A Black-Box Explicit Solvation Protocol for Calculation of Redox Potentials
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Improved Prediction of Solvation Free Energies by Machine-Learning Polarizable Continuum Solvation Model
Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model Amin Alibakhshi1,*, Bernd Hartke1 Theoretical Chemistry, Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24118 Kiel, Germany Corresponding Author’s email: [email protected] Abstract Theoretical estimation of solvation free energy by continuum solvation models, as a standard approach in computational chemistry, is extensively applied by a broad range of scientific disciplines. Nevertheless, the current widely accepted solvation models are either inaccurate in reproducing experimentally determined solvation free energies or require a number of macroscopic observables which are not always readily available. In the present study, we develop and introduce the Machine- Learning Polarizable Continuum solvation Model (ML-PCM) for a substantial improvement of the predictability of solvation free energy. The performance and reliability of the developed models are validated through a rigorous and demanding validation procedure. The ML-PCM models developed in the present study improve the accuracy of widely accepted continuum solvation models by almost one order of magnitude with almost no additional computational costs. A freely available software is developed and provided for a straightforward implementation of the new approach. Introduction Free energy of solvation is one of the key thermophysical properties in studying thermochemistry in solution, where the majority of real-life chemistry happens. -
FORCE FIELDS for PROTEIN SIMULATIONS by JAY W. PONDER
FORCE FIELDS FOR PROTEIN SIMULATIONS By JAY W. PONDER* AND DAVIDA. CASEt *Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 51. Louis, Missouri 63110, and tDepartment of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 I. Introduction. ...... .... ... .. ... .... .. .. ........ .. .... .... ........ ........ ..... .... 27 II. Protein Force Fields, 1980 to the Present.............................................. 30 A. The Am.ber Force Fields.............................................................. 30 B. The CHARMM Force Fields ..., ......... 35 C. The OPLS Force Fields............................................................... 38 D. Other Protein Force Fields ....... 39 E. Comparisons Am.ong Protein Force Fields ,... 41 III. Beyond Fixed Atomic Point-Charge Electrostatics.................................... 45 A. Limitations of Fixed Atomic Point-Charges ........ 46 B. Flexible Models for Static Charge Distributions.................................. 48 C. Including Environmental Effects via Polarization................................ 50 D. Consistent Treatment of Electrostatics............................................. 52 E. Current Status of Polarizable Force Fields........................................ 57 IV. Modeling the Solvent Environment .... 62 A. Explicit Water Models ....... 62 B. Continuum Solvent Models.......................................................... 64 C. Molecular Dynamics Simulations with the Generalized Born Model........ -
Water Quality Monitoring System Operating Manual February 2002
Water Quality Monitoring System Operating Manual February 2002 (Revision A) Hydrolab Corporation 8700 Cameron Road, Suite 100 Austin, Texas 78754 USA (800)949-3766 or (512)832-8832 fax: (512)832-8839 www.hydrolab.com Quanta•G Display Operations Tree Calib Salin SpC TDS DO DO% ORP pH BP Depth 00:002 mg/L 100% YMDHM [Standard, Scale Factor, or BP] Calib Review Screen Store [Index#] Screen 1⇔2⇔32 [Index#] Clear ClearAll Screen Screen Review Screen Setup Circ Temp Salin/TDS Depth On Off °C °F PSS g/L m ft Setup Notes: 1. Pressing the Esc ∞ key always exits to the previous operation level except at the top level where it toggles the circulator on or off. 2. RTC calibration (Calib ! 00:00) and Screen 3 are only available if the RTC/PC-Dump option is installed. 3. If the RTC/PC-Dump option is installed, pressing and holding the Esc ∞ key down during power-up causes the Quanta Display to enter PC-Dump mode. Table of Contents 1 Introduction ...........................................................................................................................1 1.1 Foreword.........................................................................................................................1 1.2 Specifications..................................................................................................................1 1.3 Components ....................................................................................................................2 1.4 Assembly.........................................................................................................................3 -
Biomolecularelectrostaticsandsol
Quarterly Reviews of Biophysics 45, 4 (2012), pp. 427–491. f Cambridge University Press 2012 427 doi:10.1017/S003358351200011X Printed in the United States of America Biomolecular electrostatics and solvation: a computational perspective Pengyu Ren1, Jaehun Chun2, Dennis G. Thomas2, Michael J. Schnieders1, Marcelo Marucho3, Jiajing Zhang1 and Nathan A. Baker2* 1 Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA 2 Pacific Northwest National Laboratory, Richland, WA 99352, USA 3 Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249, USA Abstract. An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models. 1. -
Wookey: USB Devices Strike Back
WooKey: USB Devices Strike Back Ryad Benadjila, Mathieu Renard, Philippe Trebuchet, Philippe Thierry, Arnauld Michelizza, Jérémy Lefaure [email protected] ANSSI Abstract. The USB bus has been a growing subject of research in recent years. In particular, securing the USB stack (and hence the USB hosts and devices) started to draw interest from the academic community since major exploitable flaws have been revealed by the BadUSB threat [41]. The work presented in this paper takes place in the design initiatives that have emerged to thwart such attacks. While some proposals have focused on the host side by enhancing the Operating System’s USB sub-module robustness [53, 54], or by adding a proxy between the host and the device [12, 37], we have chosen to focus our efforts on the de- vice side. More specifically, our work presents the WooKey platform: a custom STM32-based USB thumb drive with mass storage capabilities designed for user data encryption and protection, with a full-fledged set of in-depth security defenses. The device embeds a firmware with a secure DFU (Device Firmware Update) implementation featuring up-to-date cryptography, and uses an extractable authentication token. The runtime software security is built upon EwoK: a custom microkernel implementa- tion designed with advanced security paradigms in mind, such as memory confinement using the MPU (Memory Protection Unit) and the integra- tion of safe languages and formal methods for very sensitive modules. This microkernel comes along with MosEslie: a versatile and modular SDK that has been developed to easily integrate user applications in C, Ada and Rust. -
Tackling Solvent Effects by Coupling Electronic and Molecular Density Functional Theory Guillaume Jeanmairet, Maximilien Levesque, Daniel Borgis
Tackling Solvent Effects by Coupling Electronic and Molecular Density Functional Theory Guillaume Jeanmairet, Maximilien Levesque, Daniel Borgis To cite this version: Guillaume Jeanmairet, Maximilien Levesque, Daniel Borgis. Tackling Solvent Effects by Coupling Electronic and Molecular Density Functional Theory. Journal of Chemical Theory and Computation, American Chemical Society, 2020, 10.1021/acs.jctc.0c00729. hal-02989427 HAL Id: hal-02989427 https://hal.archives-ouvertes.fr/hal-02989427 Submitted on 5 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Tackling solvent effects by coupling electronic and molecular Density Functional Theory , Guillaume Jeanmairet,⇤ † Maximilien Levesque,¶ and Daniel Borgis¶ Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes † Interfaciaux, PHENIX, F-75005 Paris, France. Réseau sur le Stockage Électrochimique de l’Énergie (RS2E), FR CNRS 3459, 80039 ‡ Amiens Cedex, France PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne ¶ Université, CNRS, 75005 Paris, France Maison de la Simulation, CEA, CNRS, Université Paris-Sud, UVSQ, Université Paris- § Saclay, 91191 Gif-sur-Yvette, France E-mail: [email protected] Abstract Solvation effects can have a tremendous influence on chemical reactions. However, precise quantum chemistry calculations are most often done either in vacuum neglect- ing the role of the solvent or using continuum solvent model ignoring its molecular nature. -
Rust and IPC on L4re”
Rust and Inter-Process Communication (IPC) on L4Re Implementing a Safe and Efficient IPC Abstraction Name Sebastian Humenda Supervisor Dr. Carsten Weinhold Supervising Professor Prof. Dr. rer. nat. Hermann Härtig Published at Technische Universität Dresden, Germany Date 11th of May 2019 Contents 1 Introduction 5 2 Fundamentals 8 2.1 L4Re . 8 2.2 Rust....................................... 11 2.2.1 Language Basics . 11 2.2.2 Ecosystem and Build Tools . 14 2.2.3 Macros . 15 3 Related Work 17 3.1 Rust RPC Libraries . 17 3.2 Rust on Other Microkernels . 18 3.3 L4Re IPC in Other Languages . 20 3.4 Discussion . 21 3.4.1 Remote Procedure Call Libraries . 21 3.4.2 IDL-based interface definition . 22 3.4.3 L4Re IPC Interfaces In Other Programming Languages . 23 4 L4Re and Rust Infrastructure Adaptation 24 4.1 Build System Adaptation . 25 4.1.1 Libraries . 26 4.1.2 Applications . 27 4.2 L4rust Libraries . 29 4.2.1 L4 Library Split . 29 4.2.2 Inlining vs. Reimplementing . 30 4.3 Rust Abstractions . 31 4.3.1 Error Handling . 31 4.3.2 Capabilities . 32 5 IPC Framework Implementation 35 5.1 A Brief Overview of the C++ Framework . 36 5.2 Rust Interface Definition . 37 5.2.1 Channel-based Communication . 37 5.2.2 Macro-based Interface Definition . 39 5.3 Data Serialisation . 43 2 5.4 Server Loop . 46 5.4.1 Vector-based Service Registration . 46 5.4.2 Pointer-based Service Registration . 48 5.5 Interface Export . 52 5.6 Implementation Tests . -
Arxiv:1809.04152V1 [Physics.Chem-Ph] 11 Sep 2018
Modeling Electronic Excited States of Molecules in Solution Tim J. Zuehlsdorff1, a) and Christine M. Isborn1, b) Chemistry and Chemical Biology, University of California Merced, N. Lake Road, CA 95343, USA (Dated: 13 September 2018) The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent configuration, explicit solute-solvent interactions are key to understanding solution-phase reactiv- ity and spectroscopy, simulating accurate inhomogeneous broadening, and predict- ing absorption spectra. In this tutorial review, we give an overview of factors to consider when modeling excited states of molecules interacting with explicit solvent. We provide practical guidelines for sampling solute-solvent configurations, choosing a solvent model, performing the excited state electronic structure calculations, and computing spectral lineshapes. We also present our recent results combining the vertical excitation energies computed from an ensemble of solute-solvent configu- rations with the vibronic spectra obtained from a small number of frozen solvent configurations, resulting in improved simulation of absorption spectra for molecules in solution. The presence of solvent around a molecule affects its energy, properties, dynamics, and reactivity, in both the ground and excited state. Because many excited state phenomena of chemical interest happen in solution and in complex interfacial -
A Microkernel Written in Rust
Objectives Introduction Rust Redox A microkernel written in Rust Porting the UNIX-like Redox OS to Arm v8.0 Robin Randhawa Arm February 2019 Robin Randhawa (arm) FOSDEM 2019 A microkernel written in Rust Objectives Introduction Rust Redox I want to talk about on Robin Randhawa (arm) FOSDEM 2019 A microkernel written in Rust Objectives Introduction Rust Redox Redox is written in Rust - a fairly new programming language Robin Randhawa (arm) FOSDEM 2019 A microkernel written in Rust Objectives Introduction Rust Redox So it is important to discuss Rust too Robin Randhawa (arm) FOSDEM 2019 A microkernel written in Rust Objectives Introduction Rust Redox My goals with this presentation are ● Lightweight intro to the Rust language ● Unique features that make it shine To primarily ● Explain why Rust is interesting for arm talk about ● Rust’s support for arm designs these ● Introduce Redox’s history, design, community ● Status, plans … and some relevant anecdotes from the industry Robin Randhawa (arm) FOSDEM 2019 A microkernel written in Rust Objectives Introduction Rust Redox Open Source Software Division System Software Architecture Team Safety Track Track Charter Firmware Kernel Middleware Platform “Promote the uptake of Arm IP in safety critical domains using open source software as a medium” Robin Randhawa (arm) FOSDEM 2019 A microkernel written in Rust Objectives Introduction Rust Redox My areas of Interest Systems programming languages Operating Arm system architecture design extensions Arm based Open source system communities design Software -
Graduate Division
Offshore Application of Self-Potential Prospecting Robert Frederic Corwin ,'/ B.S. (university of Missouri at ~olla)1964 M.S. (university of ~alifornia)1969 DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY iR Engineering in the GRADUATE DIVISION . "-I 1 . of the UNIVERSITY OF CALIFORMIA, BERKELEY Committee in Charge OFFSHORE APPLICATION OF SELF-POTENTIAL PROSPECTING ABSTRACT Robert Frederic Corwin Degree: Ph .D. Eng inear i rlg Geosc ience Ocean Eng i neering An offshore self-potential prospecting system, consisting of a portable chart recorder and a pair of towed electrodes, is shown to be capable of locating both onshore and submerged offshore deposits of conductive minerals. The silver - silver chloride electrodes, specially designed for this work, are shown to have a small and predictable response to changes in environmental parameters. The background noise level is generally less than a few tenths of a millivolt, allowing visual recognition of offshore self- potential anomalies with a gradient in excess of one miiiivolt over the electrode sepa ration. However, somc man-made str-uctures, or areas of geothermal activity, may generate fields large enough to interfere with self-potential profiling. 1 :! 4:"'4 extending from a reducing sea floor into oxidizing sea water, generates a potential field consistent in magnitude and polarity with those seen over sulfide ore bodies on land. As an oxidation - reduction mechanism appears to offer the best explanation for the self- potential -
Effect of Textural Properties and Presence of Co-Cation on NH3-SCR Activity of Cu-Exchanged ZSM-5
catalysts Article Effect of Textural Properties and Presence of Co-Cation on NH3-SCR Activity of Cu-Exchanged ZSM-5 Magdalena Jabło ´nska 1,* , Kinga Góra-Marek 2 , Miha Grilc 3 , Paolo Cleto Bruzzese 4 , David Poppitz 1, Kamila Pyra 2 , Michael Liebau 1, Andreas Pöppl 4, Blaž Likozar 3 and Roger Gläser 1 1 Institute of Chemical Technology, Universität Leipzig, Linnéstr. 3, 04103 Leipzig, Germany; [email protected] (D.P.); [email protected] (M.L.); [email protected] (R.G.) 2 Faculty of Chemistry, Jagiellonian University in Kraków, Gronostajowa 2, 30-387 Kraków, Poland; [email protected] (K.G.-M.); [email protected] (K.P.) 3 Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; [email protected] (M.G.); [email protected] (B.L.) 4 Felix Bloch Institute for Solid State Physics, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany; [email protected] (P.C.B.); [email protected] (A.P.) * Correspondence: [email protected] Abstract: Comparative studies over micro-/mesoporous Cu-containing zeolites ZSM-5 prepared by top-down treatment involving NaOH, TPAOH or mixture of NaOH/TPAOH (tetrapropylammonium hydroxide) were conducted. The results of the catalytic data revealed the highest activity of the Cu-ZSM-5 catalyst both in the absence and presence of water vapor. The physico-chemical charac- terization (diffuse reflectance UV-Vis (DR UV-Vis), Fourier transform infrared (FT-IR) spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, temperature-programmed desorption of NOx Citation: Jabło´nska,M.; Góra-Marek, (TPD-NO ), and microkinetic modeling) results indicated that the microporous structure of ZSM-5 K.; Grilc, M.; Bruzzese, P.C.; Poppitz, x D.; Pyra, K.; Liebau, M.; Pöppl, A.; effectively stabilized isolated Cu ion monomers. -
The Kinetic and Radiolytic Aspects of Control of the Redox Speciation of Neptunium in Solutions of Nitric Acid
AN ABSTRACT OF THE DISSERTATION OF Martin Precek for the degree of Doctor of Philosophy in Chemistry presented on August 29, 2012. Title: The Kinetic and Radiolytic Aspects of Control of the Redox Speciation of Neptunium in Solutions of Nitric Acid Abstract approved: ________________________________________________ Alena Paulenova Neptunium, with its rich redox chemistry, has a special position in the chemistry of actinides. With a decades-long history of development of aqueous separation methods for used nuclear fuel (UNF), management of neptunium remains an unresolved issue because of its not clearly defined redox speciation. Neptunium is present in two, pentavalent (V) and hexavalent (VI) oxidation states, both in their dioxocation O=Np=O neptunyl form, which differ greatly in their solvent extraction behavior. While the neptunium(VI) dioxocation is being very well extracted, the dioxocation of pentavalent neptunium is practically non-extractable by an organic solvent. As a result, neptunium is not well separated and remains distributed in both organic and aqueous extraction phases. The aim of this study was to develop or enhance the understanding of several key topics governing the redox behavior of neptunium in nitric acid medium, which are of vital importance for the engineering design of industrial-scale liquid-liquid separation systems. In this work, reactions of neptunium(V) and (VI) with vanadium(V) and acetohydroxamic acid - two redox agents envisioned for adjusting the neptunium oxidation state in aqueous separations – were studied in order to determine their kinetic characteristics, rate laws and rate constants, as a function of temperature and nitric acid concentration. Further were analyzed the interactions of neptunium(V) and (VI) with nitrous acid, which is formed as a product of radiolytic degradation of nitric acid caused by high levels of radioactivity present in such systems.