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FF12MC: a Revised AMBER Forcefield and New Protein Simulation Protocol
bioRxiv preprint doi: https://doi.org/10.1101/061184; this version posted July 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. FF12MC: A revised AMBER forcefield and new protein simulation protocol Yuan-Ping Pang Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN 55905, USA Corresponding author: Stabile 12-26, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA; E-mail address: [email protected] Short title: FF12MC: A new protein simulation protocol Keywords: Protein folding; Protein dynamics; Protein simulation; Protein structure refinement; Molecular dynamics simulation; Force field; Chignolin; CLN025; Trp-cage; BPTI. bioRxiv preprint doi: https://doi.org/10.1101/061184; this version posted July 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. ABSTRACT Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened C– H bonds, (ii) removal of torsions involving a nonperipheral sp3 atom, and (iii) reduced 1–4 interaction scaling -
Refinement of Protein Conformations Using a Macromolecular Energy Minimization Procedure
J. Mol. Biol. (1969) 46, 269-279 Refinement of Protein Conformations using a Macromolecular Energy Minimization Procedure MICHAEL LEVITT AND SHNEIOR LIFSON Weixmann Institute of Science Rehovot, Israel (Received 3 December 1968, and in revised form 29 July, 1969) This paper presents a rapid refinement procedure capable of deriving the stable conformation of a macromolecule from experimental model co-ordinates. All the degrees of freedom of the molecule are allowed to vary and all parts of the structure are refined simultaneously in a general force-field. The procedure has been applied to myoglobin and lysozyme. The deviations of peptide bonds from planar conformation and of various bond angles from their respective average values are found to contribute significantly to the retied protein conformation. Hydrogen atoms are not included in the present refinement. A set of non-bonded potential functions, applicable to the equilibrium of a folded protein in an aqueous medium, is described and tested on myoglobin. 1. Introduction The Cartesian co-ordinates of a protein molecule have been obtained from measure- ments on a rigid wire model, built according to electron density maps derived from X-ray diffraction measurements. The errors inherent in measuring a mechanical model give rise to highly strained bond lengths and angles. Much of this strain can be relieved without affecting the relative orientation of parts of the molecule. Diamond (1966) proposed a co-ordinate refinement procedure which varied certain dihedral and bond angles to give the best fit to the rough measured co-ordinates. The fixed bond lengths and angles of each amino acid residue were obtained from crystallographic studies of small molecules. -
IYUNIM Multidisciplinary Studies in Israeli and Modern Jewish Society
IYUNIM Multidisciplinary Studies in Israeli and Modern Jewish Society IYUNIM Multidisciplinary Studies in Israeli and Modern Jewish Society Volume 31 2019 Editors: Avi Bareli, Ofer Shiff Assistant Editor: Orna Miller Editorial Board: Avi Bareli, Avner Ben-Amos, Kimmy Caplan, Danny Gutwein, Menachem Hofnung, Paula Kabalo, Nissim Leon, Kobi Peled, Shalom Ratzabi, Ilana Rosen, Ofer Shiff Founding Editor: Pinhas Ginossar Style Editing: Ravit Delouya, Herzlia Efrati, Keren Glicklich, Yeal Ofir, Meira Turetzky Proofreading: Margalit Abas-Gian, Leah Lutershtein Abstracts Editing: Moshe Tlamim Cover Design: Shai Zauderer Production Manager: Hadas Blum ISSN 0792-7169 Danacode 1246-10023 © 2019 All Rights Reserved The Ben-Gurion Research Institute Photo Typesetting: Sefi Graphics Design, Beer Sheva Printed in Israel at Art Plus, Jerusalem CONTENTS Society Uri Cohen Shneior Lifson and the Founding of the Open University, 1970-1976 7 Oded Heilbronner Moral Panic and the Consumption of Pornographic Literature in Israel in the 1960s 60 Danny Gutwein The Chizbatron and the Transformation of the Palmach’s Pioneering Ethos, 1948-1950 104 Defense Yogev Elbaz A Calculated Risk: Israel’s Intervention in Jordan’s Civil War, September 1970 152 Nadav Fraenkel The Etzion Bloc Settlements and the Yishuv’s Institutions in the War of Independence 182 Mandate Era Ada Gebel Yitzhak Breuer and the Question of Sovereignty in the Land of Israel 215 Dotan Goren The Hughes Land Affair in Transjordan 244 Culture and Literature Liora Bing-Heidecker Choreo-trauma: The Poetics of Loss in the Dance Works of Judith Arnon and of Rami Beer 272 Or Aleksandrowicz The Façade of Building: Exposed Building Envelope Technologies in Modern Israeli Architecture 306 Michael Gluzman David Grossman’s Writing of Bereavement 349 Abbreviations 381 List of Participants 382 English Abstracts i ABSTRACTS ABSTRACTS Shneior Lifson and the Founding of the Open University, 1970-1976 Uri Cohen The idea of an Open University in Israel gained traction in 1970 and in 1976 it opened its doors for classes. -
Required Readings
HPS/PHIL 93872 Spring 2006 Historical Foundations of the Quantum Theory Don Howard, Instructor Required Readings: Topic: Readings: Planck and black-body radiation. Martin Klein. “Planck, Entropy, and Quanta, 19011906.” The Natural Philosopher 1 (1963), 83-108. Martin Klein. “Einstein’s First Paper on Quanta.” The Natural Einstein and the photo-electric effect. Philosopher 2 (1963), 59-86. Max Jammer. “Regularities in Line Spectra”; “Bohr’s Theory The Bohr model of the atom and spectral of the Hydrogen Atom.” In The Conceptual Development of series. Quantum Mechanics. New York: McGraw-Hill, 1966, pp. 62- 88. The Bohr-Sommerfeld “old” quantum Max Jammer. “The Older Quantum Theory.” In The Conceptual theory; Einstein on transition Development of Quantum Mechanics. New York: McGraw-Hill, probabilities. 1966, pp. 89-156. The Bohr-Kramers-Slater theory. Max Jammer. “The Transition to Quantum Mechanics.” In The Conceptual Development of Quantum Mechanics. New York: McGraw-Hill, 1966, pp. 157-195. Bose-Einstein statistics. Don Howard. “‘Nicht sein kann was nicht sein darf,’ or the Prehistory of EPR, 1909-1935: Einstein’s Early Worries about the Quantum Mechanics of Composite Systems.” In Sixty-Two Years of Uncertainty: Historical, Philosophical, and Physical Inquiries into the Foundations of Quantum Mechanics. Arthur Miller, ed. New York: Plenum, 1990, pp. 61-111. Max Jammer. “The Formation of Quantum Mechanics.” In The Schrödinger and wave mechanics; Conceptual Development of Quantum Mechanics. New York: Heisenberg and matrix mechanics. McGraw-Hill, 1966, pp. 196-280. James T. Cushing. “Early Attempts at Causal Theories: A De Broglie and the origins of pilot-wave Stillborn Program.” In Quantum Mechanics: Historical theory. -
Kosmas 2018 Ns
New Series Vol. 1 N° 2 by the Czechoslovak Society of Arts and Sciences KOSMAS CZECHOSLOVAK AND CENTRAL EUROPEAN JOURNAL KOSMAS ISSN 1056-005X ©2018 by the Czechoslovak Society of Arts and Sciences (SVU) Kosmas: Czechoslovak and Central European Journal (Formerly Kosmas: Journal of Czechoslovak and Central European Studies, Vols. 1-7, 1982-1988, and Czechoslovak and Central European Journal, Vols. 8-11, (1989-1993). Kosmas is a peer reviewed, multidisciplinary journal that focuses on Czech, Slovak and Central European Studies. It publishes scholarly articles, memoirs, research materials, and belles-lettres (including translations and original works), dealing with the region and its inhabitants, including their communities abroad. It is published twice a year by the Czechoslovak Society of Arts and Sciences (SVU). Editor: Hugh L. Agnew (The George Washington University) Associate Editors: Mary Hrabík Šámal (Oakland University) Thomas A. Fudge (University of New England, Australia) The editors assume no responsibility for statements of fact or opinion made by contributors. Manuscript submissions and correspondence concerning editorial matters should be sent via email to the editor, Hugh L. Agnew. The email address is [email protected]. Please ensure that you reference “Kosmas” in the subject line of your email. If postal correspondence proves necessary, the postal address of the editor is Hugh L. Agnew, History Department, The George Washington University, 801 22nd St. NW, Washington, DC, 20052 USA. Books for review, book reviews, and all correspondence relating to book reviews should be sent to the associate editor responsible for book reviews, Mary Hrabík Šámal, at the email address [email protected]. If postal correspondence proves necessary, send communications to her at 2130 Babcock, Troy, MI, 48084 USA. -
A. Personal Statement B. Positions, Honors and Review Service
Program Director/Principal Investigator (Last, First, Middle) : LEVITT, Michael BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES. NAME POSITION TITLE Michael LEVITT eRA COMMONS USER NAME (credential, e.g., agency login) Professor LEVITT.MICHAEL EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) INSTITUTION AND LOCATION DEGREE FIELD OF STUDY (if applicable) MM/YY King's College, London, England B.Sc. 06/1967 Physics Royal Society Fellow, Weizmann Institute Israel N/A 09/1968 Conformation Analysis Cambridge University, England Ph.D. 12/1971 Computational Biology A. Personal Statement I pioneered of computational biology setting up the conceptual and theoretical framework for a field that I am still actively involved in at all levels. More specifically, I still write and maintain computer programs of all types including large simulation packages and molecular graphics interfaces. I have also developed a high-level of expertise in Perl scripting, as well as in the advanced use of the Office Suite of programs (Word, Excel and PowerPoint), which is more important and rare than it may seem. My research focuses on three different but inter-related areas of research. First, we are interested in predicting the folding of a polypeptide chain into a protein with a unique native-structure with particular emphasis on how the hydrophobic forces affect the pathway. We expect hydrophobic interactions to energetically favor structure that are more native-like. -
John Von Neumann's “Impossibility Proof” in a Historical Perspective’, Physis 32 (1995), Pp
CORE Metadata, citation and similar papers at core.ac.uk Provided by SAS-SPACE Published: Louis Caruana, ‘John von Neumann's “Impossibility Proof” in a Historical Perspective’, Physis 32 (1995), pp. 109-124. JOHN VON NEUMANN'S ‘IMPOSSIBILITY PROOF’ IN A HISTORICAL PERSPECTIVE ABSTRACT John von Neumann's proof that quantum mechanics is logically incompatible with hidden varibales has been the object of extensive study both by physicists and by historians. The latter have concentrated mainly on the way the proof was interpreted, accepted and rejected between 1932, when it was published, and 1966, when J.S. Bell published the first explicit identification of the mistake it involved. What is proposed in this paper is an investigation into the origins of the proof rather than the aftermath. In the first section, a brief overview of the his personal life and his proof is given to set the scene. There follows a discussion on the merits of using here the historical method employed elsewhere by Andrew Warwick. It will be argued that a study of the origins of von Neumann's proof shows how there is an interaction between the following factors: the broad issues within a specific culture, the learning process of the theoretical physicist concerned, and the conceptual techniques available. In our case, the ‘conceptual technology’ employed by von Neumann is identified as the method of axiomatisation. 1. INTRODUCTION A full biography of John von Neumann is not yet available. Moreover, it seems that there is a lack of extended historical work on the origin of his contributions to quantum mechanics. -
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SPRING 1991 85 Inbetweenness: Spatial Folds in Theatre Historiography Michal Kobialka Thought thinks its own history (the past), but in order to free itself from what it thinks (the present) and be able finally to "think otherwise" (the future). Gilles Deleuze, Foucault In his recent book, Soundings in Critical T7ieoryy Dominick LaCapra discusses the critical and self-critical nature of historiography. Noteworthy is a passage introducing the dialogic exchanges between the theoretical systems of Marx, Derrida, Foucault, and other contemporary theoreticians, in which LaCapra talks about the nature of criticism today: Any assembly of "critics" today will have representatives of various established departments who are uneasy with their own represent ative function and may find more to say, listen to, or at least argue about with other critics than with more securely "representative" members of their own department or field. Indeed contemporary critics are no longer content with interdisciplinary efforts that simply combine, compare, or synthetically unify the methods of existing academic disciplines. Their questioning of established disciplines both raises doubts about internal criteria of purity or autonomy and unsettles the boundaries and protocols of given fields. Criticism in this sense is a discursive agitation running across a variety of Michal Kobialka has published articles and reviews in Journal of Dramatic Theory and Criticism, Theatre History Studies, Medieval Perspectives, The Drama Review, Theatre Journal, Stages, Slavic and East European Journal, and Soviet and East-European Drama, Theatre and Film. He is currently working on a book on Taduesz Kantor and his Cricot 2 theatre. 86 Journal of Dramatic Theory and Criticism disciplines and having an uneasy relation to its own institutional ization. -
Required Readings
HPS/PHIL 687 Fall 2003 Historical Foundations of the Quantum Theory Required Readings: Topic: Readings: Planck and black-body radiation. Martin Klein. “Planck, Entropy, and Quanta, 1901- 1906.” The Natural Philosopher 1 (1963), 83-108. Einstein and the photo-electric effect. Martin Klein. “Einstein’s First Paper on Quanta.” The Natural Philosopher 2 (1963), 59-86. The Bohr model of the atom and spectral series. Max Jammer. “Regularities in Line Spectra”; “Bohr’s Theory of the Hydrogen Atom.” In The Conceptual Development of Quantum Mechanics. New York: McGraw-Hill, 1966, pp. 62-88. The Bohr-Sommerfeld “old” quantum theory; Max Jammer. “The Older Quantum Theory.” In Einstein on transition probabilities. The Conceptual Development of Quantum Mechanics. New York: McGraw-Hill, 1966, pp. 89-156. The Bohr-Kramers-Slater theory. Max Jammer. “The Transition to Quantum Mechanics.” In The Conceptual Development of Quantum Mechanics. New York: McGraw-Hill, 1966, pp. 157-195. Bose-Einstein statistics. Don Howard. “‘Nicht sein kann was nicht sein darf,’ or the Prehistory of EPR, 1909-1935: Einstein’s Early Worries about the Quantum Mechanics of Composite Systems.” In Sixty-Two Years of Uncertainty: Historical, Philosophical, and Physical Inquiries into the Foundations of Quantum Mechanics. Arthur Miller, ed. New York: Plenum, 1990, pp. 61-111. Schrödinger and wave mechanics; Heisenberg and Max Jammer. “The Formation of Quantum matrix mechanics. Mechanics.” In The Conceptual Development of Quantum Mechanics. New York: McGraw-Hill, 1966, pp. 196-280. De Broglie and the origins of pilot-wave theory. James T. Cushing. “Early Attempts at Causal Theories: A Stillborn Program.” In Quantum Mechanics: Historical Contingency and the Copenhagen Hegemony. -
PDF Book, Philosophy of Physics
This content has been downloaded from IOPscience. Please scroll down to see the full text. Download details: IP Address: 170.106.34.90 This content was downloaded on 23/09/2021 at 15:07 Please note that terms and conditions apply. You may also be interested in: Physics as a useful tool for learning English Jesús Fidalgo and Juan Ramón Gallástegui Don't overlook the beauty in physics Leon Lederman Pregnancy and physics: can they mix? What is mathematical physics? Vladimir I Arnol'd Get set for The Physics Congress 2001 Philosophy of Physics Philosophy of Physics Robert P Crease Stony Brook University, New York, US IOP Publishing, Bristol, UK ª IOP Publishing Ltd 2017 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the publisher, or as expressly permitted by law or under terms agreed with the appropriate rights organization. Multiple copying is permitted in accordance with the terms of licences issued by the Copyright Licensing Agency, the Copyright Clearance Centre and other reproduction rights organisations. Permission to make use of IOP Publishing content other than as set out above may be sought at [email protected]. Robert P Crease has asserted his right to be identified as the author of this work in accordance with sections 77 and 78 of the Copyright, Designs and Patents Act 1988. ISBN 978-0-7503-1542-5 (ebook) DOI 10.1088/978-0-7503-1542-5 Version: 20171001 Physics World Discovery ISSN 2399-2891 (online) British Library Cataloguing-in-Publication Data: A catalogue record for this book is available from the British Library. -
Yaakov Levy, B
Prof. Yaakov (Koby) Levy February 2019 The Morton and Gladys Pickman professional chair in Structural Biology Department of Structural Biology Weizmann Institute of Science Rehovot 76100, Israel Tel: +972 (8) 934-4587 Fax: +972 (8) 934-4136 E-mail: [email protected] CURRICULUM VITAE Personal details Date & Place of Birth March 22, 1972; Tel-Aviv, Israel Citizenship Israeli Marital Status Married, three children Homepage http://www.weizmann.ac.il/Structural_Biology/Levy/ Languages Hebrew (mother language), English, Spanish 6/1994 – 6/1997 Military service in the Israel Defense Forces Education 6/1997 – 6/2002 Tel-Aviv University, Tel-Aviv, Israel. Ph.D., Department of Chemical Physics, School of Chemistry Theoretical and computational biophysics, Thesis title: "Multidimensional Potential Energy Surfaces of Biological Macromolecules". Prof. Joshua Jortner and Dr. Oren Becker. 1991 – ‘94 Technion- Israel Institute of Technology, Haifa, Israel. B.Sc., in Chemistry (summa cum laude). Teaching Experience 2008, 2009 Protein Structure Function I, WIS 2007, 2015, 2017 Protein Structure Function II, WIS 2007, 2011, 2013, Computational Molecular Biophysics, WIS 2019 1998 – ‘02 Teaching special courses in General Chemistry (The School of Dental Medicine and the Pre- University project, Tel-Aviv University). 1 Teaching Assistant in General and Physical Chemistry courses (The School of Medicine, Tel- Aviv University), Laboratory course (General Chemistry), Statistical Thermodynamics and in analytical chemistry courses (The School of Chemistry, Tel-Aviv University). 1999 – ‘01 Member in the center for improving teaching in Tel-Aviv university. 1993 – ‘94 Teaching chemistry (for matriculation), “Shuv” High-School, Haifa. Honors and Awards 1992, 1993, President's award for high academic achievements (Technion, Israel Inst. -
Report of the Committee on Post-Secondary Education
DOCUMENT RESUME ED 059 709 JC 720 062 AUTHOR Lefs-n, Shneior TITLE Repor of the Committee on Post-Secondary Education. INSTITUTION Ministry of Education and Culture, Jerusalem (Israel). PUB DATE Dec 71 NOTE 72p. EDRS PRICE MF-$0.55 HC-$3.29 DESCRIPTORS *Educational Development; *Educational Planning; *Foreign Countries: *Institutional Role: *Junior Colleges IDENTIFIERS *Isr6.e1 ABSTRACT This report was produced by a committee appointed by the Council for Higher Education of the Ministry of Education and culture (Israel) to perform the following three major tasks: (1) review all facets of post-secondary education excluding university activities; (2) suggest principles on which to base the development of post-secondary education; and (3) make long- and short-run suggestions for planning and directing various types of post-secondary education. Other major efforts were to initiate discussion regarding communication between different educational levels; the nature and value of awarded certificates; the possibility of using television, radio, and postal services for instructional purposes; and the concept of post-secondary institutions offering a wide variety of courses. The main part of the report consists of a review of post-secondary educational institutions and their role. Such areas as admissions, distribution of students in morning and evening courses, geographical distribution of institutions, program potential, and the role of teacherm are discussed. Tables of descriptive statistics relating to Israeli education in general as well as post-secondary education are appended. (A14 U.S. DEPARTMENT OF HEALTH. EDUCATION & WELFARE OFFICE OF EDUCATION THIS DOCUMENT HAS BEEN REPRO- DUCED EXACTLY AS RECEIVED FROM THE PERSON OR ORGANIZATION ORIG- INATING IT POINTS OF VIEW OR ORIN- IONS STATED DO NOT NECESSARILY REPRESEN1 OFFICIAL OFFICE OF EuL).