How to Modify LAMMPS: from the Prospective of a Particle Method Researcher
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Olaseni Sode
Olaseni Sode Work Address: 5735 S. Ellis Ave. [email protected] Searle 231 +1 (314) 856-2373 The University of Chicago Chicago, IL 60615 Home Address: 1119 E Hyde Park Blvd [email protected] Apt. 3E +1 (314) 856-2373 Chicago, IL 60615 http://www.olaseniosode.com Education University of Illinois at Urbana-Champaign Urbana, IL Ph.D. in Chemistry September 2012 – Supervisor: Professor So Hirata – Thesis title: A Theoretical Study of Molecular Crystals – Transferred from the University of Florida in 2010 with Prof. Hirata Morehouse College Atlanta, GA B.S. & B.A. in Chemistry and French December 2006 – Studied at the Université de Nantes, Nantes, France (2004-2005) Research Experience The University of Chicago Chicago, IL Postdoctoral Research – research advisor: Dr. Gregory A. Voth 2012–present – Studied proposed proton transport minimum free-energy pathways in [FeFe]-hydrogenase via molecular dynamics simulations and the multistate empirical valence bond technique. – Collaborated to develop the multiscale string method to accelerate refinement of chemical reaction pathways of adenosine triphosphate (ATP) hydrolysis in globular and filamentous actin proteins. University of California, San Diego La Jolla, CA Visiting Scholar – research advisor: Dr. Francesco Paesani 2014, 2015 – Developed and implemented a reactive molecular dynamics scheme for condensed phase systems of the hydrated hydronium ions. University of Illinois at Urbana-Champaign Urbana, IL Doctoral Research – research advisor: Dr. So Hirata 2010-2012 – Characterized the vibrational structure of extended systems including infrared and Raman-active vibrations, as well as phonon dispersions and densities of states in the first Brillouin zone. – Developed zero-point vibrational energy analysis scheme for molecular clusters using a fragmented, local basis scheme. -
Pysimm: a Python Package for Simulation of Molecular Systems
SoftwareX 6 (2016) 7–12 Contents lists available at ScienceDirect SoftwareX journal homepage: www.elsevier.com/locate/softx pysimm: A python package for simulation of molecular systems Michael E. Fortunato a, Coray M. Colina a,b,∗ a Department of Chemistry, University of Florida, Gainesville, FL 32611, United States b Department of Materials Science and Engineering and Nuclear Engineering, University of Florida, Gainesville, FL 32611, United States article info a b s t r a c t Article history: In this work, we present pysimm, a python package designed to facilitate structure generation, simulation, Received 15 August 2016 and modification of molecular systems. pysimm provides a collection of simulation tools and smooth Received in revised form integration with highly optimized third party software. Abstraction layers enable a standardized 1 December 2016 methodology to assign various force field models to molecular systems and perform simple simulations. Accepted 5 December 2016 These features have allowed pysimm to aid the rapid development of new applications specifically in the area of amorphous polymer simulations. Keywords: ' 2016 The Authors. Published by Elsevier B.V. Amorphous polymers Molecular simulation This is an open access article under the CC BY license Python (http://creativecommons.org/licenses/by/4.0/). Code metadata Current code version v0.1 Permanent link to code/repository used for this code version https://github.com/ElsevierSoftwareX/SOFTX-D-16-00070 Legal Code License MIT Code versioning system used git Software code languages, tools, and services used python2.7 Compilation requirements, operating environments & Linux dependencies If available Link to developer documentation/manual http://pysimm.org/documentation/ Support email for questions [email protected] 1. -
Mercury 2.4 User Guide and Tutorials 2011 CSDS Release
Mercury 2.4 User Guide and Tutorials 2011 CSDS Release Copyright © 2010 The Cambridge Crystallographic Data Centre Registered Charity No 800579 Conditions of Use The Cambridge Structural Database System (CSD System) comprising all or some of the following: ConQuest, Quest, PreQuest, Mercury, (Mercury CSD and Materials module of Mercury), VISTA, Mogul, IsoStar, SuperStar, web accessible CSD tools and services, WebCSD, CSD Java sketcher, CSD data file, CSD-UNITY, CSD-MDL, CSD-SDfile, CSD data updates, sub files derived from the foregoing data files, documentation and command procedures (each individually a Component) is a database and copyright work belonging to the Cambridge Crystallographic Data Centre (CCDC) and its licensors and all rights are protected. Use of the CSD System is permitted solely in accordance with a valid Licence of Access Agreement and all Components included are proprietary. When a Component is supplied independently of the CSD System its use is subject to the conditions of the separate licence. All persons accessing the CSD System or its Components should make themselves aware of the conditions contained in the Licence of Access Agreement or the relevant licence. In particular: • The CSD System and its Components are licensed subject to a time limit for use by a specified organisation at a specified location. • The CSD System and its Components are to be treated as confidential and may NOT be disclosed or re- distributed in any form, in whole or in part, to any third party. • Software or data derived from or developed using the CSD System may not be distributed without prior written approval of the CCDC. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
Instructions on Making Pdf Files Containing 3D
Detailed Instructions for Creating an Embedded Virtual 3-D Image of a Molecule Creating the documents with embedded virtual three-dimensional images may be done fairly easily by repeating the following procedures. Once you have embedded your first image, the use of that image is limited only by your imagination. The following instructions are written in extreme detail with annotated screen shots of the four programs you will use throughout for clarification. Once you are familiar with the procedure embedding a structure of interest should take less than 20 min., limited only by the speed with which you can click a mouse. In practice most of our embedded 3-D images have been created by our undergraduate student collaborators. Step 1. Creating a 2-D image in ChemSketch Using ACD ChemSketch 11.0 Freeware (http://www.acdlabs.com/download/chemsk_download.html ) a two dimensional structure may be drawn as per your specific need (see Figure 1). Once the molecule is drawn, optimized it by clicking the 3-D optimization button then save as an MDL molfile (*.mol). Figure 1: A screen shot of acetone drawn with ChemSketch after 3-D optimization. Step 2. Converting the *.mol file to a *.pdb file using Open Babel The file can now be converted from a .mol file to a .pdb file, Protein Data Bank format, to be properly accessed with the Adobe Acrobat 3D Toolkit 8.1.0. The file conversion is done using Open Babel Graphical User Interface v2.2.0 (openbabel.sourceforge.net) under default settings. Step by step instructions: A. -
A Study on Cheminformatics and Its Applications on Modern Drug Discovery
Available online at www.sciencedirect.com Procedia Engineering 38 ( 2012 ) 1264 – 1275 Internatio na l Conference on Modeling Optimisatio n and Computing (ICMOC 2012) A Study on Cheminformatics and its Applications on Modern Drug Discovery B.Firdaus Begama and Dr. J.Satheesh Kumarb aResearch Scholar, Bharathiar University, Coimbatore, India, [email protected] bAssistant Professor, Bharathiar University, Coimbatore, India, [email protected] Abstract Discovering drugs to a disease is still a challenging task for medical researchers due to the complex structures of biomolecules which are responsible for disease such as AIDS, Cancer, Autism, Alzimear etc. Design and development of new efficient anti-drugs for the disease without any side effects are becoming mandatory in the recent history of human life cycle due to changes in various factors which includes food habit, environmental and migration in human life style. Cheminformaticds deals with discovering drugs based in modern drug discovery techniques which in turn rectifies complex issues in traditional drug discovery system. Cheminformatics tools, helps medical chemist for better understanding of complex structures of chemical compounds. Cheminformatics is a new emerging interdisciplinary field which primarily aims to discover Novel Chemical Entities [NCE] which ultimately results in design of new molecule [chemical data]. It also plays an important role for collecting, storing and analysing the chemical data. This paper focuses on cheminformatics and its applications on drug discovery and modern drug discovery techniques which helps chemist and medical researchers for finding solution to the complex disease. © 2012 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of Noorul Islam Centre for Higher Education. -
Baryon Resonances and Pentaquarks on the Lattice ✩
Nuclear Physics A 754 (2005) 248c–260c Baryon resonances and pentaquarks on the lattice ✩ F.X. Lee a,b,∗, C. Bennhold a a Center for Nuclear Studies, George Washington University, Washington, DC 20052, USA b Jefferson Lab, 12000 Jefferson Avenue, Newport News, VA 23606, USA Received 17 December 2004; accepted 22 December 2004 Available online 21 January 2005 Abstract We review recent progress in computing excited baryons and pentaquarks in lattice QCD. 2004 Elsevier B.V. All rights reserved. 1. QCD primer Quantum Chromodynamics (QCD) is widely accepted as the fundamental theory of the strong interaction. The QCD Lagrangian density can be written down simply in one line (in Euclidean space) 1 L = Tr F F µν +¯q γ µD + m q, (1) QCD 2 µν µ q where Fµν = ∂Aµ − ∂Aν + g[Aµ,Aν] is the gluon field strength tensor and Dµ = ∂µ + gAµ is the covariant derivative which provides the interaction between the gluon and quark terms. The action of QCD is the integral of the Lagrangian density over space– 4 time: SQCD = LQCD d x. QCD is a highly non-linear relativistic quantum field theory. It is well known that the theory has chiral symmetry in the mq = 0 limit and the symmetry is spontaneously broken in the vacuum. At high energies, it exhibits asymptotic freedom, ✩ Based on plenary talk by F.X. Lee at HYP2003, JLab. * Corresponding author. E-mail address: [email protected] (F.X. Lee). 0375-9474/$ – see front matter 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.nuclphysa.2004.12.072 F.X. -
Getting Started in Jmol
Getting Started in Jmol Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingResources/jmol/jmolTraining/started.html Introduction Physical models of proteins are powerful tools that can be used synergistically with computer visualizations to explore protein structure and function. Although it is interesting to explore models and visualizations created by others, it is much more engaging to create your own! At the MSOE Center for BioMolecular Modeling we use the molecular visualization program Jmol to explore protein and molecular structures in fully interactive 3-dimensional displays. Jmol a free, open source molecular visualization program used by students, educators and researchers internationally. The Jmol Training Guide from the MSOE Center for BioMolecular Modeling will provide the tools needed to create molecular renderings, physical models using 3-D printing technologies, as well as Jmol animations for online tutorials or electronic posters. Examples of Proteins in Jmol Jmol allows users to rotate proteins and molecular structures in a fully interactive 3-dimensional display. Some sample proteins designed with Jmol are shown to the right. Hemoglobin Proteins Insulin Proteins Green Fluorescent safely carry oxygen in the help regulate sugar in Proteins create blood. the bloodstream. bioluminescence in animals like jellyfish. Downloading Jmol Jmol Can be Used in Two Ways: 1. As an independent program on a desktop - Jmol can be downloaded to run on your desktop like any other program. It uses a Java platform and therefore functions equally well in a PC or Mac environment. 2. As a web application - Jmol has a web-based version (oftern refered to as "JSmol") that runs on a JavaScript platform and therefore functions equally well on all HTML5 compatible browsers such as Firefox, Internet Explorer, Safari and Chrome. -
Ghost-Free Scalar-Fermion Interactions
PHYSICAL REVIEW D 98, 044043 (2018) Ghost-free scalar-fermion interactions † ‡ Rampei Kimura,1,2,* Yuki Sakakihara,3, and Masahide Yamaguchi2, 1Waseda Institute for Advanced Study, Waseda University, 1-6-1 Nishi-Waseda, Shinjuku, Tokyo 169-8050, Japan 2Department of Physics, Tokyo Institute of Technology, Tokyo 152-8551, Japan 3Department of Physics, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan (Received 15 June 2018; published 28 August 2018) We discuss a covariant extension of interactions between scalar fields and fermions in a flat space-time. We show, in a covariant theory, how to evade fermionic ghosts appearing because of the extra degrees of freedom behind a fermionic nature even in the Lagrangian with first derivatives. We will give a concrete example of a quadratic theory with up to the first derivative of multiple scalar fields and a Weyl fermion. We examine not only the maximally degenerate condition, which makes the number of degrees of freedom correct, but also a supplementary condition guaranteeing that the time evolution takes place properly. We also show that proposed derivative interaction terms between scalar fields and a Weyl fermion cannot be removed by field redefinitions. DOI: 10.1103/PhysRevD.98.044043 I. INTRODUCTION scalar-tensor theories [4–6,13–20], vector-tensor theories [21–29], and form fields [30–32]. Construction of general theory without ghost degrees of On the other hand, generic theory with fermionic d.o.f. freedom (d.o.f.) has been discussed for a long time. has not yet been investigated well. If we could find such According to Ostrogradsky’s theorem, a ghost always appears in a higher (time) derivative theory as long as it fermionic theories which have not been explored, some is nondegenerate [1] (see also Ref. -
The Ghost Particle 1 Ask Students If They Can Think of Some Things They Cannot Directly See but They Know Exist
Original broadcast: February 21, 2006 BEFORE WATCHING The Ghost Particle 1 Ask students if they can think of some things they cannot directly see but they know exist. Have them provide examples and reasoning for PROGRAM OVERVIEW how they know these things exist. NOVA explores the 70–year struggle so (Some examples and evidence of their existence include: [bacteria and virus- far to understand the most elusive of all es—illnesses], [energy—heat from the elementary particles, the neutrino. sun], [magnetism—effect on a com- pass], and [gravity—objects falling The program: towards Earth].) How do scientists • relates how the neutrino first came to be theorized by physicist observe and measure things that cannot be seen with the naked eye? Wolfgang Pauli in 1930. (They use instruments such as • notes the challenge of studying a particle with no electric charge. microscopes and telescopes, and • describes the first experiment that confirmed the existence of the they look at how unseen things neutrino in 1956. affect other objects.) • recounts how scientists came to believe that neutrinos—which are 2 Review the structure of an atom, produced during radioactive decay—would also be involved in including protons, neutrons, and nuclear fusion, a process suspected as the fuel source for the sun. electrons. Ask students what they know about subatomic particles, • tells how theoretician John Bahcall and chemist Ray Davis began i.e., any of the various units of mat- studying neutrinos to better understand how stars shine—Bahcall ter below the size of an atom. To created the first mathematical model predicting the sun’s solar help students better understand the neutrino production and Davis designed an experiment to measure size of some subatomic particles, solar neutrinos. -
Arxiv:1908.02416V2 [Hep-Th] 21 Aug 2019
ACFI-T19-08 Unitarity, stability and loops of unstable ghosts John F. Donoghue∗ Department of Physics, University of Massachusetts Amherst, MA 01003, USA Gabriel Menezesy Department of Physics, University of Massachusetts Amherst, MA 01003, USA and Departamento de F´ısica, Universidade Federal Rural do Rio de Janeiro, 23897-000, Serop´edica, RJ, Brazil We present a new understanding of the unstable ghost-like resonance which appears in theories such as quadratic gravity and Lee-Wick type theories. Quantum corrections make this resonance unstable, such that it does not appear in the asymptotic spectrum. We prove that these theories are unitary to all orders. Unitarity is satisfied by the inclusion of only cuts from stable states in the unitarity sum. This removes the need to consider this as a ghost state in the unitarity sum. However, we often use a narrow-width approximation where we do include cuts through unstable states, and ignore cuts through the stable decay products. If we do this with the unstable ghost resonance at one loop, we get the correct answer only by using a contour which was originally defined by Lee and Wick. The quantum effects also provide damping in both the Feynman and the retarded propagators, leading to stability under perturbations. 1. INTRODUCTION Theories such as quadratic gravity [1{19] and Lee-Wick theories [20{28] have propagators which contain both quadratic and quartic momentum dependence. In addition to the pole at q2 = 0, this combination will produce a high mass pole, via 1 1 1 = − : (1) 2 q4 q2 q2 − µ2 q − µ2 The negative sign for the second term implies that this pole is ghost-like, i.e. -
Reactive Molecular Dynamics Study of the Thermal Decomposition of Phenolic Resins
Article Reactive Molecular Dynamics Study of the Thermal Decomposition of Phenolic Resins Marcus Purse 1, Grace Edmund 1, Stephen Hall 1, Brendan Howlin 1,* , Ian Hamerton 2 and Stephen Till 3 1 Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guilford, Surrey GU2 7XH, UK; [email protected] (M.P.); [email protected] (G.E.); [email protected] (S.H.) 2 Bristol Composites Institute (ACCIS), Department of Aerospace Engineering, School of Civil, Aerospace, and Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK; [email protected] 3 Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-1483-686-248 Received: 6 March 2019; Accepted: 23 March 2019; Published: 28 March 2019 Abstract: The thermal decomposition of polyphenolic resins was studied by reactive molecular dynamics (RMD) simulation at elevated temperatures. Atomistic models of the polyphenolic resins to be used in the RMD were constructed using an automatic method which calls routines from the software package Materials Studio. In order to validate the models, simulated densities and heat capacities were compared with experimental values. The most suitable combination of force field and thermostat for this system was the Forcite force field with the Nosé–Hoover thermostat, which gave values of heat capacity closest to those of the experimental values. Simulated densities approached a final density of 1.05–1.08 g/cm3 which compared favorably with the experimental values of 1.16–1.21 g/cm3 for phenol-formaldehyde resins.