DOCSLIB.ORG

Measure to Fund Upgrades

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Measure to Fund Upgrades In Sports... In Forum... Spartans upset On the bus in 10th-ranked SPARTAN San Jose: 49ers, win two of sights, sounds three games in and smells. weekend series. FORUM & OPINION See story on page 4. See column on page 2. 1'111,11,11yd for AIStith' tucr 1414 Volume 102, Number 49 Monday. April 18, 1994 Measure to fund upgrades New building By Laurel Anderson The money will be divided almost oumi, associate executive vice presi- The $901; ntillion to fund the pro- in the works siranan Daily Staff Writer equally among the three systems. dent of facilities development and jects comes In the state's selling of genti.t1 /bligation bonds to investors By Laurel Anderson A bond measure to fund Califor- The CSU's project list covers an operations. Sintruui Day St41 Writer nia college campus improvements estimated 80 projects at all 20 Bentley-Adler said, "In who earn interest on the money they will be on the June 1994 ballot. The campuses. 1990 when Proposition 143 loan to the state. The total cost to the A plan to construct and renovate campus projects include modernization and "The bond measure is the ALIFORNIA failed, that set us back a cou- state is $1.6 billion, because an addi- facilities will proceed if SJSU receives funding remodeling of facilities, updating only way to remodel and ple years in building and tional $700 million will be paid in from a $900 million bond measure. safety standards and replacing aging repair some of our facilities," TATE remodeling projects, so if interest. Proposition IC, The Higher Education equipment. chancellor's office spokesper- NIVERSITT this one were to fail, it would The bonds are similar to mortgage Facilities Bond Act of June 1994, will finance Proposition IC, The Higher Edu- son Colleen Bentley-Adler set us back even farther. loans because the bonds allow the the construction, remodeling and upgrading cation Facilities Bond Act of June said. "That just hurts thou- state to borrow money and pay it of facilities on California State University, Uni- 1994 will provide $900 million for "If these projects are sands of incoming students. back over a period of '25 to 30 years. versity of California, and California Commtini- projects at the CSU campuses, Uni- deferred, all the other projects we are Hundreds of thousands of eligible Concern has bet, \ii essed that ty College campuses. The bond measure pro versity of California campuses and hoping to accomplish would be students will not be served if we can't 107 California Community Colleges. pushed back," said Mohammad Qay- upgrade buildings." Sc BONDS. page 5 See CONSTRUCTION. page 5 Black colleges offer a different perspective By Joan Burke and Marci. Spears Spartrin Daily Staff Writers rently there are 117 predomi- education for blacks. These "1 wanted to be around other nantly black schools in the Unit- schools simply have a high per- black folks. I was tired of being For a white student whose ed States. centage of black students the only black in class. I wanted race represents a large percent Historically, black colleges enrolled. to be in school with black people of the total student population, were founded during the segre- Junior criminal justice major who had the same experiences college life can be satisfying. Stu- gation era. The Second Morrill Shabazz Allah has been on an and would face the same prob- dents feel more accepted Act of 1890 provided for academic journey that lems in the job market," Allah because the student body, teach- the use of land-grant took him from De Anza said. "I learn better, and am ers and classmates are usually of funds for the mainte- College to Florida A & more eager to learn at a black the same race and have the same nance and establishment M University (FAMU), school because the people rep- views and backgrounds. of colleges for blacks. MIN and finally to SJSU. He resent me. I understand the talk For black students, this is not The purpose of these left FAMU for SJSU to and mannerisms and the classes always the case. Unless they institutions was to pro- diversity deal with family matters are more personal." attend a predominantly black vide theoretical and in California. He wants Junior engineering major institution, blacks will be in the practical higher education with to ultimately return to the Flori- Destah Owens has attended minority among their classmates. an emphasis on agriculture and da college. both types of schools. After two Some SJSU and Bay Area stu- mechanical arts. Allah has always wanted to years at UCLA he received a bas- dents have experienced both Predominantly black institu- attend a black college. During ketball scholarship to the Uni- predominantly black and pre- tions were not founded with the his one-year stay at FAMU, his SJSU junior Shabazz Allah attended Florida A&M, an all-black college dominantly white schools. Cur- sole purpose of providing higher wish was granted. Sec COLLEGES page 6 but had to return to San Jose for family reasons. Campus to evacuate Culture Night fanfare in quake disaster drill By Gera],I \ nLU 0it Staley will coordinate the fifth *Arun 1)1.1' s,-111 annual exercise with the help of An all-campus building-es:aro- safety personnel including anent exercise designed to give police officers. cadets, parking safety personnel an opportunity garage supenisors and other vol- to practice emergency tech- unteers who will use radios to niques will take place :weep campus build- tomorrow at 10:10 am. around April is Earthquake People will be t/ )1/I to Preparedness Month 4atlicr at specific areas and the 20-minute exer- , designated for each cise will show the SJSU 1/1tilding while the- safe- campus community how campus : .crsonnel check for to "beat the quake" and cijil tes, casualties. how to cope with other di...- structural damage and haz- "Disasters and emergent ies ardous chemical leaks. occur without warning. It is a A "senior building p matter of when these incidents tor" will he assigned to each will happen, not if they will hap- building and will give the final pen. This is serious stuff," said approval once the buildings Rich Stales'. emenzet i v info 'rum- v DRILL. page 8 Body-fat analysis simple with current technology I3y Ittlit.t ken cll Funding tot the $6,tiou device Spartan I )aih Still Warr crimes horn the Cita le of Friends, a group of students, SJSU sophomore Amy Mendoza, a member of the Akbayan club, amphitheater. The club is rehearsing for Culture Night. which will be In an age of technological alumni and faculty front the practices Singkil, a Filipino folk dance, Sunday at the Student Union presented at the Santa Clara Convention Center in June advam is. measuring body fat nutrition and food science' stands ight on the cutting edge. deparunent. In addition to spon- The Hitt-electric Impedance soring a yearly project. the asso- Analv.i. i III 1f . measuring body ciation }ma-ides students a link Consumers pay for ticket resellers' high overhead fat s a .111.111. high-freque ticv to professionals in the nutrition eft( liii / la rent. will soon grace field. By Cara Broglia percent of a ticket's value by phone room, labor, postage, et purchases also lowers the cost. the c lass!, s >MS of the 19S1 nutri- The first B1A demonstration Spartan Daily Staff Writer banks for cred- envelopes and Administration of justice tion and food ./ iiii depart- will be held tomorrow at a pri- Beware concert-goers: if you it-card purchas- tickets. senior Steve Weichert said that ment. vate Circle of Friends reception purchase your tickets at a BASS es. Discounts On average, he and his friends found a way to nil! giu .indents the featuring John W. Farquhar. an 1,, }ha, experience internationally recognized or Ticketmaster location, you are given to 'BASS is ridiculous It Levinson said beat the system. ())pm tunas might be paying for more than people who pay that BASS earns "BASS is ridiculous. It seems with equipment iii their field," authority in disease prevention you counted on. cash. seems like the charges only $3 to $4 per like the charges go up every senior nun Mon major Dawn and health promotion. Convenience fees, or service Outlets such go up every year.' ticket despite the year," Weichert said. Shues said, excited about her Fatcpihai produces public- charges, can cost the consumer as the Where- Siie of the service 'They're (The Wherehouse) department's state-of-the-art health campaigns that attempt up to $18 for a $350 ticket, as in house and charge the con- being very particular about how addition. to motivate' people to change the case of the Barbara Streisand Tower Records sumer pays. they sell their tickets. We-just go Passing through the right atm their diet and exercise. concert in June. take another Things such as to the (San Jose) Arena because down to the r lain leg and foot, "It's one thing to know to eat Steve Weichert and the RI a (tut cut creates an elec- a low-fat diet and a whole other Some people want to know portion of the lenfor, adminkuration of Jultire sporting events we can spend the night the reason for all the fees. fees to cover arc not as expen- don't have to pay the set vice tric al field in the subject's body. thing to convince people." said In the April 12 issue of the computer costs, sive. charges." The pen icit tagt of Is gh tat is Fee.
Load more

Recommended publications
  • The Molecular Sciences Software Institute
    The Molecular Sciences Software Institute T. Daniel Crawford, Cecilia Clementi, Robert Harrison, Teresa Head-Gordon, Shantenu Jha*, Anna Krylov, Vijay Pande, and Theresa Windus http://molssi.org S2I2 HEP/CS Workshop at NCSA/UIUC 07 Dec, 2016 1 Outline • Space and Scope of Computational Molecular Sciences. • “State of the art and practice” • Intellectual drivers • Conceptualization Phase: Identifying the community and needs • Bio-molecular Simulations (BMS) Conceptualization • Quantum Mechanics/Chemistry (QM) Conceptualization • Execution Phase. • Structure and Governance Model • Resource Distribution • Work Plan 2 The Molecular Sciences Software Institute (MolSSI) • New project (as of August 1st, 2016) funded by the National Science Foundation. • Collaborative effort by Virginia Tech, Rice U., Stony Brook U., U.C. Berkeley, Stanford U., Rutgers U., U. Southern California, and Iowa State U. • Total budget of $19.42M for five years, potentially renewable to ten years. • Joint support from numerous NSF divisions: Advanced Cyberinfrastructure (ACI), Chemistry (CHE), Division of Materials Research (DMR), Office of Multidisciplinary Activities (OMA) • Designed to serve and enhance the software development efforts of the broad field of computational molecular science. 3 Computational Molecular Sciences (CMS) • The history of CMS – the sub-fields of quantum chemistry, computational materials science, and biomolecular simulation – reaches back decades to the genesis of computational science. • CMS is now a “full partner with experiment”. • For an impressive array of chemical, biochemical, and materials challenges, our community has developed simulations and models that directly impact: • Development of new chiral drugs; • Elucidation of the functionalities of biological macromolecules; • Development of more advanced materials for solar-energy storage, technology for CO2 sequestration, etc.
    [Show full text]
  • A Command-Line Interface for Analysis of Molecular Dynamics Simulations
    taurenmd: A command-line interface for analysis of Molecular Dynamics simulations. João M.C. Teixeira1, 2 1 Previous, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain 2 DOI: 10.21105/joss.02175 Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Software Canada • Review Summary • Repository • Archive Molecular dynamics (MD) simulations of biological molecules have evolved drastically since its application was first demonstrated four decades ago (McCammon, Gelin, & Karplus, 1977) and, nowadays, simulation of systems comprising millions of atoms is possible due to the latest Editor: Richard Gowers advances in computation and data storage capacity – and the scientific community’s interest Reviewers: is growing (Hospital, Battistini, Soliva, Gelpí, & Orozco, 2019). Academic groups develop most of the MD methods and software for MD data handling and analysis. The MD analysis • @amritagos libraries developed solely for the latter scope nicely address the needs of manipulating raw data • @luthaf and calculating structural parameters, such as: MDAnalysis (Gowers et al., 2016; Michaud- Agrawal, Denning, Woolf, & Beckstein, 2011); (McGibbon et al., 2015); (Romo, Submitted: 03 March 2020 MDTraj LOOS Published: 02 June 2020 Leioatts, & Grossfield, 2014); and PyTraj (Hai Nguyen, 2016; Roe & Cheatham, 2013), each with its advantages and drawbacks inherent to their implementation strategies. This diversity License enriches the field with a panoply of strategies that the community can utilize. Authors of papers retain copyright and release the work The MD analysis software libraries widely distributed and adopted by the community share under a Creative Commons two main characteristics: 1) they are written in pure Python (Rossum, 1995), or provide a Attribution 4.0 International Python interface; and 2) they are libraries: highly versatile and powerful pieces of software that, License (CC BY 4.0).
    [Show full text]
  • EPSRC Service Level Agreement with STFC for Computational Science Support
    CoSeC Computational Science Centre for Research Communities EPSRC Service Level Agreement with STFC for Computational Science Support FY 2016/17 Report and Update on FY 2017/18 Work Plans This document contains the 2016/17 plans, 2016/17 summary reports, and 2017/18 plans for the programme in support of CCP and HEC communities delivered by STFC and funded by EPSRC through a Service Level Agreement. Notes in blue are in-year updates on progress to the tasks included in the 2016/17 plans. Text highlighted in yellow shows changes to the draft 2017/18 plans that we submitted in January 2017. Contents CCP5 – Computer Simulation of Condensed Phases .......................................................................... 4 CCP5 – 2016 / 17 Plans (1 April 2016 – 31 March 2017) ...................................................... 4 CCP5 – Summary Report (1 April 2016 – 31 March 2017) .................................................... 7 CCP5 –2017 / 18 Plans (1 April 2017 – 31 March 2018) ....................................................... 8 CCP9 – Electronic Structure of Solids .................................................................................................. 9 CCP9 – 2016 / 17 Plans (1 April 2016 – 31 March 2017) ...................................................... 9 CCP9 – Summary Report (1 April 2016 – 31 March 2017) .................................................. 11 CCP9 – 2017 / 18 Plans (1 April 2017 – 31 March 2018) .................................................... 12 CCP-mag – Computational Multiscale
    [Show full text]
  • Lawrence Berkeley National Laboratory Recent Work
    Lawrence Berkeley National Laboratory Recent Work Title From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape. Permalink https://escholarship.org/uc/item/4sm897jh Journal Chemical reviews, 121(8) ISSN 0009-2665 Authors Kowalski, Karol Bair, Raymond Bauman, Nicholas P et al. Publication Date 2021-04-01 DOI 10.1021/acs.chemrev.0c00998 Peer reviewed eScholarship.org Powered by the California Digital Library University of California From NWChem to NWChemEx: Evolving with the computational chemistry landscape Karol Kowalski,y Raymond Bair,z Nicholas P. Bauman,y Jeffery S. Boschen,{ Eric J. Bylaska,y Jeff Daily,y Wibe A. de Jong,x Thom Dunning, Jr,y Niranjan Govind,y Robert J. Harrison,k Murat Keçeli,z Kristopher Keipert,? Sriram Krishnamoorthy,y Suraj Kumar,y Erdal Mutlu,y Bruce Palmer,y Ajay Panyala,y Bo Peng,y Ryan M. Richard,{ T. P. Straatsma,# Peter Sushko,y Edward F. Valeev,@ Marat Valiev,y Hubertus J. J. van Dam,4 Jonathan M. Waldrop,{ David B. Williams-Young,x Chao Yang,x Marcin Zalewski,y and Theresa L. Windus*,r yPacific Northwest National Laboratory, Richland, WA 99352 zArgonne National Laboratory, Lemont, IL 60439 {Ames Laboratory, Ames, IA 50011 xLawrence Berkeley National Laboratory, Berkeley, 94720 kInstitute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794 ?NVIDIA Inc, previously Argonne National Laboratory, Lemont, IL 60439 #National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373 @Department of Chemistry, Virginia Tech, Blacksburg, VA 24061 4Brookhaven National Laboratory, Upton, NY 11973 rDepartment of Chemistry, Iowa State University and Ames Laboratory, Ames, IA 50011 E-mail: [email protected] 1 Abstract Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems.
    [Show full text]
  • PLUMED User's Guide
    PLUMED User’s Guide A portable plugin for free-energy calculations with molecular dynamics Version 1.3.0 – Nov 2011 Contents 1 Introduction 5 1.1 What is PLUMED?.........................5 1.2 Supported codes . .6 1.3 Features . .7 1.4 New in version 1.3 . .8 1.5 Restrictions . .9 1.6 The PLUMED package . .9 1.7 Online resources . 10 1.8 Credits . 11 1.9 Citing PLUMED ........................... 11 1.10 License . 11 2 Installation 13 2.1 Compiling PLUMED ......................... 13 2.1.1 Compiling the ACEMD plugin with PLUMED ...... 17 2.2 Including reconnaissance metadynamics . 18 2.3 Testing the installation . 19 2.4 Back to the original code . 21 2.5 The Python interface to PLUMED ................. 21 3 Running free-energy simulations 23 3.1 How to activate PLUMED ..................... 23 3.2 The input file . 25 3.3 A note on units . 27 3.4 Metadynamics . 27 3.4.1 Typical output . 27 3.4.2 Bias potential . 28 3.4.3 Well-tempered metadynamics . 29 1 3.4.4 Restarting a metadynamics run . 30 3.4.5 Using GRID ........................ 30 3.4.6 Multiple walkers . 35 3.4.7 Monitoring a collective variable without biasing it . 35 3.4.8 Defining an interval . 36 3.4.9 Inversion condition . 38 3.5 Running in parallel . 40 3.6 Replica exchange methods . 40 3.6.1 Parallel tempering metadynamics . 41 3.6.2 Bias exchange simulations . 42 3.7 Umbrella sampling . 45 3.8 Steered MD . 46 3.8.1 Steerplan . 46 3.9 Adiabatic Bias MD .
    [Show full text]
  • Assessing the Feasibility of Genome-Wide DNA Methylation Profiling
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.04.455090; this version posted August 5, 2021. 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. Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling Federico Rossi1,13*, Alessandro Crnjar2, Federico Comitani3,4, Rodrigo Feliciano5,6, Leonie Jahn1,7, George Malim2, Laura Southgate8, Emily Kay1,9, Rebecca Oakey1, Richard Buggs8.10, Andy Moir11, Logan Kistler12, Ana Rodriguez Mateos5, Carla Molteni2*, Reiner Schulz1*, 1 King's College London, Department of Medical and Molecular Genetics, London, UK 2 King's College London, Department of Physics, London, UK 3 University College London, Department of Chemistry, London, UK 4 The Hospital for Sick Children, Toronto, Ontario, Canada 5 King's College London, Department of Nutrition, London, UK 6 University of Dusseldorf, Division of Cardiology, Pulmonology and Vascular Medicine, Dusseldorf, Germany 7 Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Kemitorvet, Denmark 8 Royal Botanical Gardens, Department of Natural Capital and Plant Health, Richmond, UK 9 CRUK Beatson Institute, Glasgow, UK 10 Queen Mary University of London, School of Biological and Chemical Sciences, London, UK 11 Tree-Ring Services Limited, Mitcheldean, UK 12 National Museum Of Natural History, Smithsonian Institution, Department of Anthropology, Washington, DC, USA 13 IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy * Corresponding author Abstract Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions.
    [Show full text]
  • PLUMED Tutorial
    PLUMED Tutorial A portable plugin for free-energy calculations with molecular dynamics CECAM, Lausanne, Switzerland September 28, 2010 - October 1, 2010 This document and the relative computer exercises have been written by: Massimiliano Bonomi Davide Branduardi Giovanni Bussi Francesco Gervasio Alessandro Laio Fabio Pietrucci Tutorial website: http://sites.google.com/site/plumedtutorial2010/ PLUMED website: http://merlino.mi.infn.it/∼plumed PLUMED users Google group: [email protected] PLUMED reference article: M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Rai- teri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia and M. Par- rinello, PLUMED: a portable plugin for free-energy calculations with molecular dynamics, Comp. Phys. Comm. 2009 vol. 180 (10) pp. 1961- 1972. 1 Contents 1 Compilation 4 1.1 PLUMED compilation . 4 1.1.1 Compile PLUMED with GROMACS . 5 1.1.2 Compile PLUMED with QUANTUM ESPRESSO 9 1.1.3 Compile PLUMED with LAMMPS . 10 2 Basics: monitoring simulations 13 2.1 Syntax for collective variables . 14 2.2 Monitoring a CV . 16 2.3 Postprocessing with driver ............... 19 3 Basics: biasing simulations 23 3.1 Restrained/steered molecular dynamics . 23 3.1.1 An umbrella sampling calculation. Alanine dipep- tide. 23 3.1.2 A steered molecular dynamics example: targeted MD. 27 3.1.3 A programmed steered MD with steerplan. 30 3.1.4 Soft walls . 32 3.2 Committment analysis . 33 3.3 Metadynamics . 35 3.4 Restarting metadynamics . 38 3.5 Free-energy reconstruction . 38 3.6 Well-tempered metadynamics . 41 4 Parallel machines 43 4.1 Exploiting MD parallelization .
    [Show full text]
  • Open Source Molecular Modeling
    Accepted Manuscript Title: Open Source Molecular Modeling Author: Somayeh Pirhadi Jocelyn Sunseri David Ryan Koes PII: S1093-3263(16)30118-8 DOI: http://dx.doi.org/doi:10.1016/j.jmgm.2016.07.008 Reference: JMG 6730 To appear in: Journal of Molecular Graphics and Modelling Received date: 4-5-2016 Accepted date: 25-7-2016 Please cite this article as: Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes, Open Source Molecular Modeling, <![CDATA[Journal of Molecular Graphics and Modelling]]> (2016), http://dx.doi.org/10.1016/j.jmgm.2016.07.008 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Open Source Molecular Modeling Somayeh Pirhadia, Jocelyn Sunseria, David Ryan Koesa,∗ aDepartment of Computational and Systems Biology, University of Pittsburgh Abstract The success of molecular modeling and computational chemistry efforts are, by definition, de- pendent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. 1. Introduction What is Open Source? Free and open source software (FOSS) is software that is both considered \free software," as defined by the Free Software Foundation (http://fsf.org) and \open source," as defined by the Open Source Initiative (http://opensource.org).
    [Show full text]
  • Molecular Modeling in Drug Design
    molecules Molecular Modeling in Drug Design Edited by Rebecca C. Wade and Outi M. H. Salo-Ahen Printed Edition of the Special Issue Published in Molecules www.mdpi.com/journal/molecules Molecular Modeling in Drug Design Molecular Modeling in Drug Design Special Issue Editors Rebecca C. Wade Outi M. H. Salo-Ahen MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editors Rebecca C. Wade Outi M. H. Salo-Ahen HITS gGmbH/Heidelberg University Abo˚ Akademi University Germany Finland Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Molecules (ISSN 1420-3049) from 2018 to 2019 (available at: https://www.mdpi.com/journal/molecules/ special issues/MMDD) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-614-1 (Pbk) ISBN 978-3-03897-615-8 (PDF) c 2019 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Special Issue Editors ..................................... vii Preface to ”Molecular Modeling in Drug Design” ..........................
    [Show full text]
  • Metadynamics Metainference with PLUMED
    Metadynamics Metainference with PLUMED Max Bonomi University of Cambridge [email protected] Outline • Molecular Dynamics as a computational microscope: - sampling problems - accuracy of force fields • Enhanced sampling with biased MD: - metadynamics - recent developments • Combining simulations with experiments: Metainference • Addressing sampling and accuracy issues: M&M • The open source library PLUMED A computational microscope Molecular Dynamics (MD) evolves a system in time under the effect of a potential energy function How? By integrating Newton’s equations of motion m R¨ = V i i rRi The potential (or force field) is derived from - Higher accuracy calculations - Fitting experimental observables Limitations: • time scale accessible in standard MD • accuracy of classical force fields The time scale problem In MD, sampling efficiency is limited by the time scale accessible in typical simulations: ★ Activated events B ★ Slow diffusion A Dimensional reduction It is often possible to describe a physical/chemical process in terms of a small number of coarse descriptors of the system: S = S(R)=(S1(R),...,Sd(R)) Key quantity of thermodynamics is the free energy as a function of these variables: 1 1 F (S)= ln P (S) where β = −β kBT βU(R) canonical dβRF (Sδ()S S(R)) e− PF((SS))=e− − ensemble dR e βU(R) / R − R Examples Isomerization: dihedral angle Protein folding: gyration radius, number of contacts, ... Phase transitions: lattice vectors, bond order parameters, ... Rare events simplified likely unlikely likely How can we estimate a free energy
    [Show full text]
  • SCM: Required Citations
    Required citations ADF Program System Release 2014 Scientific Computing & Modelling NV Vrije Universiteit, Theoretical Chemistry De Boelelaan 1083; 1081 HV Amsterdam; The Netherlands WWW: www.scm.com E-mail: [email protected] Copyright © 1993-2014: SCM / Vrije Universiteit, Theoretical Chemistry, Amsterdam, The Netherlands All rights reserved 1 Table of Contents Required citations .......................................................................................................................................... 1 Table of Contents ........................................................................................................................................... 2 General References........................................................................................................................................ 4 ADF ......................................................................................................................................................... 4 BAND ...................................................................................................................................................... 4 GUI .......................................................................................................................................................... 5 COSMO-RS............................................................................................................................................. 5 DFTB......................................................................................................................................................
    [Show full text]
  • Optimization of Molecular Dynamics Simulations of C-MYC1-88—An Intrinsically Disordered System
    life Article Optimization of Molecular Dynamics Simulations of c-MYC1-88—An Intrinsically Disordered System Sandra S. Sullivan and Robert O.J. Weinzierl * Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-(0)-20-7594-5236 Received: 29 May 2020; Accepted: 7 July 2020; Published: 10 July 2020 Abstract: Many of the proteins involved in key cellular regulatory events contain extensive intrinsically disordered regions that are not readily amenable to conventional structure/function dissection. The oncoprotein c-MYC plays a key role in controlling cell proliferation and apoptosis and more than 70% of the primary sequence is disordered. Computational approaches that shed light on the range of secondary and tertiary structural conformations therefore provide the only realistic chance to study such proteins. Here, we describe the results of several tests of force fields and water models employed in molecular dynamics simulations for the N-terminal 88 amino acids of c-MYC. Comparisons of the simulation data with experimental secondary structure assignments obtained by NMR establish a particular implicit solvation approach as highly congruent. The results provide insights into the structural dynamics of c-MYC1-88, which will be useful for guiding future experimental approaches. The protocols for trajectory analysis described here will be applicable for the analysis of a variety of computational simulations of intrinsically disordered proteins. Keywords: oncoproteins; c-MYC; molecular dynamics simulations 1. Introduction Intrinsically disordered proteins (IDPs) exhibit vastly different structural dynamics as compared to folded proteins. Instead of folding predictably, according to their amino acid sequence, IDPs exist as a rapidly changing ensemble of conformations.
    [Show full text]