Self-Consistent Field, VSCF, and several variants and extensions, especially Correlation Corrected VSCF, CC- VSCF). A major advantage of the algorithms developed is that they are directly applicable to potential surfaces from electronic structure calculations, i.e. to cases where the force field is available only on a grid of points in configuration space and not as an analaytic function. The research in the period of the report focused on applications to spectroscopy of biological molecules. This work included both contributions of the calculations to the interpretation of experimental data, in collaboration with the experimentalists, and the development of potential functions of quality, as tested by comparison with experiment. The main achievement in this direction was a study of the spectroscopy of the G···C complex of nucleotide bases. This work was done jointly with M. de Vries and coworkers (UCSB), who measured the vibrational spectroscopy of this system in a highly elegant molecular beam study. We also cooperated in this work with the group of P. Hobza (Prague), who carried out ab initio calculations. This work led to a satisfactory interpretation of the spectrum and also established the high quality of the Improved PM3 potential surface used in the calculations. Also, the results provide insights into the anharmonic couplings between different pairs of modes in this system. All in all, this work led to the determination of a high quality anharmonic potential surface for this important prototypical system. The calculations of this project were done by Dr. B. Brauer, a postdoc in our group. A paper based on this work was very strongly reviewed(1). Another result in this area of research are our calculations of the spectrum of DHU (dihydrouracile), and its complex with water(2). Also this study demonstrates the power of the VSCF methods, and the apparent success of the Improved PM3 potentials developed by our group for biological molecules. (1) B. Brauer, R.B. Gerber, M. Kabelac, P. Hobza, J.M. Bakker, A.G. Abu Rizik, J. Phys. Chem. A 109, 6974 (2005). (2) A. Adesokan, E. Fredj, E.C. Brown and R.B. Gerber, Mol. Phys. 103, 1505 (2005).

2. Vibrational Spectroscopy of Atmospherically-Important Molecules and Clusters Our calculations of the anharmonic vibrational spectra of molecules and clusters that (1) (2) include HNO3, HNO3-H2O, H2SO4, H2SO4-H2O provide the atmospheric chemistry community with useful experimental data in the study of these species. The most important new results are the calculations of overtone and combination mode transitions, that have hitherto not been available. The results provide insights into the nature of the anharmonic couplings between different modes. 28

This work was done by Yifat Miller, a research student in our group. (1) Y. Miller, G.M. Chaban and R.B. Gerber, Chem. Phys. 313, 213 (2005). (2) Y. Miller, G.M. Chaban and R.B. Gerber, J. Phys. Chem. A 109, 6565 (2005).

3. Photoionization Dynamics of Small Biological Molecules We have pursued the dynamics of small biological molecules (glycine, tryptophane) following single and two photon ionization. Despite the fundamental importance of photoionization in mass spectrometry, little is known on the dynamics of these processes. Our approach is based on classical dynamics using realistic potential surfaces from electronic structure theory in "on the fly" simulations (PM3 potentials, including variants and improvements). Some of the main results obtained are as follows: (a) Photoionization of glycine was found to result in fast internal rotation around the C-C bond, an effect that persists for at least 10 ps. This is an interesting prediction of a new effect.(1) (b) There are substantial deviations from RRKM behavior both for conformational transitions and for fragmentation processes for short timescales (t ≤ 10 ps). It seems that IVR is very incomplete on these timescales.(1)

(c) Photoionization seems highly selective with regards to the initial conformer. Different conformers give rise to different reactions on short timescales (t ≤ 10 ps).

We also carried out simulations of ionization of glycine adsorbed on a silicon cluster(3) (as a model for glycine on silicon surfaces). Work on this topic was done by Dorit Shemesh, a research student in our group. The work on glycine adsorbed on silicon clusters was done in cooperation with Professor Roi Baer. (1) D. Shemesh, G.M. Chaban and R.B. Gerber, J. Phys. Chem. A 108, 11477 (2004). (2) D. Shemesh and R.B. Gerber, J. Chem. Phys. 122, 241104 (2005). (3) D. Shemesh, R. Baer, T. Seideman and R.B. Gerber, J. Chem. Phys. 122, 184704 (2005).

29

2.5 Ronnie Kosloff

Cold matter studies

Creating Ground State Molecules with Optical Feshbach Resonances in Tight Traps

Together with Christiane P. Koch, Francoise Masnou-Seeuws we studied the proposal to create ultracold ground state molecules in an atomic Bose-Einstein condensate by adiabatic crossing of an optical Feshbach resonance. We envision a scheme where the laser intensity and possibly also frequency are linearly ramped over the resonance. Our calculations for 87Rb show that for sufficiently tight traps it is possible to avoid spontaneous emission while retaining adiabaticity, and conversion efficiencies of up to 50% can be expected.

Control of Ultracold Collisions with Frequency-Chirped Light

Together with M. J. Wright, S. D. Gensemer, J. Vala, and P. L. Gould, we report on ultracold atomic collision experiments utilizing frequency-chirped laser light. A rapid chirp below the atomic resonance results in adiabatic excitation to an attractive molecular potential over a wide range of internuclear separation. This leads to a transient inelastic collision rate which is large compared to that obtained with fixed-frequency excitation. The combination of high efficiency and temporal control demonstrates the benefit of applying the techniques of coherent control to the ultracold domain.

Intensity and wavelength control of a single molecule reaction: Simulation of photodissociation of cold-trapped MgH+

In collaboration with Solvejg Jørgenson and Michael Drewsen we carried out a simulation of the photodissociation of cold magnesium hydride ions MgH+ leading to either Mg+ + H or Mg + H+ from first principles. The purpose was to study the possibility of single molecule control of the products in the presence of two laser fields. The system evolves on four electronic potential-energy curves. These potential-energy curves are calculated from first principles using multireference self-consistent field theory. The accuracy of the electronic potential curves has been checked by calculating the energies of the rovibrational eigenstates and comparing them to experimental findings. The photodissociation dynamics has furthermore been simulated by solving the time-dependent Schrödinger equation. It is shown that the branching ratio of the two dissociation channels, Mg+ + H or Mg + H+, can be controlled by changing the intensity and wavelength of the two driving laser fields.

Study of improvised explosives

Decomposition of Triacetone Triperoxide Is an Entropic Explosion

With Faina Dubnikova, Joseph Almog, Yehuda Zeiri, Roland Boese, Harel Itzhaky, Aaron Alt and Ehud Keinan we studied both X-ray crystallography and electronic structure calculations using the cc-pVDZ basis set at the DFT B3LYP level were employed to study the explosive 30 properties of triacetone triperoxide (TATP) and diacetone diperoxide (DADP). The thermal decomposition pathway of TATP was investigated by a series of calculations that identified transition states, intermediates, and the final products. Counterintuitively, these calculations predict that the explosion of TATP is not a thermochemically highly favored event. It rather involves entropy burst, which is the result of formation of one ozone and three acetone molecules from every molecule of TATP in the solid state.

Atomistic-Scale Simulations of the Initial Chemical Events in the Thermal Initiation of Triacetonetriperoxide

With Adri C. T. van Duin, Yehuda Zeiri, Faina Dubnikova, Ronnie Kosloff, and William A. Goddard, we studied the initial chemical events related to the detonation of triacetonetriperoxide (TATP) and performed a series of molecular dynamics (MD) simulations. In these simulations we used the ReaxFF reactive force field, which we have extended to reproduce the quantum mechanics (QM)-derived relative energies of the reactants, products, intermediates, and transition states related to the TATP unimolecular decomposition. We find excellent agreement between the QM-predicted reaction products and those observed from 100 independent ReaxFF unimolecular MD cookoff simulations. Furthermore, the primary reaction products and average initiation temperature observed in these 100 independent unimolecular cookoff simulations match closely with those observed from a TATP condensed-phase cookoff simulation, indicating that unimolecular decomposition dominates the thermal initiation of the TATP condensed phase. Our simulations demonstrate that thermal initiation of condensed- phase TATP is entropydriven (rather than enthalpy-driven), since the initial reaction (which mainly leads to the formation of acetone, O2, and several unstable C3H6O2 isomers) is almost energy-neutral. The O2 generated in the initiation steps is subsequently utilized in exothermic secondary reactions, leading finally to formation of water and a wide range of small hydrocarbons, acids, aldehydes, ketones, ethers, and alcohols.

Nonadiabatic electronic processes

Nonadiabatic Charge Transfer Processes of Oxygen on Metal Surfaces

With Gil Katz and Yehuda Zeiri we studied the dynamics of charge transfer processes of oxygen on metal surfaces. Two theoretical frameworks, the adiabatic and the nonadiabatic, are compared with experiment. The O2/Al system is chosen as a representative example. In the adiabatic approach there is no barrier to dissociation. This fact contradicts experimental observations of an increase of the dissociation probability with incident energy. In this study a nonadiabatic framework is formulated where the encounter takes place simultaneously on four electronic surfaces, each representing a different charged oxygen species. The dynamics, starting from an oxygen molecule in the gas phase, is followed by solving the multichannel time dependent Schrödinger equation. The transition from the diabatic to the adiabatic limit is explored by varying the nonadiabatic coupling terms. By so doing the dissociation probability dependence on incident energy changes from a strong monotonic increase in the diabatic case, to a flat dependence in the adiabatic case. The influence of electronic quenching is also studied, based on a numerical solution of the Liouville von Neumann equation. The dynamics subject to 31 quenching shows a stronger initial dependence on incident kinetic energy leading to saturation. The general trend is quite similar to the dynamics without quenching.

The role of vibrationally excited NO in promoting electron emission when colliding with a metal surface: A non adiabatic dynamic model

With Gil Katz and Yehuda Zeiri we studied a non adiabatic quantum dynamic model developed to study the process of electron emission from a low work function metal surface. The process is initiated by scattering a highly vibrationally excited NO molecule from a surface composed of a Cs layer covering a Ru crystal. The model addresses the increasing quantum yield of the electron emission as a function of the molecular vibrational excitation and incident kinetic energy. The reaction mechanism is identi_ed as a long range harpooning electron transfer to a molecular ion which is then accelerated toward the surface. Upon impact, the molecular ion emits its excess electron. Dissipative dynamics of a system passing through a conical intersection: ultrafast pump-probe observables With David Gelman, Gil Katz and Mark A. Ratner we studied the dynamics of a system incorporating a conical intersection, in the presence of a dissipative environment. The purpose was aimed at identifying observable ultrafast spectroscopic signatures. A model system consisting of two vibronically coupled electronic states with two nuclear degrees of freedom is constructed. Dissipation is treated by two different methods, Lindblad semi-group formalism and the Surrogate Hamiltonian approach. Pump-probe experimental expectation values such as transient emission and transient absorption are calculated and compared to the adiabatic and diabatic population transfer. The ultrafast population transfer reecting the conical intersection is not mirrored in transient absorption measurements such as the recovery of the bleach. Emission from the excited state can be suppressed on the ultrafast time scale, but the existence of a conical intersection is only one of the possible mechanisms that can provide ultrafast damping of emission.

Quantum problems

On the temperature dependence of the interaction-induced entanglement.

With Michael Khasin we studied both direct and indirect weak nonresonant interactions are shown to produce entanglement between two initially disentangled systems prepared as a tensor product of thermal states, provided the initial temperature is sufficiently low. Entanglement is determined by the Peres-Horodecki criterion, which establishes that a composite state is entangled if its partial transpose is not positive. If the initial temperature of the thermal states is higher than an upper critical value Tuc the minimal eigenvalue of the partially transposed density matrix of the composite state remains positive in the course of the evolution. If the initial temperature of the thermal states is lower than a lower critical value Tlc ≤ Tuc the minimal eigenvalue of the partially transposed density matrix of the composite state becomes negative which means that entanglement develops. We calculate the lower bound Tlb for Tlc and show that the negativity of the composite state is negligibly small in the interval Tlb < T < Tuc. Therefore the lower bound temperature Tlb can be considered as the critical 32 temperature for the generation of entanglement. It is conjectured that above this critical temperature a composite quantum system could be simulated using classical computers.

1. Faina Dobnikova, Ronnie Kosloff, Joseph Almog, Yehuda Zeiri, Roland Boese, Harel Izhaky, Aaron Alt and Ehud Keinan Decomposition of TATP is an entropic explosion 2. J. Am. Chem. Soc. 127, 1146-1159 (2005). Christiane P. Koch, Françoise Masnou-Seeuws, and Ronnie Kosloff Creating Ground State Molecules with Optical Feshbach Resonances in Tight Traps Phys. Rev. Lett. 94, 193001 (2005). 3. Gil Katz, Yehuda Zeiri, Ronnie Kosloff Nonadiabatic Charge Transfer Processes of Oxygen on Metal Surfaces Isr. J. Chem. 45, 27 (2005). 4. M. J. Wright, S. D. Gensemer, J. Vala, R. Kosloff, and P. L. Gould Control of Ultracold Collisions with Frequency-Chirped Light Phys. Rev. Lett. 95, 063001 (2005) . 5. A. C. T. van Duin, Y. Zeiri, F. Dubnikova, R. Kosloff, W. A. Goddard III Atomistic-Scale Simulations of the Initial Chemical Events in the Thermal Initiation of Triacetonetriperoxide J. Am. Chem. Soc. 127, 11053 (2005). 6. Solvejg Jørgensen, Michael Drewsen, and Ronnie Kosloff Intensity and wavelength control of a single molecule reaction: Simulation of photodissociation of cold-trapped MgH+ J. Chem. Phys. 123, 094302 (2005). 7. G. Katz, Y. Zeiri, R. Kosloff, Role of Vibrationally Excited NO in Promoting Electron Emission When Colliding with a Metal Surface: A Nonadiabatic Dynamic Model J. Phys. Chem. B. 109, 18876 (2005 ) 8. Michael Kashin and Ronnie Kosloff On the temperature dependence of the interaction-induced entanglement Phys. Rev. A, 72, 052303 (2005). 9. David Gelman, Gil Katz and Mark A. Ratner, and Ronnie Kosloff Dissipative dynamics of a system passing through a conical intersection: ultrafast pump-probe observables. J. Chem. Phys. 123, 134112 (2005). 33

2.6 Raphael D. Levine

1. Objectives

The objective of this research effort remains unchanged: A theoretical and computational understanding of chemistry and physics under extreme conditions (which is characteristic of many situations of direct interest to the Air Force) and/or application to new experimental results for such processes.

2. Status of effort

Several papers have been submitted/published since the previous report. A complete list is included below. As written in the earlier report, scientists from different laboratories emphasize that for a variety of aerospace related applications it is necessary to better understand light emission from both natural and human-induced perturbations of the atmosphere. We have looked at possible molecular-level mechanisms for such processes. We chose water because our earlier work has stimulated the performance of a systematic experiment and the experiment used water. We believe that this could be the start of an organized exploration of the field of collision induced emission. This work is in progress and we hope to report on it soon. In the meantime we have a paper accepted on the extension of this work to reactive collisions.

3. New Findings

We believe that our completely new work on high energy density matter, as described in the appendix, is both of methodological interest in its own right and provides useful quantitative insights for the kind of densities that can be reached under realistic conditions.

4. Transitions:

On January 15, 2005 the book “Molecular Reaction Dynamics” has been officially published by Cambridge University Press, NY.

5. Honors/Awards:

In September 2004 R D Levine received the MOLEC 2004 award∗ at the MOLEC (MOLEcular Collisions) conference in Holland.

APPENDIX

∗ The citation reads ‘In honor of his outstanding studies of, and pioneering contributions to The Dynamics of Chemical Reactions’. 34

Transitory Ultra-High Pressure During Cluster-Surface Impact

Abstract

High energy density and compressed matter can be generated by a collision of a hypersonic cluster with a surface. The ultrahigh pressure interlude lasts only briefly from the impact until the cluster shatters. Pressures in the Mbar range are indicated for rare gas clusters. The pressure is computed using the virial theorem of mechanics that is shown valid also for a motion under constraint. The law of corresponding states is not satisfied at such high energy densities but a new form where the scale factor for the pressure is the impact energy per particle per unit cell volume is derived.

Matter under ultra-high pressure exhibits novel modes of behavior1. The high energy impact of clusters at a surface 2-5 offers a way offers a technique for compressing atoms or molecules together as is evident by formation of energy rich products that require close-in collisions. The high energy impact of clusters at a surface produces only a transient high pressure regime because the hot and compressed cluster rapidly shatters to many small fragments 6. Still, the high pressure interlude must last long enough for a number of collisions to take place, sufficient to scramble the memory of the initial conditions so that the emerging small fragments are distributed as in thermal equilibrium 4,7,8. It is therefore appropriate to ask how high a pressure is achieved during the compression stage. This letter offers a theoretical approach to the definition of pressure in a system such as a hot cluster and a computational implementation using constrained molecular dynamics. We report that pressures in the teraPascal range can be reached in clusters of heavy particles, e.g., Xe. An important dissipation channel of the hot and dense cluster is electronic excitation followed by ionization4,5. This is to be expected on the basis of the united atom limit 9,10. This is a correlation diagram, as a function of interatomic distance, between the electronic states of two separated atoms and the states of a ‘united’ atom with a nuclear charge as the sum of the charges of the two atoms. The correlation shows that low-lying states of the atoms correlate to higher excited states of the united limit. Therefore, upon compression electronic states are expected to cross. A detailed examination10 shows that many such crossings occur already when the two atoms approach within a separation not much below the equilibrium value. In this letter we assume that the compression occurs electronically adiabatically. Therefore we can take it that the atoms of the cluster interact by a velocity-independent potential. The available experimental4 and theoretical evidence is that this limits the impact velocity to be below about 10 kms-1 . Above this threshold there is a rapid rise in the yield of ionization. Theory attributes such an onset behavior to the inefficiency of inducing large changes in the translational momentum of the atoms11. There are two contributions to the pressure exerted by the atoms of the cluster. One is the reversal of their momentum under the influence of the constraining force (that under ordinary circumstances is due to the wall of the container). The other contribution is the change in momentum of an atom due to the force of the other atoms. This is the contribution that is known to chemists as the internal pressure. It represents deviation from an ideal gas behavior and it is often represented by a virial expansion12. For a bounded system the contribution of the interatomic forces to the pressure can be represented exactly as what is known12,13 as the virial of the force. 35

W = ∑ (r − r ) f (1) α i iα cmα iα The atoms of the cluster are indexed as i = 1,.., N , riα is the coordinate of atom i in the direction α, α = x, y, z , cm designates the center of mass and fiα is the force on the atom due to the other atoms and due to the surface at which the impact occurs. The force can be derived as the gradient of the interatomic potential provided that such a configuration-dependent potential is a valid approximation. The conventional derivation of the virial expression for the pressure exerted by a system requires that the motion of the system be bounded. The pressure is then derived as a long time average over the trajectory of the particles of the system12,13. If we confine the cluster to a container and wait then it will come to equilibrium and the pressure can be computed. But this is not the pressure that we here want to determine. We seek an instantaneous, time-dependent pressure that reflects first the compression and then the fast expansion of the cluster and the corresponding steep rise followed by decline in the pressure. A time-dependent pressure need not exhibit ultrafast fluctuations due to individual atom-atom or atom-surface collisions because first of all the potentials that we use have a finite range so that a collision is not instantaneous but takes time, albeit short, and, because the numbers of atoms in the cluster is finite but not small, different collisions overlap in time. We do find structure in the pressure computed as a function of time but this structure can be shown to reflect collective rather than uncorrelated atom motions. To derive an equation for the time-dependence of the pressure we start, as in the derivation of the virial theorem, with the time evolution of the hyperradius ρα (t). For a cluster of N 2 identical atoms rate of change of ρα (t) is  2 N G α ≡=Mtραα()/2 m∑i = 1()ric−rmα(riα−rcmα) (2) where M = mN is the mass of the cluster. The force Fiα on particle i is defined by the Newton equation of motion of the particle in the direction α, Fiα = mriα . We resolve Fiα as the sum c Fiα = fiα + fiα of the force due to a constraint and the force fiα derived from the unconstrained mechanical motion. The time derivative of G is α 2 NNc N2 Mtραα( )/2=−∑∑ii==11()ricrmαfiα+()ricα−rmαfiα+2∑i=1(m/2)()ricα−rmα (3) The force on the particle due to the constraint is equal in magnitude and opposite in sign to the force that the particles exert, the force that gives rise to the pressure. To express the contribution of the constraint force as an integral of this force acting along the normal to the surface we replace the summation over all particles by integration over the volume and then use Green’s theorem 12,14 to convert the volume to a surface integral. Thereby the instantaneous pressure is defined c PVα =-∑i (rricαα− m)fiα (4) Just as for a gas at ordinary temperatures and density, the pressure is defined by confining the motion. At equilibrium we specify the constraint that G as defined by equation (2) is14 α ‘constant or at least does not exhibit a secular increase with time’. This constraint insures that the long time average of dG / dt is zero and hence defines the pressure as the long time average of the right hand side of equation (3). We want to define an instantaneous pressure and 36 so we impose the constraint that G is constant or, equivalently that the instantaneous value α of dGα / dt is zero. To impose the constraint that G as defined by equation (2) stays constant at its value at the α time τα the computation proceeds as follows. An unconstrained molecular dynamics simulation of cluster impact is performed up to the time point τα at which point the constraint is imposed. We can thereby compute the pressure at any time t ≥ τα . What we mean by the instantaneous pressure is the pressure just past the time τα at which the constraint is imposed. A sequence of values of τα defines the time-dependent pressure, P (τα ) as a function of τα . In practice a single trajectory (with some back integration at every time point τα ) can be used to generate the entire τα -dependent pressure function. The constraint that G stays constant is non-holonomic because G is a function of the α α velocities and not only of the configuration. However G is linear in the velocities and for this α special case of a non-holonomic constraint it is well understood how to add the force of constraint to the Newton equations of motion15. In terms of a, thus far undetermined, Lagrange multiplier λα (t) the equation to be solved is mrjjα =−f ααλ ()t ∂G α∂r jα,t ≥τα (5) 13 This value for rjα is used in the Gear routine for integration of Newton’s equations of motion. For an impact along the surface normal the equation of motion in the α = x direction, where the distance x is measured from the surface is mxii=−()∂V ()r d x −(∂U (x)d xi)(1+Γ xi) (6) V (r) is the interatomic potential energy function. We use a sum of two body potentials, each of the Lennard-Jones 12,6 form of depth ε and range σ. U(x) is the repulsive potential, ε(σ / x)12 , for the interaction of the atom and the surface. We allow energy dissipation to the surface by introducing a frictional force, proportional to the velocity, which only operates very near to the surface. By setting the magnitude of the friction coefficient Γ, dimensions of inverse velocity, we impose ca 40% energy loss. Equation (6) defines the force fix . For t ≥ τ x there is also the contribution due to the force of the constraints as shown in equation (5). In the directions parallel to the surface the force fiα , α = y, z is derived only from the potential V (r) . The Gear algorithm propagates the coordinates (and velocities and acceleration) to the next time point, t + δt by Taylor expansion about the present values. Then the predicted values are used to update the value of the force and thereby provided corrected values. We modify this routine as follows. The values are first corrected using the force fiα . These are the unconstrained corrected values. Now we make a second correction whereby the unconstrained corrected values are used to compute the force of the constraint and update to a set of constrained corrected values. The constrained corrected values depend on a yet unknown value of the Lagrange multiplier at the new time point λα (t + δt) . The value of the constraint is now used to compute the new value of the Lagrange multiplier. It is now possible to compute the pressure by equation (4) that reads explicitly 37

2 PVα ()tt()=-λαα()tm∑i (ric((t) − rmαt)),t≥τα (7) At the time τα or very close thereafter the value of the Lagrange multiplier is noisy due to the discontinuity in the accelerations since an additional force is imposed at the time τα . By the pressure at the time τα we therefore mean at a time very shortly past when the numerical noise has subsided. The volume is also time dependent because the cluster compresses or expands. We approximate the volume of the cluster as that of an ellipsoid where the principal radii are 2ρα , α = x, y, z . To express the pressure in dimensionless units we first note that there are inherent length and energy scale factors provided by the range σ and depth ε of the potential. If, furthermore, time is scaled by the period (mσ 2 / ε)1/2 of the motion in the potential well, also the kinetic energy scales as ε. The pressure as computed by the virial theorem will then scale as ε / σ 3 . This is the scaling familiar from equilibrium statistical mechanics but it does not reproduce the trends in the simulations we performed. The problem appears to be with the scaling of time. In hypersonic impact the initially directed kinetic energy very rapidly gets randomized8. The duration of an atom-atom collision therefore scales as σ / v where v is the velocity of impact. If σ / v is used as the scale of time it is found that the scale factor that brings the pressure to dimensionless form is mv2 σ 3 . Figure 1 shows that this scaling works for comparing collisions of Ar and Xe clusters at a given impact velocity. m / σ 3 equals 1.01 and 1.96 amu ⋅ Å−3 for the two elements respectively. The results are plotted in a ‘double X’- ‘double Y’ format. The Shown is the pressure vs. time. The spacing of tick marks fort the two axes of time is in the ratio of the σ’s, i.e., 1.17 .The spacings between tick marks of the two ordinates are in the ratio of 1.94. In this way the absolute value of the pressure, several Mbars, can be directly read from the plot. The scaling with the velocity of impact is shown in figure 2. 38

Figure 1. The pressure component in the direction parallel to the surface, solid line, in Mbar units, exerted by a cluster of 125 Ar atoms, left ordinate, or 125 Xe atoms, right ordinate, incident at 10 kms-1 in a direction normal to the surface, vs. time in fs. As discussed in the text the scale of the two ordinates is in a ratio of 1.94/1. This brings the two plots of the pressure to be nearly superposable except at the very peak where the pressure of the Xe cluster is somewhat higher. The pressure is computed from the virial theorem as a sum of two components shown, for Xe, as dashed and dotted curves. Dash- pressure due to the random kinetic energy of the atoms. Before the impact all the kinetic energy is directed. At longer time the cluster shatters, its volume rapidly increases and the pressure decreases. Dots- pressure due to the repulsive interaction between the atoms. Due to the rapid expansion this component decreases earlier.

Results for molecular dynamics simulations for the pressure exerted in a direction parallel to the surface of impact as a function of time are shown in figure 1. This is the simpler case because the surface is taken to be not corrugated so there is no force in exerted by the surface in the parallel direction. There are then only two contributions to the pressure, cf. equation (3), the random kinetic energy and the internal pressure. The two contributions are seen to be roughly comparable in magnitude and to have the same sign. This means that the internal pressure is very strongly repulsive. This is another indication of the high density within the cluster. The total pressure is the solid curve. It is computed from the virial theorem as the sum of the random kinetic energy and the internal pressure. The alternative expression in terms of the force of the constraint, cf. equation (7), yields essentially identical values. Note that at this high velocity and for the heavy rare gas the pressure can reach 0.3 teraPascal. 39

Figure 2. The pressure component in the direction normal to the surface, in Mbar units, exerted by a cluster of 125 Xe atoms, incident at 5 kms-1 left ordinate and bottom abscissa, or incident at 10 kms-1 , ordinate on the right and top abscissa, vs. time in fs. As discussed in the text the scale of the two ordinates is in a ratio of 4/1 while the ratio of the two times scales is 2/1. The negative values immediately after impact is due to the repulsive force from the surface. This force dominates at early times.

The time scale σ / v for an impact velocity of 10 kms-1 is 40.6 fs for Xe and 34 fs for Ar. This is seen to be of the order of the period of the structure in the pressure vs. time plot shown in figure 1. We attribute this structure to a few vibrations executed by the front atoms of the cluster that are caught between the surface and the bulk of the cluster. There is also a motion with a longer period due to a shock wave that transverses the cluster from the surface to the other end of the cluster and back3,16. But this motion is much more clearly seen in the pressure in the direction normal to the surface as shown in figure 2. The new feature in the pressure component in the direction normal to the surface is the pressure due to the steeply repulsive potential U(x) between the atoms and the surface, cf. equation (6). The initial response to this force is the compression of the cluster in that direction. This unlike the behavior in the direction parallel to the surface where upon impact the cluster immediately expands17. The initial compression means physically that at early times after the impact the pressure has an opposite sign as shown in figure 2. The force due to the surface has a negative sign because we regard it as an internal force of the system. If we chose to regard it as an external force and move the corresponding virial to the left hand side of equation (3) then the same force will appear as a positive pressure due to the cluster. Another manifestation of the force due to the surface is the few vibrations of those atoms at the front of the cluster that are trapped between the repulsion from the bulk of the cluster, a repulsion that 40 pushes them towards the surface and the repulsion in the opposite direction due to the surface. The net effect is the fast oscillatory modulation, period ca. σ / v that is seen in both figures 1 and 2. At a given mass of the atoms the scale factor for the pressure increases as the square of the impact velocity. The scale factor for the time decreases inversely as the impact velocity. As shown in figure 2 these scale factors do account for the main trends in the results of the simulations. The increase in the pressure with the kinetic energy of impact per particle is tempting as a route to even higher pressures but our simulations are not physically reliable at even higher incidence velocities because in the physical system there will be an onset of copious ionization4,5,18. A cluster compacted by hypersonic impact at a surface can reach enormous energy density. The kinetic energy can be characterized by its random part or equivalently by a temperature. We argued that the potential energy can be characterized by the virial of its force, ∑atoms r⋅f , and that the two contributions are about equal in magnitude. The pressure characterizes the sum of the two. Molecular dynamics simulations suggest that the peak transient pressure can reach the teraPascal range and that we understand the scaling of the pressure with the prime variables of the systems.

1 H. G. Drickamer, Ann. Rev. Phys. Chem. 33, 25 (1982); E. G. A.F. Goncharov, H.-k. Mao, Z. Liu, R.J. Hemley, Phys. Rev. Lett. 85, 1262 (2000); R. J. Hemley, Ann. Rev. Phys. Chem. 51, 763 (2000); M. Bastea, A. C. Mitchell, and W. A. Nellis, Phys. Rev. Lett. 86, 3108 (2001); D. Beule, W. Ebeling, A. Forster, H. Juranek, R. Redmer, and G. Ropke, Phys. Rev. E. 63, 060202 (2001); W. D. Mattson, D. Sanchez-Portal, S. Chiesa, and R. M. Martin, Phys. Rev. Lett. 93, 125501 (2004); Y. Q. Yang, S. F. Wang, Z. Y. Sun, and D. D. Dlott, Journal of Applied Physics 95 (7), 3667 (2004); V. V. Brazhkin and A. G. Lyapin, Nature materials 3, 497 (2004); P. F. McMillan, Nature materials 1, 19 (2002). 2 U. Even, I. Schek, and J. Jortner, Chem. Phys. Lett. 202, 303 (1993); W. Christen and U. Even, European Physical Journal D 9, 29 (1999); H. Yasumatsu, A. Terasaki, and T. Kondow, J. Chem. Phys. 106, 3806 (1997); T. Raz and R. D. Levine, in Atomic and Molecular Beams, edited by R. Campargue (Springer, Berlin, 2000); M. Gupta, E.A. Walters, and N. C. Blais, J. Chem. Phys. 104, 100 (1996); T. Raz and R. D. Levine, J. Phys. Chem. 99, 7495 (1995); H. Yasumatsu and T. Kondow, Reports on Progress in Physics 66 (10), 1783 (2003); R. J. Beuhler and L. Friedman, Chem. Rev. 86, 521 (1986). 3 T. Raz, I. Schek, M. Ben-Nun, U. Even, J. Jortner, and R. D. Levine, J. Chem. Phys. 101, 8606 (1994). 4 E. Hendell and U. Even, J. Chem. Phys. 103, 9045 (1995). 5 U. Even, P. J. d. Lange, H. T. Jonkman, and J. Kommandeur, Phys. Rev. Lett. 56, 965 (1986). 6 E. Hendell, U. Even, T. Raz, and R. D. Levine, Phys. Rev. Lett. 75, 2670 (1995); W. Christen, U. Even, T. Raz, and R. D. Levine, Int'l J. Mass Spectrom. & Ion Proc. 174, 35 (1998); U. Even, T. Kondow, R. D. Levine, and T. Raz, Com. At. Mol. Phys. (1999). 7 H. Yasumatsu, S. Koizumi, A. Terasaki, and T. Kondow, J. Chem. Phys. 105, 9509 (1996); W. Christen, U. Even, T. Raz, and R. D. Levine, J. Chem. Phys. 108, 10202 (1998). 8 T. Raz and R. D. Levine, Chem. Phys. 213,, 263 (1996). 9 W. Lichten, Phys. Rev. 164, 131 (1967). 41

10 G. Herzberg, Molecular Spectra and Molecular Structure I. Spectra of Diatomic Molecules. (Van Nostrand, Princeton, 1950). 11 R. D. Levine, Molecular Reaction Dynamics. (The University Press, Cambridge, 2005). 12 J. O. Hirschfelder, C. F. Curtiss, and R. B. Bird, Molecular Theory of Gases and Liquids. (John Wiley, New York, 1954). 13 M. P. Allen and D. J. Tildesey, Computer Simulations of Liquid. (Clarendon, Oxford, 1987). 14 R. H. Fowler, Statistical Mechanics. (University Press, Cambridge, 1936). 15 S.-P. Liu, Am. J. Phys. 49, 750 (1981); E. J. S. J.V. Jose, Classical Dynamics: A Contemporary Approach. (Cambridge University Press, 1998); J. R. Ray, Am. J. Phys. 40, 179 (1972); D. J. Evans and G. P. Morriss, Computer Phys Reports 1, 297 (1984). 16 I. Schek and J. Jortner, J. Chem. Phys. 104, 4337 (1996); I. Schek, J. Jortner, T. Raz, and R. D. Levine, Chem. Phys. Lett. 257, 273 (1996). 17 A. Gross, H. Kornweitz, T. Raz, and R. D. Levine, Chem. Phys. Lett. 354, 395 (2002). 18 Y. L. Beyec, Intl J Mass Spectrometry Ion Phys 174, 101 (1998).

42

PART II

STATUS REPORT

for

December 2005

BACKGROUND

• Brief history of the center

• Members and personnel

• The Beirat

• Operation

• Space

• The computer unit

UPDATE

• Research and support staff

• Symposia supported by the Center

43

Part II

Status Report

3. Background

3.1. Brief history of the center

The Fritz Haber Research Center for Molecular Dynamics has been established by the Minerva Society and The Hebrew University to strengthen the synergy between theory and experiment, to support research in molecular dynamics and to encourage cooperation between German and Israeli scientists. The center, which supports theoretical research in all branches of chemical and molecular physics, began its activities in January 1981. The agreement between The Minerva Society of the Federal Republic of Germany and the Hebrew University, providing an endowment fund for the Fritz Haber Research Center, was signed in August 1981. The computer facility started operation in November 1981. The official inauguration of the Center took place on May 26, 1983. The initial endowment fund was 1,000,000 DM. On the occasions of the fifth anniversary of the Center in 1986 and the tenth anniversary in 1991, Minerva announced increases in the endowment fund. In 1986 the endowment was increased by 1,000,000 DM and in January 1992 by 500,000 DM. In July 1997 the endowment was further increased by 1,000,000 DM. The annual budget stems from the endowment’s interest, matched by Hebrew University support. Because of the drastic drop in interest rates and the decrease in USD/EU exchange rate, the average annual budget which was about 200,000 EU until 2001, has dropped to about 75,000 EU in recent years. It should be emphasized that the entire budget is dedicated to the joint activities of the center and its infrastructure. In addition, members of the center are funded by external agencies on a per-project basis. There are about 23 such current projects, with a total annual budget of over 500,000 USD. At inception, headed by its first director, Professor R.D. Levine, the Fritz Haber center numbered about ten members and a similar number of associate members, including both experimentalists and theoreticians from the Hebrew University and other universities in Israel. Prof. E.W. Schlag has served as the first Chairman of the center’s scientific advisory board (the Beirat) and accompanied its activities and development until 1998. From 1998 to 2005, the Beirat’s Chair was Prof. G. Comsa. From 2006 the chair is Professor W. Domcke, and the other members of the Beirat are: Professors H. Bercovier (HU Vice President for Research), G. Meijer, H. Grübmuller, N. Moiseyev, M. Asscher and A. Nitzan. Prof. R.B. Gerber served as the second director of the center, from 1989 until 1991; Prof. R. Kosloff took over in 1991 until 1998; and from 1998 the director is Prof. A. Ben-Shaul. The academic activities and scientific achievements of the center have been thoroughly evaluated twice, by review committees composed of world leaders in molecular dynamics and theoretical chemistry. First in 1994 and then in 2002. In both cases the reports of the review committees were very positive. They also contained some suggestions for improvement which we gladly accepted and implemented. 44

Following the establishment of other Minerva centers, including two which are based at the institute of chemistry of the Hebrew University (the Lise Meitner center for Computational Quantum Chemistry and the Farkas center for Light-Induced Processes), Minerva and the Hebrew University have established new regulations, stipulating that a researcher cannot belong to more than one center, and there can be no associate members. Thus, cur- rently, the Fritz Haber center consists of six research groups (Agmon, Ben-Shaul, Buch, Gerber, Kosloff, Levine). As mentioned in the introduction, two younger scientists are supposed to join the center within less than a year from now. Thanks to generous special Minerva grants and partial support from the Hebrew University, as well as other occasional contributions, the center has been able to frequently update its central computational facilities. Presently, most research groups possess personal multi-cpu clusters dedicated to their specific research. Several high performance multi-processor machines are still operational and provide cooperative computational abilities. Regrettably, for many years now, no support for renewing our central computing facilties has been forthcoming.

3.2. Scientific scope

Originally, and in accordance with its name, research at the center has been mostly concerned with molecular reaction dynamics and closely related topics, such as laser-molecule and surface-molecule interactions. In the spirit of the period, the research has focused on processes involving small molecules and state-to-state processes, usually in the gas phase. Twenty five years later, part of the research carried out at the center is still concerned with molecular rate processes but emphasis has shifted towards larger and more complex systems, such as molecular clusters, reactions in solution and protein dynamics. This comprehensive definition of the center’s scientific goals has been approved, even encouraged, by both evaluation committees, in 1994 and 2002. Indeed, we find that while strong expertise and the existence of a ’critical mass’ of researchers in a specific field (molecular dynamics in our case) is imperative for success, the dialogue with researchers in neighboring fields of science is invaluable. Similarly, as attested by many joint publications, close collaboration with experimental groups is a characteristic of all research groups at the center. Overall, research at the center spans a broad spectrum of systems, phenomena and theoretical approaches. The systems investigated range from coherent light-matter interaction, noble gas molecules, hydrogen-bonded systems, and molecule-surfaces interactions, through van der Waals and hydrogen bonded clusters, nanoparticles, surfaces, Bose-Einstein condensates, impact-heated clusters, all the way to ligand-protein binding kinetics, the assmebly mechanism of viral particles, and cell locomotion. The phenomena of interest, dealing mainly with dynamical, kinetic, and radiative processes, also involve a wide spectrum of inter-particle interactions and diverse molecular properties. A number of research projects are concerned with quantum effects such as chemical selectivity mediated by the coherent control of laser-matter interaction, ultra cold (nano K) chemistry, or novel architectures of quantum dots towards the development of chemically synthesized computers. At least three groups at the Center are engaged in the research of molecular clusters. These studies include the dynamics and thermodynamics of cluster-surface encounters and, on a more microscopic level, the internal dynamics, structure, spectroscopy and photochemistry of molecular clusters, especially water oligomers and ion-water complexes. 45

The theoretical understanding of the systems and phenomena mentioned above requires the development of new theoretical methods and sophisticated computational algorithms. As in the past, all members of the Center have been involved in such developments. Their record of theoretical contributions to molecular reaction dynamics, quantum dynamics, algebraic methods, coherent control, statistical and information theoretic approaches, diffusion kinetics, spectroscopy, quantum chemistry, protein structure and dynamics, as well as the statistical thermodynamics of complex fluids and biophysical systems, are well recognized. The various research interests of the members and the research topics pursued in their groups during the last seven years have been thoroughly described in the 2002 hepta-annual report and updated in Part I of the this report.

3.3. Academic activities

The scientific activity at the center has always been intense. Usually, about fifty scientists participate in this activity, including graduate students, post-doctoral fellows, visitors and faculty. There have been many added values to this activity, in addition to the many publications summarizing the research in the various groups. The weekly Fritz Haber seminar, now running continuously for over twenty years, has become an “institution”, hosting and attracting numerous scientists - from world leaders in their field to graduate students delivering their first public talk. The center and its activities have attracted numerous young scientists to carry out their post- doctoral research or graduate studies at the Hebrew University. Over the years we have benefited from the presence of many dozens of post-doctoral fellows from Europe, the US and other countries around the world. Even during the difficult intifada times in Israel, and especially here in Jerusalem, there were several foreign post-doctoral fellows actively pursuing research at the Fritz Haber center. Our many young excellent graduate students have always been an enthusiastic and exciting element in the center. Many of our former graduate students are now serving as senior scientists in various industrial companies, as well as in government and private research laboratories. Many others are among the leading scientists in academic institutes in Israel. Many are faculty members in leading foreign universities. The center has a well established tradition of organizing and supporting scientific meetings in Israel on Molecular Dynamics and related fields, notably those where center members are involved in the organization. To encourage theoretical chemistry research in Israel, The Fritz Haber Center has initiated and organized a comprehensive theoretical chemistry conference (The first TheoChem meeting), which took place in Jerusalem in October 2002. This meeting has been a great success and has paved the way for more successful meetings since then. Several international meetings involving members of the center which took place afterwards are listed in Sec. 4.2 below. In particular, in March 2005, on the ocaassion of the Beirat meeting we held a special symposium on Biophysical Dynamics where, apart from several German and other distinguished speakers, most lectures were given by young faculty members from different Israeli institutes. This has been a very successful and inspiring meeting.

46

3.4. Personnel

The center’s administrative and technical staff are well trained and highly dedicated. Our complex and diverse computing services are taken care of by a professional system manager helped by a part time assistant system manager. The current system manager is Mr. Grigory Rashkovan, who performs an excellent job in maintaining and upgrading our computational infrastructure. Most valuable help in maintaining and developing the computing facility in the center is provided by Merav Dehan, who works at the center part time. The entire administrative work at the center which involves following up and allocating funds to the many budgetary items, the purchase of equipment, taking care of all the visitors and students, and coordinating these activities with the Hebrew University’s administration - all this workload is shouldered most efficiently by Ms. Geula Levy. Mrs. Eva Guez, the center’s secretary since its inception, has retired in September 2001. Eva is still helping us on a part time basis, including in the preparation of this report. The Institute of Chemistry supports the basic salary of the system manager. The part time system manager assistant; extra hours and many other benefits are paid from the center’s budget. No support is provided for administrative services.

3.5. Interaction with the Institute of Chemistry All members of the center are faculty members at the Department of Physical Chemistry, The Institute of Chemistry at The Hebrew University. In practice, the Fritz Haber Center constitutes the theoretical chemistry group at the Institute of Chemistry. As faculty members of the Institute of Chemistry, all members of the center participate in all the academic and teaching activities, e.g., serving as members and chairs of various university committees. The center provides and supports a framework for research activity, but all academic and technical appointments are made via the Institute of Chemistry. The academic and administrative interaction with the Institute of Chemistry is generally cooperative and fruitful.

3.6. The computer unit

The System Manager since April 2005 is Grigory Rashkovan, and his assistant, Merav Dehan, are responsible for the maintenance and development of our computer services, which include both equipment of the Center, and machines used by individual groups. Computational research activities in all the groups depend heavily on the smooth functioning of the unit. All the members and their research groups work on personal workstations managed by the unit. There are currently about 50 workstations, mostly running RedHat Linux on PC hardware, but there are also many Windows PCs, laptops, Macs, and a few SGI workstations. All of the workstations and servers are connected by a switched 100Mb Ethernet network with a 1Gb backbone network. Also, laptop owners can use the recently installed wireless connection network with a 54Mb speed. All UNIX servers share a central file server with over 800 GB of RAID protected storage. For Windows users we also maintain two Windows 2003 active directory servers with 300GB of shared storage. In addition to the personal workstations, the center provides several computational platforms for running heavy simulations. Some of these are for specific groups, and others are shared by all groups. These include an aging Silicon Graphics (SGI) Origin 2000 (Ouzo and Gustav) with 8 CPUs and 8 GB or RAM, an upgraded 47

SGI Origin 300 (Born) with 8 CPU and 8 GB, Six Linux cluster running the Mosix cluster management. These are running on single and dual Pentium 3 and 4 computers. There are a total of 100 nodes on these clusters.

3.7. The Beirat

The Beirat is requested to report to Minerva on the program, budget and activities of the Center. Annually, the center submits a report to the Beirat, detailing the scientific progress and activity, as well as a financial report and a budget proposal for the next year. In recent years, the Beirat convenes every second year. The last meeting was held in Jerusalem in March 2005 and included a successful international symposium on Biophysical Dynamics. The Chairman of the Beirat and the Jerusalem Director work jointly on an online basis. The Beirat oversees and advises as to the operations of the Center. The current Members of the Beirat are:

Prof. W. Domcke (Munich, Germany), Chairman Prof. Bercovier, H. (Jerusalem, Israel, Vice President for R&D, Hebrew University). Prof. H. Meijer (Berlin, Germany), Prof. H. Grubmüller (Göttingen, Germany) Prof. N. Moiseyev (Haifa, Israel) Prof. A. Nitzan (Tel-Aviv, Israel) Prof. M. Asscher (Jerusalem, Israel)

The members of the center would like to sincerely thank the present and past members of the Beirat for their constant advice, encouragement, constructive criticism and support through all the years, some of which were difficult in many respects.

48

4. Update

4.1 Research and support staff

There are usually over 50 scientists at the Center, including professors, visitors, post- doctoral fellows and graduate students. Two system managers are responsible for the maintenance and frequent upgrading of the diverse computing facilities of the Center and those of its members. An administrative assistant is in charge of all budgets, student fellowships, purchase orders, visitors’ arrangements, meetings, seminars, etc. We list below the staff, students and long term visitors in the center during the last year.

A. Members of the Center:

N. Agmon, Ph.D., Professor of Theoretical Chemistry A. Ben-Shaul, Ph.D., Sherman Professor of Theoretical Chemistry V. Buch, Ph.D., Professor of Theoretical Chemistry R.B. Gerber, D.Phil., Fiedler Professor of Chemistry R. Kosloff, Ph.D., Sonneborn Professor of Theoretical Chemistry R.D. Levine, Ph.D., D.Phil., Max Born Professor of Natural Philosophy

B. Visiting faculty for 2004/5 (long visits):

Dr. Ch. Koch (Germany) Dr. F. Remacle (University of Liege) Dr. V. Teif (Inst. of Bio-Organic Chemistry, Belarus Nat. Acad. Sci., Minsk) Dr. M. Vatasescu (Inst. for Space Sciences, Bucharest, Romania)

C. Postdoctoral fellows and research associates (temporary positions):

Brauer, B., Ph.D. (Israel) Brown, E., Ph.D., (USA) Kallush, S., Ph.D., (Israel) Kurzweil, Y., Ph.D., (Israel) Sheng, L., Ph.D., (China),

D. Graduate students:

Adesokan, A., M.Sc., Amshalem, M., B.A., Ansbacher, T., B.Sc., Baer, L., B.Sc., Brill, Y., M.Sc., Cohen, A., M.Sc., Eshet, C., B.Sc., Gelman, D., B.Sc., Goldstein, M., M.Sc., Granot, R., M.Sc., Gross, A., M.Sc., Grumbach, M. B.Sc., Hassin, M., M.Sc., Jacobi, S., M.Sc., Klein, M., B.A., Kogan, K., B.A., Lavie-Tzafrir, Z., M.Sc., Lifshitz, E., M.Sc., Markowitz, O., B.A., Miller, Y., M.Sc., Nidal, S., B.Sc., Razak, Y., B.Sc., Rejwan, M., M.Sc., Richka, N., B.Sc., Segev, E., M.Sc., Sharir, A., B.Sc., Shai, N., M.Sc., Shemesh, D., M.Sc., Slavin, O., Steinberg, M., M.Sc., Steinitz, D., M.Sc., Suvan, M., M.A., Tokarski, S., B.Sc., Tzivyon, U.O., B.A., Tzlil, S., M.Sc. 49

E. Technical staff: System Administrators: Grigory Rashkovan, Merav Dehan (Assistant) Administrator: Geula Levy

4.2. Symposia supported by the Center

The Center and Members have organized numerous international meetings and symposia since its foundation. The Center also supports, generally modestly, symposia in research fields related to its scientific activities; especially symposia involving the Center’s members in the organizing committees, or as invited speakers. Below, is the list of meetings supported since 1998. (Recall that during the last several years, owing to the difficult political situation in Israel, organizing scientific meetings in Israel was quite difficult. )

From Clusters to Nano-Wires and Surfaces Symposium

This one day (13 May, 1998) Symposium, partially supported by the Center, was organized by Prof. M. Asscher in honor of the Wolf Prize Laureates in Chemistry.

Proton Solvation and Proton Mobility Conference

This four-day conference was held at Neve Ilan (Oct. 18-22, 1998), organized by Prof. N. Agmon and partially supported by the Center.

Workshop on Protein Folding and Dynamics

This workshop (August to December 1998) was organized and coordinated by Prof. R. Elber under the auspices of The Institute for Advanced Studies of The Hebrew University and was widely attended by Members of the Center, their students and visitors.

Frontiers in Chemistry and Material Science

The Center contributed to the organization of the 4’th joint symposium between the Technical University of Berlin and the Institute of Chemistry of The Hebrew University. Four members of the Center served as discussion leaders or delivered invited lectures. The meeting was held in Jerusalem on February 20-25, 1999.

50

Diffusion Assisted Reactions

Prof. N. Agmon has served on the organizing committee of the workshop on ”Dif- fusion Assisted Reactions” which was held at the Weizmann Institute in March 14-19, 1999.

Self-Assembly of Biological and Synthetic Amphiphiles

Prof. A. Ben-Shaul has served as a member of the organizing Committee of the ISF workshop on ”Self-Assembly of Biological and Synthetic Amphiphiles”, held at the Weizmann Institute, June 29-30, 1999. Five of the foreign invited speakers at this meeting came from Germany.

Molec 2000 - European Conference on Dynamics of Molecular Collisions

Prof. Kosloff served on the organizing committee of this conference. Prof. Levine delivered an invited talk at this conference which took place in Jerusalem, September 17-21, 2000.

Advances in Finite-Time Thermodynamics

Prof. Kosloff organized this symposium which took place in Jerusalem, 12-14 November, 2000.

The James Franck Beirat Meeting

The Fritz Haber Center partially supported the James Franck Beirat Meeting which was held at the same time as the FH Beirat Meeting, February 2001.

Israel TheoChem I

The Fritz Haber Center initiated this first Israeli meeting on Theoretical Chemistry. It was organized by Professor B. Gerber, V. Buch, N. Agmon and R. Baer. It took place in Jerusalem in 9-10, October 2002.

Ein Gedi Workshop II: Non Adiabatic Processes at Surfaces

Prof. Kosloff was on the organizing committee of this symposium which took place at Ein Gedi, 11-15 January, 2004.

The Gentner Symopsium, in honor of Professor Erich Sackmann: Physics of Biomaterials and Soft Matter

Professor Ben-Shaul was on the organizing committee of this MINERVA - Gentner symposium, which took place in the Nirvana hotel, Dead Sea, March 14-17, 2004

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The Safed Workshop on Quantum Dissipation

Professor Kosloff was on the organizing committee of this workshop which was held at the Hotel Merkazi in Safed, August 29 to September 4, 2004.

The Fritz Haber Symposium on Biophysical Dynamics

Professor Kosloff and Professor Agmon were on the organizing committee of this workshop, which was held at the Jerusalem Mt Zion Hotel, March 13-14, 2005.

At least two additional symposia will be supported by the center in 2006.

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PART III

APPENDICES, 2000-2005

• List of visitors and seminar topics

• List of publications*

(*Under the auspices of the Fritz Haber Center)

53

Part III

Appendices

5. List of visitors and seminars, 2000-2005

4.1.00 Prof. J. Jortner, Tel-Aviv University Charge Transfer and Transport in Molecular Systems 9.1-7.2.00 Ch. Koch, FH Inst., Berlin Surrogate Hamiltonian with Application to Quenching in Nickel Oxide 9.1-7.2.00 S. Thiel, FH Inst.Berlin Solution of the Schr ¨odinger Equation to Describe Photolysis on Oxide Surfaces 12.1.00 Prof. R.S. Eisenberg, Rush Medical College, Chicago Selectivity in Ionic Channels: A Mean Spherical Approximation 16-22.1.00 Prof. J.P. Devlin, Oklahoma State University Structure, Dynamics and Adsorbate Interactions of Ice Particles in the 4-80 Range 17-31.1.00 Dr. F. Masnou-Seeuws, Lab. Aime Cotton, Orsay Formation of Ultra-Cold Molecules 25.1.00 Dr. F. Masnou-Seeuws, Lab. Aime Cotton, Orsay Formation of Ultra-Cold Molecules Through Photoassociation 7-8.2.00 Dr. I. Bivas, Bulgarian Acad. Sci. Mechanical Properties of Lipid Bilayers, Containing Grafted Lipids 8-16.2.00 Prof. S. May, Jena Membrane-Macromolecule Interaction 16-27.2.00 Dr. J. Sadlej, Warsaw Hydrogen Bonding in Water Clusters 19.2-1.3.00 Prof. M. Severson, Oakland Univ. Quantum Monte Carlo Simulation of Excited Intermolecular Vibrational States in Water Clusters 23.2.00 Prof. K. Kern, MPI f. Festkoerperforschung, Stuttgart Atomic & Molecular Architecture at Surfaces 29.2.00 Prof. M.S. de Vries, Inst. of Chemistry, HU Shedding Light on Life’s Building Blocks, One by One 7.3.00 Dr. V. Kokoouline, FH Jerusalem & CNRS Paris One and Two Dimensional Mapped Fourier Grid Hamiltonian Method & Appliaction to Cold Molecules & Application to Cold Molecules 15.3.00 Prof. L. Diosi, Particle & Nuclear Physics Research Inst., Budapest Coupling Classical & Quantum Dynamics 18.3-1.4.00 Dr. M. Br¨andle, Chemistry Inf. Center, ETH Z ¨urich Quantum Chemistry & Potential Functions Applied to Large Unit Cell Oxide Materials: Zeolites & Vanadium Oxide Nanotubes 54

28.3-4.4.00 Dr. L. Pesce, FU Berlin Coherent Control of Li2 3.4.00 Prof. I. Last, Tel-Aviv University Semiempirical Treatment of Molecular Systems with Charge Transfer 4.4.00 Dr. F. Remacle, Liege University Charge Transfer and Site Selective Reactivity in Small Peptide Cations 8-13.4.00 Prof. S. Xantheas, Battelle Memorial Inst., Pacific Northwest Labs., Richland, Wa Cooperative Effects in Water 18.4.00 Dr. Y. Bohbot, Caltech Discovering New Ordered Phases of Block Copolymer Melts 30.4-31.5.00 Ch. Koch, FH Inst. Berlin Surrogate Hamiltonian with Applications 2.5.00 Prof. M. Baer, Soreq N. R.C., Yavne Topological Effects in Molecular Systems:An Attempt Toward a Complete Theory 16.5.00 Prof. R. Nechushtai, Life Sciences, HU Industry - Academia Relationship. The HU Experience 23.5.00 Prof. S. Baer, Phys. Chem., HU Entropy - Structure Relationship in Strong Repulsive Systems 30.5.00 Prof. H. Reiss, UCLA Comments on Statistical Geometry of Hard Particle Systems 30.5.00 Prof. J. Faeder, Weizmann Inst. Molecular Dynamics Simulations of the Interior of Aqueous Reverse Micelles 5.6.00 Dr. N. Lukzen, Theoretcial Chem. Tomography Center, Novosibirsk, Russia Integral Encounter Theory of Multistage Reactions. Kinetic Equations 6.6.00 Dr. N. Wright, Durham University UK Direct Calculation of Anharmonic Vibrational Spectroscopy: Testing Density Functional Theory 10-17.6.00 Prof. J. Manz, FU Berlin Control and Analysis of Chemical Reaction Dynamics 10-17.6.00 M. Schr ¨oder, FU Berlin Photodissociation of Recombination of Diatomic Molecules in Solids 11-25.6.00 Dr. G. Darling, Univ. of Liverpool Ion Production in High Energy Collisions 13.6.00 Dr. B. Ilan, Chemistry Dept., Cornell Univ. Dynamical Heterogeneity at the Glass Transition of Polymer Melts 14-21.6.00 Prof. E. Carter, UCLA Electronic Structure of Large Systems Taking into Account Electron Correlation 22.8.00 Prof. B. Lavenda, Camerino, Italy Heisenberg’s Gitterwelt Revisied 14-28.9.00 Dr. F. Masnou-Seeuws, Lab. Aime Cotton, Orsay Cold Atom Collisions 17-30.9.00 Dr. F. Rebentrost, MPI Munich Direct Observation of Molecular Collisions 17-27.9.00 Prof. J. Grosser, University of Hannover Observation of Atom-Atom & Atom-Molecule Collisions 55

10.10.00 Prof. G. Witt, Stockholm Atmospheric Clustering and Particle Generation 24.10-30.11.00 Ch. Koch, FH Inst., Berlin Nickel Oxide; Electron Quenching; Photodesorption 31.10.00 Prof. D. Neuhauser, UCLA Interaction of Matter with Extremely Strong Laser Pulses: A Molecular Approach 31.10-19.11.00 Ms. M. Schr ¨oder, Freie Universit¨at Berlin Photochemistry in Matrices 4-11.11.00 Dr. S. May, University of Jena Membrane Elasticity 9.11.00 Dr. B.S. Tsukerblat, Moldova Acad. Sci. Mixed-Valence Systems: Double Exchange and Vibronic Interactions 10-12.11.00 Prof. R. Coalson, University of Pittsburgh Biological Systems 11-18.10.00 Prof. P. Devlin, University of Oklahoma Ice Surface Spectra 12-14.11.00 Prof. G. Witt, Stockholm Atmospheric Clustering and Particle Generation at Low Temperature - The Mystery of Mesospheric Clouds and Radar Echoes 15.11.00 Dr. E. Barkai, MIT Theoretical Analysis of Low Temperature Single Molecule Spectroscopy 21.11.00 Dr. S. Adhikari, IACS, Calcutta, India Complexity of Molecule-Surface Reactions 28.11.00 Prof. S. Kais, Purdue University Quantum Phase Transitions and Stability of Atomic and Molecular Systems 5.12.00 J. Vala, FH Research Center, Jerusalem Coherent Control Using a Chirped Field: Photoassociation of Alkali Atoms 13.12.00 Dr. E. Schneidman, Computer Science, HU Universality & Individuality in a Neural Code 14.12.00 Prof. H. Meirovitz, Florida State University Solvation Models for Predicting the Structures of Cyclic Peptides and Surface Loops in Proteins 19.12.00 Dr. C. Brif, Princeton University Decoherence of Molecular Vibrational Wavepackets: Mechanism, Observable Manifestations & Control 26.12.00 Prof. E. Pollak, Weizmann Institute Theory & Control of Thermal Photodinduced Polyatomic Reactions 2.1.01 Prof. O. Biham, Racah Inst. of Physics, HU Modeling of Hydrogen Recombination on Dust Grains in the Interstellar Medium 3-24.1.01 Dr. S. Jorgensen, University of Copenhagen Quantum Dynamics 6-25.1.02 Dr. B. Schaefer-Burg, Humboldt Univ., Berlin Coherent Control 8-24.1.01 Dr. D.M. Lockwood, Northwestern University Dephasing Dynamics 9.1.01 Prof. D.C. Rapaport, Bar-Ilan University Emergent Behavior in Many-Particle Systems 56

21.1-5.2.02 Dr. M. Vatasescu, Inst. of Space Science, Bucharest Cold Molecules 23.1.01 Dr. G. Ashkenazi, Science Teaching Dept., HU From Cavity Resonance to Cognitive Dissonance 4-16.2.01 Dr. J. Kindt, UCLA Self-assembly & Phase Transitions of Semiflexible Chain-forming Particles 21.2.01 SPECIAL FH SYMPOSIUM Prof. R. Kosloff, HU: Impulsive Control of Ground Surface Dynamics Ms. S. Tzlil, HU: Loading, Structure & Ejection of Viral DNA Prof. W. Domcke, TU Munich: Photoinduced Electron & Proton Transfer Processes in Molecules & Clusters: Exploring Photochemical Reaction Mechanisms by Ab Initio Quantum Chemistry 8.3.01 Dr. R. Granek, Weizmann Institute Anomalous Diffusion in Polymers, Membranes, and Active Biological Systems 22.3.01 Dr. S. Srebnik, Div. of Environmental Sciences, HU Modeling Molecular Recognition 27.3.01 Prof. W. Thiel, MPI Kohlenforschung, M ¨ulheim Theoretical Models for Large Molecules 4-8.4.01 J. Uhde, M. Tristl and B. Lorz (Students of Prof. E. Sackmann, Physics, TU M ¨unchen) Membrane Biophysics 19-24.4.01 Dr. Th. Kluener, FH Inst., Berlin Ab initio Simulation of Photochemsitry on Surfaces 19.4-18.5.01 Ch. Koch, FH Inst. Berlin Nickel Oxide; Electron Quenching; Photodesorption 26.4-6.5.01 S.O. Volkkonen, University of Helsinki Photochemistry in Matrices 3.5.01 Prof. U. Even, TA University Small Helium Clusters on Aromatic Molecules 10.5.01 G. Katz, Physical Chemistry, HU Charge Transfer Processes of Oxygen over Metals 17.5.01 Dr. I. Arkin, Biological Chem., HU Structures of Membrane Proteins Without Crystals or Magnets? 22.5.01 Prof. D.J. Kouri, Houston Generalized Coherent States, Relative Minimum Heisenberg Uncertainty, & the Non-Hermitian Harmonic Oscillator 24.5.01 Prof. Y. Klafter, Tel-Aviv University ”Atomic” Scale Friction: Basic Characteristics to Control 31.5.01 Prof. I. Procaccia, Weizmann Institute Fractal Growth Patterns and Iterated Conformal Maps 3-9.6.01 Prof. J.P. Devlin, Oklahoma State University The Ice Surface Region: a) The Nature of Adsorbed HCl and b) The Mobility of Point Defects 4.6.01 Dr. I. Borukhov, UCLA Elastically-Driven Linker Aggregation between Two Semi-Flexible Polyelectrolytes 57

12.6.01 Dr. A. Vardi, ITAMP, Harvard Smithsonian Center Quanum Dynamics of Bose Einstein Condensates 11-12.6.01 Prof. M. Schick, Univ. of Washington Statistical Mechanics of Complex Fluids 21.6.01 Dr. P. Kral, Weizmann Inst. Coherent Injection of Photo-Currents in Nanotubes 1-31.7.01 Ch. Koch, FH Inst., Berlin Quenching in Nickel Oxide 9.10-19.12.01 Dr. J. Lundell, Helsinki University New Frontiers of Rare Gas Chemistry: The Rare Gas Hydrides 30.10.01 Prof. D. Tannor, Weizmann Inst. Laser Cooling of Molecules: A Theory of Purity Increasing Transformations 8.11.01 Prof. R. Coalson, Pittsburgh University Theory of Ion Permeation through Biological Channels: Continuum and Atomistic Approaches 14-21.11.01 Prof. P. Devlin, Univ. of Oklahoma Ice Surface Spectra 20.11.01 Prof. R. Kosloff, Hebrew University Quantum Mechanical Heat Engines & Refrigerators 25.11-25.12.01 Ch. Koch, FH Inst., Berlin Surrogate Hamiltonian 27.11.01 Dr. S. Jorgensen, Aarhus University, Denmark Heterogeneous Solvation & Electron Transfer 1.12.01-30.4.02 Dr. Th. deJong, Free Univ., Amsterdam Dynamics of Conical Intersections 18.12.01 Dr. E. Rabani, Tel-Aviv University A New Molecular Hydrodynamic Approach to Dynamical Correlation in Quantum Liquids 25.12.01 Dr. N. Argaman, Nuclear Res. Center, Negev Thermodynamics as an Alternative Foundation for Density Functional Theory 30.12.01-13.1.02 Prof. E.E.B. Campbell, MBI Berlin Fullerene Collisions 1.1.02 Dr. A. Agnon, Inst. of Earch Sciences, HU Friction and the Brittle Instability 7.1-11.2.02 Dr. M. Roeselova, J. Hyrovsky Inst., Prague Electron Photodetachment in Halogen-Water Complexes: From Classical to Quantum Description 6-25.1.02 Dr. B. Schaefer-Burg, Humboldt Univ., Berlin Coherent Control 8.1.02 Dr. Y. Elran, Weizmann Institute Between Quantum and Classical Mechanics: Semiclassical Calculation of Molecular Dynamics 10.1-1.2.02 Dr. P. Jungwirth, Czech Acad. Sci. Large Polyatomic Systems 21.1-1.02.02 Dr. M. Vatasescu, Inst. of Space Science, Bucharest Cold Molecules 14.3.02 Prof. R.B. Gerber, Hebrew University Photochemistry and Formation of New Molecules in Low-Temperature Solids 2-9.4.02 Prof. P. Devlin, University of Oklahoma Ice Surface Systems 58

25.4.02 Prof. N. Tishby, Hebrew University Principled Selection of Relevant Variables 2.5.02 Prof. A. Kuppermann, Caltech Quantum Reaction Dynamics for Multiple Electronic States 23.5.02 Dr. R. Baer, Lise Meitner Center, HU Born-Oppenheimer Invariants Along Nuclear Paths 27.5.02 Prof. A. Goldblum, School of Pharmacy, HU Many Needles in a Haystack: Finding the Global Optimum and Best Populations on Biomolecular Systems 6.6.02 Prof. O. Agam, Hebrew University Projecting the Kondo Effect: Theory of the Quantum Mirage 16-25.6.02 Dr. E. Geva, University of Michigan Calculating Quantum Mechanical Solution-Phase Vibrational Energy Relaxation & Reaction Rate Constants 20-21.6.02 Prof. V. Mandelshtam, UC San Diego Harmonic Inversion 24.6.02 Prof. R. Schweitzer-Stenner, Univ. of Puerto Rico Structure of Tripeptides in Solution Revaled by Visible Raman. FTIR and Vibrational Spectroscopy 23-25.10.02 Prof. R. Schweitzer-Stenner, Univ. of Puerto Rice Tripeptide Structure 7-15.11.02 Prof. P. Devlin, Oklahoma State Univ. Ice Surface Spectra 26.11.02 Dr. I. Borukhov, UCLA Linker-Assisted Biopolymer Aggregation 3.12.02 Dr. D. Boese, WIS Development and Assessment of Exchange- Correlation Functionals 10.12.02 J. Kazimirski, HU Search of Low Energy Minima in Water Clusters Using Diffusion Monte Carlo 23-24.12.02 Prof. H.T. Chua, Univ. of Singapore Thermodynamics of Cooling 24.12.02 Dr. A. Shurki, USC, LA What Can Computers Tell Us About Enzyme Catalysis? 31.12.02 C. Yinnon, HU Hydrogen Bond Chemistry of Carbon Cluster Complexes - Catalysis, Vesicles, Liquid Crystals and Gene Delivery 7.1.03 Prof. M. Baer, SNRC, Yavne (G.D. Billing Memorial Lecture) Diabatization for Time-Dependent Molecular Processes 9-17.1.03 Dr. Ch. Koch, CNRS, Paris Surrogate Hamiltonian 11-15.1.03 Prof. P. Jungwirth, Czech Academy Polyatomic Quantum Simulations 14.1.03 Prof. H. Parnas, Neurobiology, HU Proteins That Are Not Expected to be Voltage Sensors were Found to be Such: Possible Mechanism for Voltage Sensitivity 21.1.03 Prof. S. Baer, HU (Get-Well Seminar for Prof. D. Kivelson) Spatial Transitons Between Local Structures in Condensed Systems 59

11.2.03 Prof. T. Seideman, Northwestern University Current-Driven Dynamics in Molecular Scale Devices 14.1.03 Prof. H. Parnas, Neurobiology, HU Proteins That Are Not Expected to be Voltage Sensors were Found to be Such: Possible Mechanism for Voltage Sensitivity 21.1.03 Prof. S. Baer, HU Spatial Transitions Between Local Structures in Condensed Systems (Get-Well Seminar for Prof. D. Kivelson) 11.2.03 Prof. T. Seideman, Northwestern University Current-Driven Dynamics in Molecular Scale Devices 20.2.03 Prof. T. Seideman, Northwestern University Controlling External Molecular Modes with Intense Light 5-8.3.03 Dr. A. Paoykova, University of Sofia, Bulgaria Atomic and Molecular Clusters 6.3.03 Dr. S. Zilberman, Chemistry, TAU Dynamics in Confined Systems: Squeeze-out of Molecular Films and Adhesion 29.4-7.5.03 Prof. P. Devlin, Oklahoma State Univ. Ice Surface Structure 1.5.03 Prof. S. Solomon, Racah Inst., HU Do Reaction-Diffusion Partial Differential Equations Represent Real Reaction Diffusion Systems? Some Strange Rigorous Results and Their Obvious Real Life Applications 8.5.03 Dr. A. Popov, FH, HU Bimolecular Reversible Reactions in Solutions 13.5.03 Prof. H. Scher, Environmental Sciences and Energy Res., WIS Anomalous Transport in Heterogeneous Media: The Origin of Fractal Stream Chemistry 22.5.03 D. Shemesh, HU Dynamics of Photoionization Processes in Biol. Molecules 25.5-5.6.03 Dr. J.Sadlej, Warsaw University Hydrogen Bonding in Water Clusters 29.5.03 D. Segal, HU Thermal Conduciton of Molecules 11-16.6.03 MINISYMPOSIUM: Ultrafast Chemical Dynamics & Reaction Control J. Manz, FU, Berlin: From Analysis via Control to Making Use of Laser Driven Reactions N. Schwentner, FU Berlin: Cage Exit, Recombination and Reorientation in Solids Investigated on the Femtosecond Timescale 19.6.03 N. Grishina, HU Computational Studies of Ice 17.7-31.8.03 Dr. J.P. Palao, Univ. of La Laguna Quantum Computing 22.7-31.8.03 Dr. Ch. Koch, CNRS, Paris Formation of Ultra Cold Molecules 27.8-4.9.03 Prof. F. Masnou, CNRS Paris Ultra Cold Molecules 21.10-4.12.03 Prof. L. Diosi, Hungarian Acad. Sci., Budapest Quantum Correction Term to Fokker-Planck Equation 6.11.03 Prof. U. Peskin, Technion The Role of Electronic Nuclear Coupling at Molecular Briges in Promoting Bridge-Assisted Electronic Tunneling 60

15.11-15.12.03 Dr. E. Brown, UC, Irvine Dynamics of Atmospheric Processes 20.11.03 Prof. Y. Band, BG University Density Functional Theory for Bose Condensed Systems 26.11-3.12.03 Prof. F. Masnou, CNRS Paris Formation of Ultracold Molecules: What Did We Learn? 2-9.12.03 Prof. P. Devlin, Oklahoma State University Ice Surface Clusters 4.12.03 Prof. S. Safran, Weizmann Inst. Membranes in Periodic Potentials: Physics of Red Blood Cells 17-18.12.03 Dr. Hui Tong, Singapore Univ. Thermodynamics 18.12.03 Dr. A. Schiller, Racah Inst. HU Coulomb Blockade and non-Fermi-Liquid Behavior in Quantum Dots 25.12.03 Dr. D. Harris, NIH Stressing Macromolecules: Osmotic Action on the Nanometer Scale 1.1.04 Prof. G. Kurizki, Weizmann Inst. Manipulation of Entanglement and Decoherence in Molecules 8.1.04 Prof. E.D. Tannenbaum, Harvard University Semiconservative Replication in the Quasispecies Model 11-15.1.04 EIN-GEDI WORKSHOP Non-Adiabatic Processes on Surfaces Organizers: M. Asscher, E. Kolodney, R. Kosloff & Y. Zeiri Dr. H.L. Abbott, University of Virginia: Vibrational State Resolved Dissociative Chemisorption of Methane on Ni(100) Prof. D. Auerbach, Hitachi Technologies: Probing Nonadiabatic Coupling in Molecular Interaction with Surfaces Prof. R. Baer, HU: Electronic Processes and Transition on Surfaces - A Time Dependent Density Functional Approach Prof. L.S. Cederbaum, Heidelberg: Beyond Born-Oppenheimer: Molecular Dynamics Through A Conical Intersection Prof. D. Chakarov, Goteborg, Sweden: Photo Physics and Photo Chemistry of Ice Films on Graphite Dr. M.P. de Lara-Castells, Inst. de Mat. y Fisica Fundamental, Madrid, Spain: Nonadiabatic Effects in the Light-Induced Desorption of O2 from the TiO2 (110) Surface Prof. V.A. Esaulov, Lab. des Collisions Atom. and Molec. Universite de Paris Sud, France: Electron Transfer Processe in Ion/Atom Scattering on Surfaces Prof. H.-J. Freund, Chem. Phys., Max Planck, Berlin: Photodesorption from Oxides and Deposited Metal Clusters: REMPI and 2PPE Investigations Prof. J.W. Gadzuk, NIST, Gaithersburg: Production and Deterction of Chemically-Induced Hot Electrons in Surface Processes: X- Ray Edges, Driven Oscillators, Friction Dr. E.D. German, Technion: Theory of Dissociative Adsorption Kinetics of Diatomic Prof. A. Gross, Physik Dept., TU Muenchen: Multidimensional Mixed Quantum-Clasical Description of the Laser- 61

Induced Desorption of Molecules Prof. I. Harrison, University of Virginia: Photoinduced Electron Transfer Chemistry and Dissociaiton of Adsorbed CO2: Harnessing A-Scale Molecular Acceleration Towards a Surface Prof. E. Hasselbrink, Chem., Duisburg-Essen: Non-adiabatic Pathways in the Dissociative Adsorption of Simple Molecules in the Al(111) Surface Prof. U. Hoefer, Physic Dept, Philipps Univ., Marburg: Time-Resolved Two-Photon Photoemission of Ar/Cu-Interface States Prof. S. Holloway, Surf. Scie. IRC, Univ. of Liverpool: Dynamics of Spin Transition in the Adsorption of Hydrogen Atoms on Metals Prof. A. Hoffman, Technion: Initial Stages of Oxygen Adsorption on Al(100) Surfaces Studied by Photoelectron Spectroscopy and Low Energy Ion Scattering Dr. S. Jorgensen, Inst. of Chemistry, HU: Adsorbate Orentational Dependent Photoinduced Desorption of CH3Br on Ru(001) Dr. A. Kaplan, Technion & University of Birmingham: Implanting Atomic Ions into Surface Adsorbed Fullerenes: The Single Collision Formation and Emission of Endohedral Complexes Prof. B. Kasemo, Chalmers and Goteborg University: Spontaneous and Photo-induced, Non-adiabatic Procesess on Extended and Nanoscale Surfaces Dr. G. Katz, Fritz Haber, HU: Abstractive Dissociation of Oxygen Over Al(111): A Nonadiabatic Quantum Model Dr. Th. Kluener, FH Inst., Berlin: Theoretical Investigation of Photochemical Reactions on Surfaces from First Principles Prof. A.C. Kummel, UC San Diego: Hyperthermal Ejection of Halogen Atoms from the Reaction of Diatomic Halogens on the Al(111) Surface: Evidence of A Vertical Electron Harpooning Mechanism Dr. Y. Lilach, HU: Steric Effect in Electron-Molecule Interaction Prof. D. Menzel, TU Munich: Ultrafast Charge Transfer and Localized Bond Breaking at Surfaces Prof. N. Moiseyev, Technion: Trapping of Electrons Due to Nonadiabatic Processes Prof. R. Naaman, Weizmann Inst.: Surprising Electronic Properties of Two Dimensional Chemical Systems Prof. A. Nitzan, Chemistry, TAU: Timescale Considerations in Electron Transfer and Electron Transmission Dr. I.D. Petsalakis, Theoret. and Phys. Chem. Inst., National Hellenic Research Foundation, Athens: Theoretical Study of Adsorption of Halogen-Substituted Benzene on a Si(111) Surface Prof. U. Peskin, Technion, Haifa: Modulations of Electronic Tunneling Rates Through Flexible Molecular Bridges by a Disspative Super- Exchange Mechanism Prof. P. Saalfrank, Chemistry, University of Potsdam: Quantum Dynamics of Non-Adiabatic Procesess at Surfaces Dr. B. Segev, BG University, Beer Sheva: The Evanescent-Wave Mirror for Cold Atoms Prof. T. Seideman, Chemistry, Northwestern University: Nonadiabatic Vibronic Dynamics as a Tool. From Surface Nanochemistry to New Forms of Molecular Machines Dr. G. Theodorakopoulos, Theoret. and Phys. Chem. Inst., 62

National Hellenic Research Foundation, Athens: Theoretical Study of Reactions of Benzene and Dibromobenzene at a Si(111) Surface Prof. M. Wolf, Freie Univ. Berlin: Ultrafast Dynamics of Non-adiabatic Processes at Interfaces: From Surface Femtochemistry to Coherent Phonon Excitation Prof. Xiaoyang Zhu, Univ. of Minnesota: Understanding Electron Transfer at Molecule- Metal Junctions: A Spectroscopic Approach 29.1.04 Dr. A. Vardi, BG University Second-sound Solutions in Ultracold Gases 15-31.1.04 Prof. T. Seideman, Chemistry, Northwestern University: Nonadiabatic Vibronic Dynamics as a Tool 14-28.2.04 M. Kjellberg, 24.2-23.3.04 Dr. Ch. Koch, CNRS, Paris Formation of Ultra Cold Molecules 4.3.04 Dr. E. Pazy, BG University pin-Based All-Optical Quantum Computation mploying Semiconducting Quantum Dots 5-19.3.04 Prof. W. Rethig, Photochemistry of Excited State Reactions 14-17.3.04 GENTNER SYMPOSIUM on The Physics of Biomaterials and Soft Matter Nirvana Hotel, Dead Sea Organizers: D. Andelman (TA), A. Ben-Shaul (J’lem), S. Safran (Weizmann) T. Bayerl (Wurzburg), H. Gaub (Munich), R. Lipowsky (Golm) and H. Mohwald (Golm) Session I: Physics of Cell Adhesion (R. Lipowsky, Chair) P.G. de Gennes (Curie): Adhesion and Friction of Soft Objects and/or cell Motions B. Geiger, (Weizmann): Mechanosensitive Interactions Association with Cell Adhesion and Migration R. Merkel (Julich): Kinetics of Single Bonds Under the Influence of Piconewton Forces D. Roux (Bordeau): Adhesion of Colloids on Cells U. Seifert (Stuttgart): Pulling on Biopolymers, Adhesion Patches and Vesicles: Theoretical Case Studies about the Effect of Forces in Model Systems M. Tanaka (Munich): Polymer Supported Membranes as Biofunctional Interfaces and Cell Surface Models M. Kozlov (Tel-Aviv): Focal Contacts as Mechanosensors: A Thermodynamic Model Session II: DNA Physics(H. Gaub, Chair) A. Minsky (Weizmann): Physical and Structural Aspects of DNA Repair: Role of Restricted Diffusion E. Braun (Technion): From DNA to Transistors by Sequence-Specific Molecular Lithography W. Helfrich (Berlin): Electro-Optically Switchable Columnar Liquid Crystals: Modeling and Conjectured Structure Session III: Cytoskeleton and Actin(H. Mohwald, Chair) E. Sackmann (Munich): Micro-viscoelasticity of Cells F. Mackintosh (Amsterdam): Elastic Response of Cytoskeletal Networks N. Gov (Weizmann): 63

Cytoskeletal Control of the Red-Blood Cell Membrane C. Safinya (UCSB): Supramolecular Assembly of Biological Molecules: From Physics to Biomedical Applications E. Frey (Berlin): Statistical Mechanics of the Cytoskeleton - Fiber Networks and Intracellular Transport J. Radler (Munich): Bits and Pieces - From Vesicles to Cell Motion A. Bernheim (Ben Gurion): Biomimetic System for the Study of Actin Based Movement Session IV: Macromolecular Assemblies(T. Bayerl, Chair) A. Bausch (Munich): Spherical Crystallography W. Gelbart (UCLA): What is the Pressure in a Virus, and Why? R. Bruinsma (UCLA): Origin of Icosahedral Symmetry in Viruses H. Strey (Amherst): Nanoporous Materials for Biomedical Applications I. Arkin (Jerusalem): Membranes Containing SARS Coronavirus Proteins S. May (Jena): Protein-Induced Demixing of Charged, Binary Lipid Membranes Session V: Dynamics of Biomaterials (J. Klein, Chair) F. Brochard (Curie): Vesicles: Transient Pores and Nanotubes R. Granek (Ben Gurion): Dynamics of Biopolymer Systems in and out of Equilibrium U. Schwarz (Golm): Stochastic Dynamics of Leukocyte Tethering in Shear Flow H. Diamant (Tel Aviv): Hydrodynamic Interactions in Confined Suspensions 17-21.3.04 S. May (Jena): Beyond Born-Oppenheimer: Molecular Dynamics Protein-Induced Demixing of Charged, Binary Lipid Membranes 23-26.3.04 Prof. L.S. Cederbaum, Heidelberg: Beyond Born-Oppenheimer: Molecular Dynamics 1.4.04 Dr. S. Keinan, Chemistry, Northwestern Computational Design of Materials 29.4.04 Prof. F. Stoddart, UCLA An Integrated Systems-Oriented Approach to Molecular Electronics 6.5.04 Dr. H. Diamant, Chemistry, TAU Confinement Effects on Colloidal Dynamics 20.5.04 D. Gelman, HU Quantum Dynamics of Fast Dissipative Processes 27.5.04 A. Zemel, HU Membrane Perforation Induced by Amphiphatic Peptides 28.5-2.6.04 Prof. J. Manz, FU Berlin Coherent Spin Control: Model Simulations for Dihalogenes in Rare-Gas Matrices 3.6.04 Prof. A. Brokman, HU Critical Morphological Transition by Elastic Interaction 4-11.6.04 Prof. P. Devlin, Oklahoma State Univ. Ice Surface Structure 9.6.04 Dr. M. Leibscher, FU Berlin Controlling Quantum Rotation: Atom Squeezing and Molecular Alignment 2-6.7.04 Prof. J. Heath, Caltech Molecular Mechanics and Electronics 1-5.8.04 Prof. H. Schubert, Fraunhofer Inst. Pfinztal Explosives 64

30.7-6.8.04 Prof. J. Oxley, Rhode Island Explosions: Explosives Not Required 12.8-10.9.04 Dr. Ch. Koch, CNRS, Paris Formation of Ultra Cold Molecules 29.8-3.9.04 SAFED WORKSHOP on QUANTUM DISSIPATION Open Problems in Open Quantum Systems Organizers: R. Kosloff (HU) and D. Tannor (Weizmann) R. Kosloff (HU): Markovian Master Equation (Lindblad Form) D. Tannor (Weizmann): Markovian Master Equation R. Coalson (Pittsburgh): Spin-Boson Dynamics U. Kleinekathofer (Berlin): Markovian Master Equation E. Rabani (Tel-Aviv): Quantum Mode-Coupling Theory E. Geva (Michigan): Classical Quantum Methods E. Pollak (Weizmann): Classical Methods R. Kosloff (HU): Surrogate Hamiltonian Method D. Cohen (Beer-Sheva): Quantum Dissipation and Classical Chaos A. Nitzan (Tel-Aviv): Molecular Conduction U. Peskin (Technion): Electron Transfer U. Kleinekathofer (Berlin): Stochastic Unravelling and Exciton Transfer D. Tannor (Weizmann): Non-Markovian Master Equation D. Cohen (Beer-Sheva): Driven Systems/Kubo N. Moiseyev (Technion): Non-Hermitian Quantum Mechanics R. Coalson (Pittsburgh): Driven Systems E. Geva (Michigan): Driven Systems Y. Imry (Weizmann): Decoherence and Noise Correlators in Mesoscopic Systems 29.8-23.9.04 S. Dittrich, FH Inst. Berlin Surface Science 21.10.04 Dr. B. Davidovitch, Harvard Div. of Eng. and Appl. Sci. Continuum Approach in Studying Nano-Scale Surface Phenomena 25-26.10.04 Dr. E. Tannenbaum Modeling Vibrational Predissociation of the van der Waals Complex ArHF 28.10.04 Dr. D. Barash, Computer Sci., Ben Gurion Univ. Computational Prediction of Mutations Causing RNA Switches 3-29.11.04 Dr. J. Palao, University of La Laguna, Spain Quantum Molecular Coupling 4.11.04 Dr. E. Pazy, Chemistry, BG University Making Bosonic Molecules from Fermionic Atoms Employing Feshbach Resonances: The Importance of Symmetry Considerations 11.11.04 Dr. O. Alon, Heidelberg Effective Orbitals for Complex Problems Methods and Applications 25.11.04 Prof. P. Zdanska, Organic Chem. and Biochem. Academy of Sciences, Czech Republic Statistical Interpretation of Complex Scaling Method 29.11-6.12.04 Prof. J.P. Devlin, Oklahoma State University Ice Surface Spectra 4-18.12.04 Dr. S. Jorgensen, Aarhus University, Denmark Single Molecular Reactions on Cold Molecular Ions 7-25.12.04 Dr. A. Yoffe, UCLA 65

Phenomenologial Model - Size and Shape of the Single-Stranded Viral RNA Genome 14-16.12.04 Prof. R. Grimm, Innsbruck University, Austria Laser-Atom Interactions 16.12.04 Prof. M. Drewsen, Physics and Astronom., Aarhus University Cold Molecular Ion Studies in Traps 30.12.04 Prof. D. Lidar, Univ. of Toronto Two Problems in the Theory of Open Quantum Systems Post-Markovian and Adiabatic Quantum Dynamics 4.1.05 Prof. A. Mogilner, UC Davis Multiscale Two-Dimensional Modeling of Migrating Keratocyte Cells 25.2-3.5.05 Dr. M. Guehr, Freie Univ. Berlin Coherent Dynamis of Small Moleculs in Rare Gas Crystals 3.3.05 Dr. V. Averbukh, Heidelberg Interatomic/Intermolecualr Coulombic Decay in Clusters: From Diatomics to Fullerenes 8.3.05 Prof. T. Saue, Louis Pasteur University, Strasbourg 4-Component Relativistic Density Functions Theory 13-14.3.05 The Fritz Haber Symposium on Biophysical Dynamics Mt Zion Hotel, Jerusalem 13-14.3.05 Prof. G. Comsa (Bonn), Participant (Beirat) Session I: Biodynamics. Ronnie Kosloff, Chair Prof. H. Gruebmuller, Goettingen Elaborate pores and complex machines: Nature’s nanotechnology benchmarks Victoria Buch: Computational studies of ether-acid solids Gilad Haran: The chemical physics of protein folding and association: Single molecules and more Session II : Benny Gerber, Chair Yossi Klafter: Single molecule dynamics: An enzyme case Nir Gov: Physics of active membranes and cytoskeleton Haim Diamant: Folding cascades in a compressed lipid monolayer Session III: Avinoam Ben-Shaul, Chair Noam Agmon: Proton pathways in green fluorescent protein Natalie Questembert-Balaban: Soft lithography for quantitative studies of biological systems Raphy Levine: Molecular logic machines and DNA computing Session IV: Roi Baer, Chair Misha Koslov: Elastic mechanism of processive capping of actin filaments by formins Nir Ben-Tal: Dynamics of peptide adsorption onto- and insertion into- membranes Shelly Tzlil: Flexible macromolecule-membrane interaction and viral budding Leonid Chernomordik: Membrane fusion: Pathways and inhibitors Session V: Victoria Buch, Chair Anne Bernheim: Formation pathway to aster and stars by actin polmerization Assaf Friedler: Biophysical studies of the tumor suppressor protein p53: A tool for the development of anti- cancer lead compounds Simha Srebnik: Adsorption behavior of model proteins embedded in a polymer brush Session VI: Noam Agmon, Chair Benny Gerber: Vibrational spectroscopy and the development of novel force fields for biological molecules Sandy Ruhman: Ultrafast spectroscopic studies of bacteriorhodopsin Wolfgang Domcke: Hydrogen bonds, conical intersections and photostability of life 17.3.05 Dr. E. Brown, UCI Molecular Spectroscopy of Atmospheric Systems: Predictions from Molecular Dynamics Simulations 66

7.4.05 Prof. F. Masnou-Seeuws, Lab. Aimee Cotton, Orsay Photoassociation of Cold Atoms with Chirped Laser Pulses: Correlation Effects in Coupled Atomic-Molecular Condensates 7-13.4.05 Prof. J. Sadlej, University of Warsaw Quantum Chemical Calculations of Spectroscopic Effects 8-14.4.05 Dr. N. Uras-Aytemiz Acid Hydrate Phases in Nanoparticles 9-17.4.05 Dr. A. van Duin, Caltech ReaxFF, A Transferable Computational Method for Atomic Scale Dynamical Simulations of Chemical Reactions 14.4.05 Prof. F. Brown, Chemistry, UCSB Simplified Models for Biomembrane Structure and Dynamics 19.4-5.5.05 Dr. U. Poschinger, Physikalisches Inst., Freiburg Ultra Cold Molecules 3-11.5.05 Prof. P. Devlin, Oklahoma State University Ice Surface Spectra 17-31.5.05 Prof. L. Diosi, Particle and Nucl. Phys. Inst., Budapest Quantum Thermodynamics 19.5.05 D. Shemesh, HU Photoionization of Biological Molecules: Conformation Selective Processes 19-24.5.05 Prof. W.D. Phillips, NIS, Gaithersburg A Bose-Einstein Condensate in an Optical Lattice Atomic Physics Meets Solid State 26.5.05 Y. Miller, HU Vibrational Spectroscopy and Photoinduced Reaction Dynamics of Atmospheric Molecules 31.5-9.6.05 Prof. M. Gordon, Iowa State University Potentials for Solvent Effects and Beyond 8.6.05 Prof. M. Ratner, Northwestern University Molecular Transport Junctions: Scattering, Disorder and Vibronics 8-10.6.05 Prof. H. Schubert, Fraunhofer Inst., Pfinztal Explosives 8-11.6.05 Prof. J. Oxley, Rhode Island Explosions and Explosives 9.6.05 Prof. I.B. Bersuker, Theoretical Chem., Univ. of Texas at Austin The Jahn-Teller Effect as a Unique Mechanism of All The Symmetry Breakings in Molecular Systems and Condensed Matter 10.11.05 Dr. I. Averbukh, Weizmann Institute Optical Kicking: Laser Control of Molecular Orientation 17.11.05 Dr. S. Kallush, Fritz Haber, Hebrew University The Quantum Governor: Automatic Quantum Control and Reduction of the Influence of Noise Without Measuring 24.11.05 Prof. J.M. Gordon, Ben Gurion University Solar Photonics for Applications in Medicie, Power Generation and Nanomaterial Synthesis 1.12.05 Dr. N. Gov, Weizmann Institute, Rehovot Active Motion and Structural Phases of Cell Membranes 8.12.05 Dr. V. Teif, Inst. Biorg. Chem., Belarus Acad. Sci. Lattice Models for DNA-Ligand Binding 67

15.12.05 Dr. C.P. Koch, The Fritz Haber, Hebrew University Making Ultracold Ground State Molecules with Optical Fields 22.12.05 Dr. D. Cohen, Physics Dept., Ben Gurion University Linear Response, Absorption of Radiation by Small Conducting Particles, Conductance of Mesoscopic Devices 2.1.06 Dr. I.N. Berezovsky, Chemistry Biol. Chem., Harvard Physical Origins and Evolution of Protein Stability and Adaptation 5.1.06 Dr. V. Teif, Bio-Organic Chem. Inst., Belarus Nat. Acad. Sci., Minsk Lattice Models for DNA-Ligand Binding 12.1.06 Prof. N. Agmon, HUJI The Remarkable Dynamics of the Green Fluorescence and its Chromophore 19.1.06 Dr. S. Zilberg, Physical Chem., HUJI Design of the Singlet-Triplet Bistable System 26.1.06 Prof. O. Biham, Racah Inst. of Physics, HUJI Molecular Hydrogen Formation and Complex Reaction Networks on Dust Grains in the Interstellar Medium 68

6. Publications

Period: 2000-2005 (Enumeration starts when the member joined the center)

6.1. Noam Agmon

88. N. Agmon Primary Events in Photoacid Dissociation, J. Mol. Liquids 85 , 87-96 (2000).

89. H. Kim, K.J. Shin and N. Agmon Excited-State Reversible Geminate Recombination with Quenching in One Dimension, J. Chem. Phys. 111 , 3791-3799 (1999).

90. K.M. Solntsev and N. Agmon Dual Asymptotic Behavior in Geminate Diffusion-Influenced Reaction, Chem. Phys. Lett. 320 , 262-268 (2000).

91. I.V. Gopich and N. Agmon Rigorous Derivation of the Long-Time Asymptotics for Reversible Binding, Phys. Rev. Lett. 84 , 2730-2733 (2000).

92. N. Agmon and I.V. Gopich Exact Long-Time Asymptotics for Reversible Binding in Three Dimensions, J. Chem. Phys. 112 , 2863-2869 (2000).

93. N. Agmon Proton Solvation and Proton Mobility, Israel J. Chem. 39 , 493-502 (1999).

94. N. Agmon Mechanism of Hydroxide Mobility, Chem. Phys. Lett. 319 , 247-252 (2000).

95. K.M. Solntsev, D. Huppert, N. Agmon and L.M. Tolbert Photochemistry of ”Super” Photoacids. 2. Excited-State Proton Transfer in Methanol/Water Mixtures, J. Phys. Chem. A 104 , 4658-4669 (2000).

96. N. Agmon Conformational Cycle of A Single Working Enzyme, J. Phys. Chem. B 32 , 7830-7834 (2000).

97. B. Cohen, D. Huppert and N. Agmon Nonexponential Smoluchowski Dynamics in Fast Acid-Base Reaction, J. Am. Chem. Soc. 122 , 9838-9839 (2000).

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98. K.M. Solntsev, D. Huppert and N. Agmon Experimental Evidence for Kinetic Transition in Reversible Reaction, Phys. Rev. Letts. 86 , 3427-3430 (2001).

99. K.M. Solntsev, D. Huppert and N. Agmon Challenge in Accurate Measurement of Fast Reversible Bimolecular Reaction, J. Phys. Chem. A 105 , 5868-5876 (2001).

100. H. Kim, K.-J. Shin and N. Agmon Diffusion-Influenced Reversible Geminate Recombination in One Dimension. II. Effect of a Constant Field, J. Chem. Phys. 114 , 3905-3912 (2001).

101. N. Agmon, W. Rettig and C. Groth Electronic Determinants of Photoacidity in Cyanonaphthols, J. Am. Chem. Soc. 124 , 1089-1096 (2002).

102. A.V. Popov and N. Agmon Three-Dimensional Simulation Verifies Theoretical Asymptotics for Reversible Binding, Chem. Phys. Letts. 340 , 151-156 (2001).

103. B. Cohen, D. Huppert and N. Agmon Diffusion-Limited Acid-Base Nonexponential Dynamics, J. Phys. Chem. A 105 , 7165- 7173 (2001).

104. A.-V. Popov and N. Agmon Three-Dimensional Simulations of Reversible Bimolecular Reactions: The Simple Target Problem, J. Chem. Phys. 115 , 8921-8932 (2001).

105. N. Agmon The Dynamics of Preferential Solvation, J. Phys. Chem. A, 106 (32), 7256-7260 (2002).

106. A.V. Popov and N. Agmon Three-dimensional simulations of Reversible Bimolecular Reactions. II. The Excited- State Target Problem with Different Lifetimes, J. Chem. Phys. 117 (9), 4376-4385 (2002).

107. A.V. Popov and N. Agmon Transition Into Non-Monotonic Approach to Equilibrium in Geminate Exchange Reac- tions, Chem. Phys. Lett. 371 (3-4), 462-468 (2003).

108. A.V. Popov and N. Agmon Exact Solution for the geminate ABCD Reaction, J. Chem. Phys. 117(12), 5770-5779 (2002).

109. A.V. Popov and N. Agmon Three-Dimensional Simulations of Reversible Bimolecular Reactions. III. The Pseudo- Unimolecular ABCS Reaction, J. Chem. Phys. 118(24), 11057-11065 (2003). 70

110. N. Agmon and A.V. Popov Accurate Solution for the ABCS Problem, Physica A 330 , 150-159 (2003).

111. N. Agmon and A.V. Popov Unified Theory of Reversible Target Reactions, J. Chem. Phys. 119(13), 6680-6690 (2003).

112. N. Agmon and A.V. Popov Unified Theory of Reversible Target Reactions, J. Chem. Phys. 119(13), 6680-6690 (2003).

113. A.V. Popov and N. Agmon Smoluchowski Theory as the Leading Term of Reversible Geminate Dissociation Kinet- ics, Polish J. Chem. 77 , 1659-1668 (2003).

114. V.-I. Arkhipov and N. Agmon Relation Between Macroscopic and Microscopic Dielectric Relaxation Times in Water Dynamics, Isr.J. Chem. 43 , 363-371 (2003).

115. A.V. Popov, N. Agmon, I.V. Gopich and A. Szabo Influence of Diffusion on the Kinetics of Excited-State Association-Dissociation Reac- tions: Comparison of Theory and Simulation, J. Chem. Phys. 120 , 6111-6116 (2004).

116. S.-H. Park, K.-J. Shin and N. Agmon Exact Solution of the Excited-State Geminate A∗BC∗ + D Reaction with Two Different Lifetimes and Quenching, J. Chem. Phys. 121 , 868-876 (2004).

117. N. Agmon Coupling of Protein Relaxation to Ligand Binding and Migration in Myoglobin, Biophys. J. 87 , 1537-1543 (2004).

118. H. Lapid, N. Agmon, M.-K. Petersen and G.A. Voth A Bond-Order Analysis of the Mechanism for Hydrated Proton Mobility in Liquid Water, J. Chem. Phys.122 , (2005).

119. N. Agmon Elementary Steps in Excited-State Proton Transfer, J. Phys. Chem. A, 109 , 13-35 (2005).

120. N. Agmon Proton Pathways in Green Fluorescence Protein, Biophys. J. 88, 2452-2461 (2005).

121. D. Dantsker, U. Samuni, J.M. Friedman and N. Agmon A Hierarchy of Functionally Importance Relaxations within Myoglobin Based on Solvent Effects, Mutations and Kinetic Model, Biochim. Biophys. Acta: and Proteomics 1749, 234-251 (2005).

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122. S.H. Park, K.J. Shin, A.V. Popov and N. Agmon Diffusion-Influenced Excited-State Reversible Transfer Reactions, A∗ + BC∗ + D, With Two Lifetimes: Theories and Simulation, J. Chem. Phys. 123, 034507 (2005).

123. P. Leiderman, D. Huppert and N. Agmon Transition in the Temperature Dependence of GFP Fluorescence: From Proton Wires to Proton Exit, Biophys. J. 90, (2006).

124. N. Agmon Reduced Parameter Set Determinable from Geminate Kinetics, Chem. Phys. Lett. 417, 530-534 (2005).

125. R. Gepshtein, D. Huppert and N. Agmon Deactivation Mechanism of the Green Fluorescent Chromophore, J. Phys. Chem. A (2006).

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6.2. Avinoam Ben-Shaul

77. K. Wagner, D. Harries, S. May, V. Kahl, J.O. R¨adler and A. Ben-Shaul Direct Evidence for Counterion Release Upon Cationic Lipid-DNA Condensation”, Lang- muir 16 , 303-306 (2000).

78. S. May, D. Harries and A. Ben-Shaul The Phase Behavior of Lamellar DNA-Lipid Complexes, Biophys. J. 78 , 1681-1697 (2000).

79. N. Ben-Tal, C. Bagdassarian, B. Honig and A. Ben-Shaul Association Entropy in Adsorption Processes, Biophys. J. 79 , 1180-1187 (2000).

80. S. May and A. Ben-Shaul A Molecualr Model for Lipid-Mediated Interaction between Proteins in Membranes, Phys. Chem. Chem. Phys. 2 , 4494-4502 (2000).

81. S. May, D. Harries and A. Ben-Shaul Lipid Demixing and Protein-Protein Interactions in the Adsorption of Charged Proteins on Mixed Membranes, Biophys. J. 79 , 1747-1760 (2000).

82. S. May and A. Ben-Shaul Molecular Theory of the Sphere to Rod Transition and the Second CMC in Micellar So- lutions, J. Phys. Chem. B 105 , 630-641 (2001).

83. J. Kindt, S. Tzlil, A. Ben-Shaul and W.M. Gelbart DNA Packing and Ejection Forces in Bacteriophage, PNAS 98 , 13671-13674 (2001).

84. D. Harries, S. May and A. Ben-Shaul Adsorption of Charged Macromolecules on Mixed Lipid Membranes, Colloids and Sur- faces A 208, 41-50 (2002).

85. S. May, D. Harries and A. Ben-Shaul Macroion-Induced Compositional Instability of Binary Fluid Membranes, Phys. Rev. Lett. 89, 268102 (2002).

86. S. May and A. Ben-Shaul Membrane-Macromolecule Interactions and their Structural Consequences, in ”Planar Lipid Bilayers (BLM’s) and their Applications”, H.T. Tien and A.L. Ottowa-Leimanov, editors. Elsevier Science B.V., Chapter 10, pp. 315-346 (2003).

87. S. Tzlil, J.T. Kindt, W.M. Gelbart and A. Ben-Shaul Force and Pressures in DNA Packaging and Release from Viral Capside, Biophys. J. 84, 1-11 (2003).

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88. A. Zemel, D.R. Fattal and A. Ben-Shaul Energetics and Self-Assembly of Amphipathic Peptide Pores in Lipid Membranes, Bio- phys. J. 84, 2242-2255 (2003).

89. D. Harries, S. May and A. Ben-Shaul Curvature and Charge Modulations in Lamellar DNA-Lipid Complexes, J. Phys. Chem. B 107, 3624-3640 (2003).

90. A. Cordova, M. Deserno, A. Ben-Shaul and W.M. Gelbart Osmotic Shock and the Strenth of Viral Capsides, Biophys. J. 85, 70-74 (2003).

91. D. Harries, A. Ben-Shaul and I. Szleifer Enveloping of Proetins by Charged Lipid Bilayers, J. Phys. Chem. B 108, 1491-1496 (2004).

92. S. May and A. Ben-Shaul Modeling of Cationic-Lipid Complexes, Current Medicinal Chemistry 11, 1241-1258 (2004).

93. A. Zemel, A. Ben-Shaul and S. May Membrane Perturbation Induced by Amphipathic Peptides, Biophys. J.86, 3607-3619 (2004).

94. S. Tzlil, M. Deserno, W.M. Gelbart and A. Ben-Shaul A Statistical-Thermodynamic Model of Viral Budding Biophys. J. 86 , 2037-2048 (2004).

95. S. May, Y. Kozlowski, A. Ben-Shaul and M. Kozlov Tilt Modulus of a Lipid Monolayer, Eur. Phys. J. 14, 299-308 (2004).

96. A. Zemel, A. Ben-Shaul and S. May Membrane Perturbation Induced by Amphiphathic Peptides, Biophys. J. 86, 3607-3619 (2004) .

97. E.C. Mbamala, A. Ben-Shaul and S. May Domain Formation Induced by the Adsorption of Charged Proteins on Mixed Lipid Mem- branes, Biophys. J.88 , 1702-1714 (2005).

98. M. Kugler, S. Park, D. Harries, A. Ben-Shaul and W.M. Gelbart DNA ”Blue Phases”: A New Twist to Double-Twist Bundles (preprint).

99. A. Zemel, A. Ben-Shaul and S. May Perturbation of a Lipid Membrane by Amphiphatic Peptides and its Role in Pore Forma- tion, Eur. Biophys. J. 34, 230-242 (2005).

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100. C.P. Chen, S. Posy A. Ben-Shaul, L. Shapiro and B.H. Honig Specificity of Cell-Cell Adhesion by Classical Cadherins: Critical Role for Low Affinity Dimerization through β-Strand Swapping, Proc. Nat’l Acad. Sci. USA 102, 8533-8538 (2005).

101. S. Tzlil and A. Ben-Shaul Flexible Charged Macromolecules on Mixed Fluid Lipid Membranes: Theory and Monte- Carlo Simulations, Biophys. J. 89, 2972-2987 (2005).

102. L. Haviv, Y. Brill-Karniely, R. Mahaffy, F. Backouche, A. Ben-Shaul, T.D. Pollard and A. Bernheim-Groswasser Lamellipodia to Filopodia Transition in a Membrane Free System, Proc. Nat’l Acad. Sci. USA (submitted).

75

6.3. Victoria Buch

32. J.P. Devlin, J. Brudermann, P. Lohbrandt, U. Buck and V. Buch Surface Vibrations of Large Water Clusters by Helium Atom Scattering, J. Chem. Phys. 112 , 11038 (2000).

33. N. Uras, V. Buch and J.P. Devlin Hydrogen Bond Surface Chemistry: Interaction of BH3 with an Ice Particle, J. Phys. Chem. B 104 , 9203 (2000).

34. J.P. Devlin, J. Sadlej and V. Buch Infrared Spectra of Large H2O Clusters: New Understanding of the Elusive Bending Mode of Ice; J. Phys. Chem. A 105 , 974 (2001).

35. U. Buck and V. Buch Isomerization and Melting Transition of Size Selected Water Nonamers, J. Phys. Chem. A 105, 974 (2001).

36. V. Buch Exploration of Multidimensional Variational Gaussian Wave Packets as a Simulation Tool, J. Chem. Phys. 117 , 4738 (2002).

37. J.P. Devlin, N. Uras, J. Sadlej and V. Buch Catching HCl in the Act of Ionizing: Observation of Frozen Solvation Stages on the Cold Ice Particle Surface, J. Phys. Chem. (feature article, to be submitted).

38. J.P. Devlin, N. Uras, M. Rahman and V. Buch Covalent and Ionic States of Strong Avid at the Ice Surface, Isr. J. Chem. 39 , 261 (1999).

39. J.P. Devlin, C. Joyce and V. Buch Infrared Spectra and Structures of Large Water Clusters, J. Phys. Chem. A 104 , 1974 (2000).

40. J. Brudermann, U. Buck and V. Buch Isomerization and Melting Transition of Size Selected Water Nonamers, J. Phys. Chem. A 106, 455 (2002).

41. J.P. Devlin, N. Uras. J. Sadlej and V. Buch Discrete Stages in the Solvation and Ionization of Hydrogen Chloride Adsorbed on Ice Particules, Nature 417, 269 (2002).

42. V. Buch, J. Sadlej, N. Aytemiz-Uras and J.P. Devlin Solvation and Ionization Stages of HCl on Ice Nanocrystals, J. Phys. Chem. A 106, 9374 (2002).

43. J. Rzepkowska, N. Uras, J. Sadlej and V. Buch Intermolecular Potentials for Ammonia-Aqueous Mixture, J. Phys. Chem. A 106, 1790 (2002).

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44. M.W. Severson, J.P. Devlin and V. Buch Librational Modes of Ice. I, J. Chem. Phys. 119, 4449 (2003).

45. N. Grishina and V. Buch Dynamics of Amorphous Water, via Migration of 3- and 5-Coordinated H2O, Chem. Phys. Lett. 379, 418 (2003).

46. J.K. Kazimirski and V. Buch Search for Low Energy Structures of Water Clusters (H2 O)n n = 20-22, 48, 123, 293, J. Phys. Chem. A 107, 9762 (2003).

47. C.A. Yinnon, V. Buch and J.P. Devlin A Monte Carlo Model for Formation of a Mixed Crystal from Two Solids in Contact, J. Chem. Phys. 120, 11200 (2004)

48. N. Grishina and V. Buch Structure and Dynamics of Orientational Defects in Ice I”, J. Chem. Phys. 120, 5217 (2004).

49. C. Steinbach, P. Andersson, J.K. Kazimirski, U. Buck, V. Buch and T.A. Ben Infrared Predissociation Spectroscopy of Large Water Clusters: A Unique Probe of Clus- ter Surfaces, J. Phys. Chem., A 108, 6165 (2004).

50. C. Steinbach, P. Andersson, M. Melzer, J.K. Kazimirski and V. Buch Detection of the Book Isomer from the OH-Stretch Spectroscopy of Size Selected Water Hexamers, Phys. Chem. Chem. Phys. 6, 3320 (2004).

51. V. Buch Calculation of Infrared Absorption Spectra Using Gaussian Variational Wave Packets, J. Chem. Phys., 121, 6961 (2004).

52. V. Buch, S. Baurecker, J.P. Devlin, U. Buck and J. Kazimirski Solid Water Clusters in the Size Range of Tens ∼ Thousands of H2O: A Combined Com- putational/Spectroscopic Outlook, Int’l Revs. Phys. Chem. 23, 375-433 (2004) (invited review) .

53. J.P. Devlin, J. Sadlej, M. Hollman and V. Buch Solvation Stages of HCl and HBr in Crystalline Phases with Methanol and Small Ethers: Acid-Ether Cluster Complexes in Amorphous and Crystal Phases, J. Phys. Chem. A 108, 2030 (2004).

54. V. Buch, F. Mohamed, M. Krack, J. Sadlej, J.P. Devlin and M. Parrinello Solvation States of HCl in Mixed Ether: Acid Crystals: A computational Study, J. Chem. Phys. 121, 12135- 12138 (2004).

55. V. Buch Calculation of Infrared Absorption Spectra Using Gaussian Variational Wave Packets, J. Chem. Phys. 121, 6961-6966 (2004).

77

56. J.P. Devlin, M. Farnik, M.A. Suhm et al. Comparative FTIR Spectroscopy of HX Adsorbed on Solid Water: Ragout-jet Water Clus- ters vs. Ice Nanocrystal Arrays, J. Phys. Chem. A 109, 955-958 (2005).

57. J.P. Devlin, D.B. Gulluru and V. Buch Rates and Mechanisms of Conversion of Ice Nanocrystals to Hydrates of HCl and HBr: Acid Diffusion in the Ionic Hydrates, J. Phys. Chem. B 109, 3392-3401 (2005).

58. J.P. Develin, M.W. Severson, F. Mohamed, V. Buch et al. Experimental and Computational Study of Isotopic Effects Within the Zundel Ion, Chem. Phys. Lett. 408, 439- 444 (2005).

59. V. Buch, K. Martonak and M. Parrinello A New Molecular-Dynamics Based Approach for Molecular Crystal Structure Search, J. Chem. Phys. 123, Art. No. 051108 (2005).

60. P. Jungwirth, D. Rosenfeld and V. Buch A Possible New Molecular Mechanism of Thundercloud Electrification, Atmospheric Re- search 76, 190-205 (2005).

61. V. Buch Molecular Structure and OH-Stretch Spectra of Liquid Water Surface, J. Phys. Chem. B 109, 17771-17774 (2005).

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6.4. Robert B. Gerber

167. N.J. Wright and R.B. Gerber Direct Calculations of Anharmonic Vibrational States of Polyatomic Molecules Using Po- tential Energy Surfaces Calculated from Density Functional Theory, J. Chem. Phys. 112 , 2598-2604 (2000).

168. G.M. Chaban, J.O. Jung and R.B. Gerber Anharmonic Vibrational Spectroscopy of Hydrogen-Bonded Systems Directly Com- puted from ab initio Potential Surfaces: (H2O)n, n = 2, 3; Cl− (H2O)n, n = 1, 2; H+ (H2O)n, n = 1, 2; H2 O − CH3OH J. Phys. Chem. A 104 , 2772-2779 (2000).

169. E.M. Knipping, M.J. Lakin, K.L. Foster, P. Jungwirth, D.J. Tobias, R.B. Gerber, D. Dabdub and B.J. Finlayson-Pitts Experiments and Molecular/Kinetics Simulations of Ion-Enhanced Interfacial Chemistry on Aqueous NaCl Aerosols, Science 288 , 301-306 (2000).

170. R. Baumfalk, N.H. Nahler, U. Buck, M.Y. Niv and R.B. Gerber Photodissociation of HBr adsorbed on the Surface and Embedded in Large Clusters, J. Chem. Phys. 113 , 329-338 (2000).

171. J. Lundell, M. Petterson, L. Khriachtchev, M. Rasanen, G.M. Chaban and R.B. Ger- ber Infrared Spectrum of HXeI Revisited: Anharmonic Vibrational Calculations and Matrix Isolation Experiments, Chem. Phys. Lett. 322 , 389-394 (2000).

172. N.J. Wright, R.B. Gerber and D.J. Tozer Direct Calculation of Anharmonic Vibrational States of Polyatomic Molecules Using Density Functional Theory: Spectroscopic Tests of Recently Developed Functionals, Chem. Phys. Lett. 324 , 206-212 (2000).

173. D. Chase, M. Manning, J.A. Morgan, G.M. Nathanson and R.B. Gerber Argon Scattering from Liquid Indium: Simulations with Embedded Atom Potentials and Experiment, J. Chem. Phys. 113 , 9279-9287 (2000).

174. R.B. Gerber, M. Korolkov, J. Manz, M.Y. Niv and B. Schmidt A Reflection Principle for the Control of Molecular Photodissociation in Solids: Model Simulations for F2 in Ar, Chem. Phys. Lett. 327 , 76-84 (2000).

175. J. Lundell, G.M. Chaban and R.B. Gerber Anharmonic Vibrational Spectroscopy Calculations for Novel Rare-Gas Containing Com- pounds: HXeH, HXeCl, HXeBr and HXeOH, J. Phys. Chem. A 104 , 7944-7952 (2000).

176. E.S. Altshuler, D.L. Mills and R.B. Gerber Simulation of Hydrogen Diffusion on BCC Metal (110) Surfaces: Coverage and Temper- ature Dependence, Surf. Sci. 452 , 95-107 (2000).

79

177. M.Y. Niv, M. Bargheer and R.B. Gerber Photodissociation and Recombination of F2 Molecules in Ar54 Clusters: Nonadiabatic Molecular Dynamics Simulations, J. Chem. Phys. 113 , 6660-6672 (2000).

178. G.M. Chaban, J.O. Jung and R.B. Gerber The Anharmonic Vibrational Spectroscopy of Glycine: Testing of Ab Initio and Empiri- cal Potentials, J. Phys. Chem. A 104 , 10035-10044 (2000).

179. J. Lundell, G.M. Chaban and R.B. Gerber Combined Ab Initio and Anharmonic Vibrational Spectroscopy Calculations for Rare- Gas Containing Fluorohydrides HRgF, Chem. Phys. Lett. 331 , 308-316 (2000).

180. A. Cohen, M.Y. Niv and R.B. Gerber Formation of Novel Rare-Gas Containing Molecules by Molecular Photodissociation in Clusters, Faraday Discuss. Chem. Soc. 118 , 269-280 (2001).

181. G.M. Chaban, R.B. Gerber, M.V. Korokolov, J. Manz, M.Y. Niv and B. Schmidt Photodissociation Dynamics of Molecular Fluorine in an Argon Matrix Induced by Ul- trashort Laser Pulses, J. Phys. Chem. A (Issue in honor of W.H. Miller) 105 , 2770-2782 (2001).

182. N.J. Wright and R.B. Gerber Extending the Vibrational Self-Consistent Field Method: Using a Partially Separable Wave Function for Calculating Anharmonic Vibrational States of Polyatomic Molecules, J. Chem. Phys. 114 , 8763-8768 (2001).

183. G.M. Chaban and R.B. Gerber Anharmonic Vibrational Spectroscopy of the Glycine- Water Complex: Calculations for Ab Initio, Empirical and Hybrid (QM/HM) Potentials, J. Chem. Phys. 115 , 1340-1348 (2001).

184. Z. Bihary, R.B. Gerber and V.A. Apkarian Vibrational Self-Consistent Field Approach to Anharmonic Spectroscopy of Molecules in Solids: Application to Iodine in Argon Matrix, J. Chem. Phys. 115 , 2695-2701 (2001).

185. G.M. Chaban, R.B. Gerber and K.C. Janda The Transition from Hydrogen Bonding to Ionization in Clusters: Consequences for An- harmonic Vibrational Spectrosopy, J. Phys. Chem. A 105 , 8223-8332 (2001).

186. Z. Bihary, M. Karavitis, R.B. Gerber and V.A. Apkarian Spectral Inhomogenety Induced by Vacancies and Thermal Phonons and Associated Ob- servables in Time- and Frequency Domain Nonlinear Spectroscopy: I2 Isolated in Argon Matrix, J. Chem. Phys. 115 , 8006-8013 (2001).

80

187. G.M. Chaban, J. Lundell and R.B. Gerber Lifetime and Decomposition Pathways of a Chemically Bound Helium Compound, J. Chem. Phys. ( Communication ) 115 , 7343-7344 (2001).

188. G.M. Chaban and R.B. Gerber Ab Initio Calculations of Anharmonic Vibrational Spectroscopy for Hydrogen Fluoride (HF)n (n = 3, 4), and Mixed Hydrogen-Fluoride /Water (HF)n(H2 O)n (n = 1, 2, 4) Clusters, Spectrochim. Acta (Special Issue on Vibrational Spectroscopy) A 58 , 887-898 (2002).

189. M. Petterson, L. Khriachtchev, A. Lignell, M. Rasanen Z. Bihary and R.B. Gerber HKrF in Solid Krypton, J. Chem. Phys. 116, 2508-2515 (2002).

190. Z. Bihary, G.M. Chaban and R.B. Gerber Vibrational Spectroscopy and Matrix-Site Geometries of HArF, HKrF, HXeCl and HXeI in Rare-Gas Solids, J. Chem. Phys. 116, 5521-5529 (2002).

191. H. Yang, N.J. Wright, A.M. Gagnon, R.B. Gerber and B.J. Finlayson-Pitts An Upper Limit to the Concentration of An Complex at the Air-Water Interface at 298K: Infrared Experiments and Ab Initio Calculatons, Phys. Chem. Chem. Phys. 4 , 1832-1838 (2002).

192. N. Matsunaga, G.M. Chaban and R.B. Gerber Degenerate Perturbation Theory Corrections for the Vibrational Self-Consistent Field Ap- proximations: Method and Applications, J. Chem. Phys. 117 , 3541-3547 (2002).

193. S.K. Gregurick,G.M. Chaban and R.B. Gerber An Initio and Improved Empirical Potentials for the Calculation of the Anharmonic Vi- brational States and Intamolecular Couplings of N-Methylacetamide, J. Phys. Chem. A 106 , 8696-8707 (2002).

194. Z. Bihary, G.M. Chaban and R.B. Gerber Stability of a Chemically Bound Helium Compound in High-Pressure Solid Helium, J. Chem. Phys (Communication) 117, 5105-5108 (2002).

195. M. Bargheer, M.Y. Niv, R.B. Gerber and N. Schwentner Ultrafast Solvent-Induced Spin-Flip and Non-Adiabatic Coupling: ClF in Argon Solids, Phys. Rev. Lett. 89, 108301/1-4 (2002).

196. G.M. Chaban, J. Lundell and R.B. Gerber Theoretical Study of Decomposition Pathways for HArF and HKrF, Chem. Phys. Lett. 364, 628-633 (2002).

81

197. M. Bargheer, R.B. Gerber, M.V. Korolkov, O. Kuhn, J. Manz, M. Schroder and N. Schwentner Subpicosecond Spin-Flip Induced by the Photodissociation Dynamics of ClF in an Ar Matrix, Phys. Chem. Chem. Phys. 4, 5554-5562 (2002).

198. R.B. Gerber, B. Brauer, S.K. Gregurick and G.M. Chaban Calculation of Anharnomic Vibrational Spectroscopy of Small Biological Molecules, Phys. Chem. Comm.142-150 (2002).

199. B. Brauer, G.M. Chaban, S.K. Gregurick and R.B. Gerber Vibrational Spectroscopy and the Development of New Force Fields for Biological Molecules, Biopolymers 68, 370-382 (2003). (Speciall Issue in Memory of S. Lifson).

200. J. Lundell, A. Cohen and R.B. Gerber Quantum Chemical Calculations on Novel Molecules from Xenon Insertion into Hydro- carbons, J. Phys. Chem. A 106, 11950-11955 (2002).

201. P. Jungwirth, R.B. Gerber and M.A. Ratner Quantum Simulations of Vibrational Dephasing of Molecules in a Cryogenic Environ- ment: HArF in an Ar Cluster, Isr. J. Chem. (Topical Issue on Quantum Dynamics) 42, 157-162 (2002).

202. L. Khriachtchev, H. Tanskanen, A. Cohen, R.B. Gerber, J. Lundell, M. Pettersson, H. Kiljunen and M. Rasanen A Gate fo Organokrypton Chemistry: HKrCCH, J. Am. Chem. Soc. (Communication) 125, 6876-6877 (2003).

203. N.H. Nahler, R. Baumfalk, U. Buck, Z. Bihary, R.B. Gerber and B. Friedrich Photodissociation of Oriented HXeI Molecules Generated from HI − Xen Clusters, J. Chem. Phys. 119, 224-231 (2003).

204. G.M. Chaban, S.S. Xantheas and R.B. Gerber Anharmonic Vibrational Spectroscopy of the F− (H2O)n Complexes, n = 1, 2, J. Phys. Chem. A 107, 4952 (2003).

205. M. Roeselova, P. Jungwirth, D.J. Tobias and R.B. Gerber Impact, Trapping and Accommodation of Hydroxyl Radical and Ozone at Aqueous Salt Aerosol Surfaces: A Molecules Dynamics Study J. Phys. Chem. B 107, 12690-12699 (2003).

206. Z. Bihary, G.M. Chaban and R.B. Gerber Delayed Formation Dynamics of HArF and HKrF in Rare-Gas Matrices, J. Chem. Phys. 119, 11278-11284 (2003).

207. A. Cohen, J. Lundell and R.B. Gerber First Compounds with Argon-Carbon and Argon-Silicon Chemical Bonds, J. Chem. Phys. (Communication) 119, 6415-6418 (2003). 82

208. R.B. Gerber Formation of Novel Rare-Gas Molecules in Low-Temperature Matrices, Ann. Rev. Phys. Chem. 55, 55-78 (2004).

209. Y. Miller, E. Fredj, J.N. Harvey and R.B. Gerber UV Spectroscopy of Large Water Clusters: Model Calculations for H2O)n , n = 8, 11, 20, 40, 50 J. Phys. Chem. 55 , 55-78 (2004).

210. B. Brauer, G.M. Chaban and R.B. Gerber Spectroscopically-Tested, Improved Semi-Empirical Potentials for Biological Molecules: Calculations for Glycine, Alanine and Proline, Phys. Chem. Chem. Phys. 6, 2543-2556 (2004).

211. N.H. Nahler, M. Farnik, U. Buck, H. Vach and R.B. Gerber Photodissociation of HCl and Small (HCl)m Complexes In and On Large Arn Clusters, J. Chem. Phys. 121, 1293-1302 (2004).

212. R.B. Gerber, G.M. Chaban, B. Brauer and Y. Miller First Principles Calculations of Anharmonic Vibrational Spectroscopy of Large Molecules, in: Theory and Applications of Computational Chemisry: The First 40 Years, edited by C.E. Dykstra, G. Frenking, K.S. Kim and G.E. Sauseria (Elsevier, Holland) (in press).

213. C.A. Brindle, G.M. Chaban, R.B. Gerber and K.C. Janda Anharmonic Vibrational Spectroscopy Calculations for (NH3 )(NF) and (NH3)(DF): Fundamental, Overtone and Combination Transitions, Phys. Chem. Chem. Phys. 7 , 945-754 (2005).

214. D. Shemesh, G.M. Chaban and R.B. Gerber Photoionization of Glycine: The First Ten Picoseconds, J. Phys. Chem. A 108 , 11477- 11484 (2004).

215. Y. Miller, G.M. Chaban and R.B. Gerber Theoretical Study of Anharmonic Vibrational Spectra of HNO3, HNO3-H2O, HNO4: Fundamental Overtone and Combination Excitations, Chem. Phys. 313 , 213-224 (2005).

216. D. Shemesh, R. Baer, T. Seideman and R.B. Gerber Photoionization Dynamics of Glycine Adsorbed on a Silicon Cluster: ”On-the-Fly”’ Sim- ulations, J. Chem. Phys. 122 , 184704 (2005).

217. E.C. Brown, A. Cohen and R.B. Gerber Prediction of a Linear Polymer Made of Xenon and Carbon, J. Chem. Phys. (Communi- cation) 122 , 171101 (2005).

218. A. Adesokan, E. Fredj, E.C. Brown and R.B. Gerber Anharmonic Vibrational Spectroscopy Calculations of 5,6 Dihydrouracil and its Complex with Water, Mol. Phys. (Special Issue in honor of J.P. Simons) 103 , 1505-1520 (2005). 83

219. R.B. Gerber New Chemistry of the Noble Gas Elements: Novel Molecules, Polymers and Crystals, Bulletin of the Israel Chem. Soc. Issue 18 , 7-14 (2005).

220. D. Shemesh and R.B. Gerber Different Chemical Dynamics for Different Conformers of Biologial Molecules: Pho- toionization of Glycine, J. Chem. Phys. (Communication) 122 , 241104-1 (2005).

221. Y. Miller, G.M. Chaban and R.B. Gerber Ab Initio Vibrational Calculations for H2SO4 and H2SO4-H2O-Spectroscopy and the Nature of the Anharmonic Couplings, J. Phys. Chem. A 109 , 6565-6574 (2005).

222. B. Brauer, R.B. Gerber, M. Kabelac, P. Hobza, J.M. Bakker, A.G. Abo Rizik and M.S. de Vries Vibrational Spectroscopy of the G...C Base Pair: Experiment, Harmonic and Anharmonic Calculations and the Nature of the Anharmonic Couplings, J. Phys. Chem. A 109 , 6974- 6984 (2005).

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6.5. Ronnie Kosloff

135. T. Feldmann and R. Kosloff Performance of Discrete Heat Engines and Heat Pumps in Finite Time, Phys. Rev. E, 61, 4774-4790 (2000).

136. D.Q. Xie, H. Guo, Y. Amatatsu and R. Kosloff Three-Dimensional Photodissociation Dynamics of Rotational State Selected Methyl Iodide, J. Phys. Chem. 104 , 1009-1019 (2000).

137. V. Kokoouline, O. Dulieu, R. Kosloff and F. Masnou-Seeuws Theoretical Treatment of Channel Mixing in Excited Rb2 and Cs2 Ultra-Cold Molecules: Determination of Predissociation Lifetimes with Coordinate Mapping, Phys. Rev. A, 62 , 032716-1 (2000).

138. L. Romm, O. Citri, R. Kosloff and M. Asscher A Remarkable Heavy Isotope Effect in the Dissociative Chemisorption of Nitrogen on Ru(001), J. Chem. Phys. 112 , 8221-8224 (2000).

139. R. Kosloff, E. Geva and J.M. Gordon The Quantum Refrigerator in Quest of the Absolute Zero, Appl. Phys. 87 , 8093-8097 (2000).

140. R. Kosloff, G. Katz and Y. Zeiri Dynamics of Charge Transfer States on Metal Surfaces: The Competition between Reactivity and Quenching, Faraday Discussions 117 , 291-301 (2000).

141. G.R. Darling, Y. Zeiri and R. Kosloff Charge-Transfer Reactions in Atom Scattering from Ionic Surfaces: A Time-Dependent Wavepacket Approach, Faraday Discussions, 117 , (2000).

142. L. Pesce, Z. Amitay, R. Uberna, S.R. Leone, M. Ratner and R. Kosloff Quantum Dynamics Simulation of the Ultrafast Photoionization of Li2, J. Chem. Phys. 114 , 1259-1271 (2001).

143. J. Vala, O. Dulieu, F. Masnou-Seeuws, P. Pillet and R. Kosloff Coherent Control of Cold- Molecule Formation through Photoassociation Using a Chirped Pulsed Laser Field, Phys. Rev. A 6301 , 3412 (2001).

144. J. Vala, and R. Kosloff Coherent Mechanism of Robust Population Inversion, Optics Express 8 , 238-245 (2001).

145. V. Kokoouline, J. Vala and R. Kosloff Tuning the Scattering Length on the Ground Triplet State of Cs2, J. Chem. Phys. 114 , 3046-3050 (2001). 85

146. A. Bartana, R. Kosloff and D.J. Tannor Laser Cooling of Molecules by Dynamically Trapped States, Chem. Phys. 267 , 195-207 (2001).

147. D. M. Lockwood, M. Ratner and R. Kosloff Energy Gap Dependence of Vibrational Dephasing Rates: A Semigroup Description, Chem. Phys. 267 ,55-64 (2001).

148. J. Vala, R. Kosloff and J.N. Harvey Ab initio and DIM Potentials for I−, 3 I2, I− 2 and I3, J. Chem. Phys. 114, 7413 (2001).

149. M. Vatasescu, O. Dulieu, R. Kosloff and F. Masnou-Seeuws Optimal Control of Photoassociation of Cold Atoms and Photodissociation of Long- Range Molecules: Characteristic Times for Wave-Packet Propagation, Phys. Rev. A 63 , 3407 (2001).

150. E. Gershgoren, J. Vala, R. Kosloff, and S. Ruhman Impulsive Control of Ground Surface Dynamics of I− 3 in Solution, J. Phys. Chem. 105 , 5081-5095, (2001).

151. S. Thiel, M. Pykavy, T. Kluner, H-J.Freund, R. Kosloff and V. Staemmler Three-Dimensional ab initio Quantum Dynamics of the Photodesorption of CO from Cr2 O3(0001): Stereodynamic Effect, Phys. Rev. Lett. 8707, 7601-7605, (2001).

152. J.P. Palao, R. Kosloff and J.M. Gordon Quantum Thermodynamic Cooling Cycle, Phys. Rev. E 64 , 056130-8 (2001).

153. D.M. Lockwood, M.A. Ratner and R. Kosloff Effects of Anharmonicity and Electronic Coupling on Photoinduced Electron Transfer in Mixed Valence Compounds, J. Chem. Phys. 117 , 10125-101332 (2002).

154. S. Thiel, M. Pykavy, T. Kluner, H.-J. Freund, R. Kosloff and V. Staemmler Rotational Alingment in the Photodesorption of CO from Cr2O3(0001): A Systematic Three- Dimensional Ab Initio Study, J. Chem. Phys. 116 , 762-773 (2002).

155. J.R. Fair, D. Schafer, R. Kosloff and D.J. Nesbitt Intramolecular Energy Flow and Nonadiabaticity in Vibrationally Mediated Chemistry: Wavepacket Studies of Cl + H2O, J. Chem. Phys. 116 , 1406-1416 (2002).

156. G. Katz, K. Yamashita, Y. Zeiri and R. Kosloff The Fourier Method for Tri-atomic Systems in the Search for the Optimal Coordinate System, J. Chem. Phys. 116, 4403-4414 (2002). 86

157. Ch. P. Koch, Th. Kluner and R. Kosloff A Complete Quantum Description of an Ultrafast Pump-Probe Charge Event in Con- densed Phase, J. Chem. Phys. 116, 7983-7996 (2002).

158. F. Dobnikova, R. Kosloff, Y. Zeiri and Z. Karpas Novel Approach to the Detection of Triperoxide (TATP): Its Structure and Its Complex with Ions, J. Phys. Chem. 106, 4951-4956 (2002).

159. R. Kosloff and T. Feldmann A Discrete Four Stroke Quantum Heat Engine Exploring the Origin of Friction, Phys. Rev. E, 65 , 055102 1-4 (2002).

160. G. Katz, Y. Zeiri and R. Kosloff Three-Dimensional Quantum Time Dependent Study of the Photodissociation Dynamics of Na...FH/D, Chem. Phys. Lett. 359 , 453-459 (2002).

161. Z. Amitay, R. Kosloff and S.R. Leone Experimental Coherent Computation of a Multiple-Input AND Gate Using Shaped Molecular Wave Packets, Chem. Phys. Lett. 359, 8-14 (2002).

162. G. Katz, Y. Zeiri and R. Kosloff Quantum Dissipative Model for the Collision Induced Ionization of In2 Impinging on a Diamond Surface, Chem. Phys. Lett. 358, 284-289 (2002).

163. R. Kosloff and M.A. Ratner Rate Constant Turnovers: Energy Spacings and Mixings, J. Phys. Chem. B 06 , 8479-8483 (2002).

164. J.P. Palao and R. Kosloff Quantum Computing by an Optimal Control Algorithm for Unitary Transformations, Phys. Rev. Lett. 89 , 188501 (2002).

165. J. Vala, Z. Amitay, B. Zhang, S.R. Leone and R. Kosloff Experimental Implementation of the Deutsch-Jozsa Algorithm for Three-Qubit Functions Using Pure Coherent Molecular Superpositions, Phys. Rev. A 66 , 062316 (2002).

166. E. Gershgoren, Z. Wang, S. Ruhman, J. Vala and R. Kosloff Investigating Pure Vibrational Dephasing of I3 in Solution: Temperature Dependence of T ∗ 2 for the Fundamental and First Harmonic of ν1 , J. Chem. Phys. 118 , 3660-3667 (2003).

167. G.R. Darling, R. Kosloff and Y. Zeiri Time-Dependent Quantum Calculations of Negative Ion Formation in Scattering of Atoms from Alkali-Halide Surfaces, Surf. Sci. 528 , 84 (2003).

168. S. Jorgensen and R. Kosloff Two-Pulse Atomic Coherent Control , Surf. Sci. 528 , 156 (2003).

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169. Ch. P. Koch, Th. Kl ¨uner, H.-J. Freund and R. Kosloff Femtosecond Photodesorption of Small Molecules from Surfaces: A Theoretical Investi- gation from First Principles, Phys. Rev. Lett. 90 , 117601 (2003).

170. D. Neuhauser, R. Baer and R. Kosloff Quantum Soliton Dynamics in Vibrational Chains (Toda Lattice): Comparison of Fully Correlated TDSCF, and Classical Dynamics, J. Chem. Phys. 118 , 5729 - 5735 (2003).

171. S. Jorgensen and R. Kosloff Two-Pulse Atomic Coherent Control (2PACC) Spectroscopy of Eley-Rideal Reactions. An Application of an Atom Laser, J. Chem. Phys. 119 , 149 (2003).

172. Ch. P. Koch, Th. Kl ¨uner, H.-J. Freund and R. Kosloff Ab initio Treatment of Electronic Relaxation in the Femtosecond Laser Induced Desorp- tion of NO/NiO(100), J. Chem. Phys. 119 , 1750-1765 (2003).

173. T. Feldmann and R. Kosloff The Quantum Four Stroke Heat Engine: Thermodynamic Observables in a Model with Intrinsic Friction, Phys. Rev. E 68 , 016101 (2003).

174. M. Binetti, O. Weiβe, E. Hasselbrink, G. Katz, R. Kosloff and Y. Zeiri The Role of Nonadiabatic Pathways and Molecular Rotations in the Oxygen Abstraction Reaction on the Al(111) Surface, Chem. Phys. Lett. 373 , 366 (2003).

175. D. Gelman and R. Kosloff Simulating Disspative Phenomena with a Random Phsae Thermal Wavefunctions, High Temperature Application of the Surrogate Hamiltonian Approach, Chem. Phys. Lett. 129, 381 (2003).

176. J.P. Palao and R. Kosloff Optimal Control Theory for Unitary Transformations, Phys. Rev. A 68 , 062308 (2003).

177. G. Katz, Y. Zeiri and R. Kosloff Abstractive Dissociation of Oxygen Over Al(111): A Nonadiabatic Quantum Model, J. Chem. Phys. 120 3931-3948 (2004).

178. G. Ashkenazi and R. Kosloff String, Ring, Sphere: Visualizing Wavefunctions on Different Topoligies, Comput. Sci. & Eng. 6 82-86 (2004).

179. Ch. Koch, J.P. Palao, R. Kosloff and F. Masnou-Seeuws Stabilization of Ultracold Molecules Using Optimal Control Theory, Phys. Rev. A 70 , 013402 (2004).

180. D. Gelman, Ch. P. Koch and R. Kosloff Dissipative Quantum Dynamics with the Surrogate Hamiltonian Approach. A Compari- son between Spin and Harmonic Baths, J. Chem. Phys. 121 , 661 (2004).

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181. S. Jorgensen and R. Kosloff A Pulse Shaping Algorithm of a Coherent Matter Wave Controlling Reaction Dynamics, Phys. Rev. A 70 , 015602 (2004).

182. E. Luc-Koenig, R. Kosloff, F. Masnou-Seeuws and M. Vatasescu Photoassociation of Cold Atoms with Chirped Laser Pulses: Time-Dependent Calcula- tions and Analysis of the Adiabatic Transfer Within a Two-State Model, Phys. Rev. A 70 , 033407 (2004).

183. S. Jorgensen, F. Dubnikova, Y. Zeiri, R. Kosloff, Y. Lilach and M. Asscher Theoretical Modeling of Steric Effect in Electron Induced Desorption: CH3Br/O/Ru(001), J. Phys. Chem. 108 , 14056 (2004).

184. T. Feldmann and R. Kosloff Characteristics of the Limit Cycle of a Reciprocating Quantum Heat Engine, Phys. Rev. E 70 , 046110 (2004).

185. G. Katz, R. Kosloff and M.A. Ratner Conical Intersections: Relaxation, Dephasing and Dynamics in a Simple Model, Isr. J. Chem. 44 , 53 (2004).

186. A. Bertelsen, S. Vogelius, S. Jorgensen, R. Kosloff and M.Drewsen Photo-Dissociation of Cold MgH+ Ions Towards Rotational Temperature Measurements and Controlled Dissociation, Euro. Phys. J. D 31 , 403-408 (2004).

187. F. Dubnikova, R. Kosloff, J. Almog, Y. Zeiri, R. Boese, H. Izhaky, A. Alt and E. Keinan Decomposition of TATP is an Entropic Explosion, J. Am. Chem. Soc. 127 , 1146-1159 (2005).

188. Ch. P. Koch, F. Masnou-Seeuws and R. Kosloff Creating Ground State Molecules with Optical Feshbach Resonances in Tight Traps, Phys. Rev. Lett. 94 , 193001 (2005).

189. G. Katz, Y. Zeiri and R. Kosloff Nonadiabatic Charge Transfer Processes of Oxygen on Metal Surfaces, Isr. J. Chem. 45 , 27 (2005).

190. M.J. Wright, S.D. Gensemer, J. Vala, R. Kosloff and P.L. Gould Control of Ultracold Collisions with Frequency-Chirped Light, Phys. Rev. Lett. 95 , 063001 (2005).

191. A.C.T. van Duin, Y. Zeiri, F. Dubnikova, R. Kosloff and W.A. Goddard III Atomistic- Scale Simulations of the Initial Chemical Events in the Thermal Initiation of Triacetonetriperoxide, J. Am. Chem. Soc. 127 , 11053 (2005).

192. S. Jorgensen, M. Drewsen and R. Kosloff Intensity and Wavelength Control of a Single Molecule Reaction: Simulation of Photodissociation of Cold-Trapped MgH+, J. Chem. Phys. 123 , 094302 (2005).

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6.6. Raphael D. Levine

322. F. Remacle and R.D. Levine The Electronic Response of Assemblies of Designer Atoms: The Metal-Insulator Transi- tion and the Role of Disorder, JACS 122 , 4084 (2000).

323. T. Raz and R.D. Levine Chemistry under Extreme Conditions Induced by Cluster Impact,

324. R.D. Levine Chemical Reaction Dynamics Looks to the Understanding of Complex Systems,

325. H. Kornweitz, T. Raz and R.D. Levine Driving High Threshold Chemical Reactions by Cluster-Surface Collisions: Molecular Dynamics Simulations for CH3I Clusters, J. Phys. Chem. 103 , 10179 (1999).

326. T. Raz and R.D. Levine Essentials of Cluster Impact Chemistry, Faraday Comm.

327. R.D. Levine Comments on Stereodynamics and Control, Faraday Disc. 113 , 77 (1999).

328. R.D. Levine Concluding Remarks On Stereodynamics and Control, Faraday Disc. 113 , 493 (1999).

329. F. Remacle and R.D. Levine Configuration Interaction Between Covalent and Ionic States in the Quantal and Semi- classical Limits with Application to Coherent and Hopping Charge Migration, J. Phys. Chem. 104 , 2341 (2000).

330. A.E. Wiskerke, S. Stolte, H.J. Loesch and R.D. Levine K + CH3I → KI + CH3 Revisited: The Total Reaction Cross Section and Its Energy and Orientation Dependence. A Case Study of an Intermolecular Electron Transfer, PCCP 2 , 757 (2000).

331. F. Remacle and R.D. Levine Architecture with Designer Atoms: Simple Theoretical Considerations, Proc. Nat’l Acad. Sci. US 97 , 553 (2000).

332. E.E.B. Campbell and R.D. Levine Delayed Ionization and Fragmentation en route to Thermionic Emission: Statistics and Dynamics, Ann. Rev. Phys. Chem. 51 , 65 (2000).

333. R.D. Levine On A Classical Limit for Electronic Degrees of Freedom Which Satisfies the Pauli Exclu- sion Principle, Nat’l Acad. Sci. US 97 , 1965 (2000).

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334. F. Remacle and R.D. Levine Broken Symmetry in the Density Electronic States of an Array of Quantum Dots as Com- puted for Scanning Tunneling Microscopy, J. Phys. Chem. 104 , 10435 (2000).

335. F. Remacle and R.D. Levine On the Classical Limit for Electronic Structure and Dynamics in the Orbital Approxima- tion, J. Chem. Phys. 113 , 4515 (2000).

336. R.S. Berry and R.D. Levine Progress in Experimental and Theoretical Studies of Clusters

337. R.D. Levine Non-Stationary Quantum Phase Transitions in Hot Clusters? Nobel Symp. on Cluster Physics , E.E.B. Campbell and M. Larsson, Eds., World Scientific (2001).

338. R.D. Levine and F. Remacle Superexchange, Localized and Domain Localized Charge States for Intramolecular Elec- tron Transfer in Large Molecules and in Arrays of Quantum Dots, J. Phys. Chem. B 105 , 2153 (2001).

339. F. Remacle and R.D. Levine Quantum Dots as Chemical Building Blocks: Elementary Theoretical Considerations, Chem. Phys. Chem. (Angew. Chem). 2 , 20 (2001).

340. K.L. Kompa and R.D. Levine A Molecular Logic Gate, Proc. Nat’l Acad. Sci. US 98 , 410 (2001).

341. F. Remacle and R.D. Levine Electron-Nuclear Dynamics in the Classical Limit for the Electronic Degrees of Freedom, J. Phys. Chem. A 105 , 2708 (2001).

342. Q. Shi, S. Kais, F. Remacle and R.D. Levine Electronic Isomerism: Symmetry Breaking and Electronic Phase Diagrams at the Large- D Limit, Chem. Phys. Chem. 2 , 434 (2001).

343. E.E.B. Campbell and R.D. Levine Dynamics of Delayed Ionization, in ”Quantum Phenomena in Clusters and Nanostruc- tures”, S.N. Khanna and A.W. Castleman, Jr., eds.

344. F. Remacle, E.W. Schlag, H. Selzle, K.L. Kompa, U. Even and R.D. Levine Logic Gates Using High Rydberg States, Proc. Nat’l Acad. Sci. US 98 , 2973 (2001).

345. Th. Witte, Ch. Bucher, F. Remacle, D. Proch, K.L. Kompa and R.D. Levine IR-UV Double-Resonance Photodissociation of Nitric Acid (HONO2) Viewed as Mole- cualr Information Processing, Angew. Chemie 40 , 2512 (2001).

346. F. Remacle and R.D. Levine Toward Molecular Logic Machines, J. Chem. Phys. 114 , 10239 (2001).

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347. F. Remacle, S. Speiser and R.D. Levine Intermolecular and Intramolecualr Logic Gates, J. Phys. Chem. A 105 , 5589 (2001).

348. Q. Shi, S. Kais, F. Remacle and R.D. Levine On the Crossing of Electronic Energy Levels of Diatomic Molecules in the Large- D Limit, J. Chem. Phys. 114 , 9697 (2001).

349. R.D. Levine On the Capture Cross-Section for Charge Neutralization, Recombination, Photoassocia- tion and Other Barrierless Reactions, Chem. Phys. 270 , 129 (2001).

350. M. Boyle, K. Hoffmann, C.P. Schulz, I.V. Hertel, R.D. Levine and E.E.B. Campbell Excitation of Rydberg Series in C60 , Phys. Rev. Lett. 87 , 273401-14 (2001).

351. J.L. Sample, P. Chandhar, K.C. Beverly, F. Remacle J.R. Heath and R.D. Levine, Conducting Arrays of Metallic Quantum Dots: An Experi- mental and Computational Study of the Role of Disorder as Probed by the Surface Poten- tial, Adv. Materials, 114 , 124 (2002).

352. D. Steinitz, F. Remacle and R.D. Levine On Spectroscopy, Control and Molecular Information Processing, Chem. Phys. Chem. 2 , 43 (2002).

353. K.C. Beverly, J.L. Sample, J.F. Sampaio, F. Remacle J.R. Heath and R.D. Levine, Quantum Dot Artificial Solids: Understanding the Static and Dynamic Role of Size and Packing Disorder, Proc. Nat’l Acad. Sci US 99 , 6456 (2002).

354. F. Remacle, R. Weinkauf, D. Steinitz, K.L. Kompa and R.D. Levine Molecular Logic Machines by Optical Spectroscopy and Charge Migration Along a Molecular Wire Realized as a Peptide, Chem. Phys. 282 , 363 (2002).

355. J.X. Wang, S. Kais and R.D. Levine Real-space Renormalization Group Study of the Hubbard Model on a Non-bipartite Lat- tice, Int’l J. Mol. Sci. 3 , 4 (2002).

356. F. Remacle, K.C. Beverly, J.R. Heath and R.D. Levine Conductivity of 2-D Ag Quantum Dot Arrays: Computational Study of the Role of Size and Packing Disorder at Low Temperatures, J. Phys. Chem. B, 106 , 4116 (2002).

357. E.A. Torres, D. Baugh and R.D. Levine Ultrashort Time Resolution From Energy Dependent Interference of Photodissociation Amplitudes, Chem. Phys. Lett.

358. A. Gross, H. Kornweitz, T. Raz and R.D. Levine Driving High Threshold Chemical Reactions During the Compression Interlude in Clus- ter Surface Impact, Chem. Phys. Lett. 354 , 395-402 (2002).

359. J.X. Wang, S. Kais, F. Remacle and R.D. Levine A Renormalization Group Approach, 92

360. E.E.B. Campbell, A.V. Glotov, A. Lassesson, R.D. Levine, Cluster-Cluster Fusion, C.R. de l’Acad. des Sci., serie II. Physique 3 , 341-352 (2002).

361. F. Remacle and R.D. Levine Voltage-Induced Non-Linear Characteristics of Arrays of Metallic Quantum Dots,. Phys. Rev. Lett. (2002).

362. D. Ben-Amotz, A.D. Gift and R.D. Levine Improved Corresponding States Scaling of the Equations of State of Simple Fluids J. Chem. Phys. 117 , 4632 (2002).

363. D. Ben-Amotz, A. Gift and R.D. Levine Updated Principle of Corresponding States, J. Chem. Ed. 81, 142 (2004).

364. J.X. Wang, S. Kais, F. Remacle and R.D. Levine Size-Effects in the Electronic Properties of the Finite Arrays of Exchange Coupled Quan- tum Dots; A Renormalization Group Approach, J. Phys. Chem. B 106, 12847-12850 (2002). (in press).

365. F. Remacle and R.D. Levine Voltage-Induced Phase Transition in Arrays of Metallic Nano Dots in Computed Trans- port and Surface Potential Structure, Appl. Phys. Letters 82, 4543-4545 (2003).

366. F. Remacle and R.D. Levine Electronic and Electrical Response of Arrays of Metallic Quantum Dots, Int. J. Quant. Chem. 99, 743-751 (2004).

367. F. Remacle and R.D. Levine Current-Voltage-Temperature Characteristisc for 2D Arrays of Metallic Quantum Dots, Is. J. Chem. 42, 269-280 (2003).

368. A. Gross and R.D. Levine Spectroscopic Characterization of Collision-Induced Electronic Deformation Energy us- ing Sum Rules, J. Chem. Phys. 119, 4283-4293 (2003).

369. F. Remacle, K.C. Beverly, J.R. Heath and R.D. Levine Gating the Conductivity of Arrays of Metallic Quantum Dots, J. Phys. Chem. , 107, 13892-13901 (2003).

370. F. Remacle and R.D. Levine Electronic and Transport Properties of Arrays of Metallic Quantum Dots: A Computa- tional Study, Chimie Nouvelle 83, 112-119 (2003).

371. A. Gross and R.D. Levine Collision-induced IR Emission Spectra of Impact Heated Clusters, J. Phys. Chem. , 107, 9567-9574 (2003).

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372. F. Remacle and R.D. Levine Electrical Transmission of Molecular Bridges, Chem. Phys. Letts. 383, 537-543 (2004).

373. F. Remacle, I. Willner and R.D. Levine Nanowiring by Molecules, J. Phys. Chem. B 108 , 18129-18134 (2004).

374. F. Remacle and R.D. Levine Conductance Spectroscopy of Low-Lying Electronic States of Arrays of Metallic Quan- tum Dots: A Computational Study, in Nanoassemblies and Superstructures , N. Kotov, Ed., Marcel Dekker, New York (2005).

375. F. Remacle and R.D. Levine Level Crossing Conductance Spectroscopy of Molecular Bridges, Appl. Phys. Lett. 85 , 1725 (2004).

376. A. Gross, M. Kjellberg and R.D. Levine Systematics of Collision-Induced Light Emission from Hot Matter, J. Phys. Chem. A 108 , 8949-8953 (2004).

377. F. Remacle and R.D. Levine Quasiclassical Computations. PNAS 101, 12091-12095 (2004).

378. H. Kornweitz, A. Gross, G. Birnbaum and R.D. Levine Probing Electronic Rearrangement During Chemical Reactions, Physica Scripta , ac- cepted (2005).

379. F. Remacle, J.R. Heath and R.D. Levine Electrical Addressing of Confined Quantum Systems for Quasiclassical Computation and Finite State Logic Machines, Proc. Natl. Acad. Sci. USA 102 5653-5658 (2005).

380. D. Remalce,I. Willner and R.D. Levine A Counter by the Electrical Input/Output Stimuli Activation of an Array of Quantum Dots, Chem. Phys. Chem. 6 , 1239 (2005).

381. F. Remacle, R. Weinkauf and R.D. Levine Molecule-Based Photonically Switched Half-Adder and Full Adder, J. Phys. Chem. A 110, 177-184 (2006). Transfer of Energy or of Charge,

382. E. Kataz, R. Baron, I. Willner, N. Richke and R.D. Levine Temperature Dependent and Friction Controlled Electrochemically-Induced Shuttling Along Molecular Strings Associated with Electrodes, Chem. Phys. Chem. (accepted).

383. F. Remacle and R.D. Levine Electrical Transport in Saturated and Conjugated Molecular Wires, Faraday Discuss. 131, 46-67 (2006).

384. G.A. Somorjai and R.D. Levine The Changing Landscape of Physical Chemistry at the Beginning of the 21st Century, J. Phys. Chem. 109 , 9853 (2005). 94

385. F. Remacle and R.D. Levine All Optical Digital Logic: Full Addition or Subtraction on a Three-State System , Phys Rev. A (submitted).

386. F. Remacle and R.D. Levine Towards Parallel Computing: Realization of a Linear Finite State Logic Machine by a Markovian Stochastic Process, (submitted).

387. A. Gross and R.D. Levine Evanescent High Pressure During Hypersonic Cluster-Surface Impact Characaterized by the Virial Theorem, J. Chem. Phys. 123, 11 pp. (194307) (2005).

390. E.W. Schlag, H.L. Selzle and R.D. Levine Dissociation Kinetics of Peptide Ions, J. Phys. Chem. (submitted).