Molecular Simulation Disciplina de Simulao Molecular PPG Fsica - - PowerPoint PPT Presentation

Mar 25, 2024 •233 likes •346 views

Molecular Simulation Disciplina de Simulao Molecular PPG Fsica - UFPel Prof. Jos Rafael Bordin What is? Important tool by many researchers in a variety of science fields to understand molecular basic theories. Experiment We

Molecular Simulation Disciplina de Simulação Molecular PPG Física - UFPel Prof. José Rafael Bordin
What is? → Important tool by many researchers in a variety of science fields to understand molecular basic theories. Experiment → We carry out computer simulations in the hope of understanding the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. → Molecular simulations have served to obtain values of various physical quantities (often inaccessible experimentally) to verify molecular-based theories and to gain insight Simulation Theory into the molecular principles underlying various processes.
→ Except for simple cases , there are no analytical What is? solutions for most of the problems in Stat. Mech. → In most cases, experiments are: Experiment Difficult or impossible to perform; ● Too dangerous to; ● Expensive and time consuming; ● Blind and too many parameters to control ● → Simulation is a powerful tool In some cases can replace experiments; ● Can provoke experiments; ● Explain and understand experiments; ● Simulation Theory Complete theories. ●
Types of MS → Molecular simulation methods can basically be separated into quantum mechanics (QM) methods, which treat electrons as the fundamental interactive particles of the system, and classical mechanics (CM) methods, which treat individual atoms or groups of atoms as the fundamental interactive particles of the system
Types of MS → Molecular simulation methods can basically be separated into quantum mechanics (QM) methods, which treat electrons as the Statistical Mechanics requires statistics fundamental interactive particles of the system, and classical mechanics (CM) methods, which treat individual atoms or groups of atoms as the fundamental interactive particles of the system
Our objects of study MONTE CARLO METHODS STOCHASTIC = RANDOM MOLECULAR DYNAMICS METHODS DETERMINISTIC/TIME EVOLUTION
Our objects of study MONTE CARLO METHODS MOLECULAR DYNAMICS METHODS
Pedagogical Methodology → On-line meeting every 14 days: https://webconf.ufpel.edu.br/b/jos-6qt-jpe → Material available in the e-aula UFPEL/Cobalto and in the website https://wp.ufpel.edu.br/bordin/molecular-simulation/ → Lists to be submited using the Cobalto System – excepted special students → Mandatory: minimal knowledge of some computer language (Fortran, C, Python, etc)
Bibliography 1) Computer Simulation of Liquids, M.P. Allen and D.J. Tildesley https://datagrid.hu/boda/Boda-sajat/Rush/Books/Allen-Tildesley.pdf 2) Understanding Molecular Simulation: From Algorithms to Applications. Daan Frenkel and Berend Smit https://datagrid.hu/boda/Boda-sajat/Rush/Books/Frenkel.pdf 3) Computational Soft Matter: From Synthetic Polymers to Proteins - Lecture Notes. Edited by Norbert Attig, Kurt Binder, Helmut Grubmüller, Kurt Kremer http://juser.fz-juelich.de/record/35298/files/nic-series-23.pdf

Recommend

4. Molecular dynamics Understanding Molecular Simulation Molecular Simulations Molecular

4. Molecular dynamics Understanding Molecular Simulation Molecular Simulations Molecular dynamics : solve equations of motion r 1 r 2 r n Monte Carlo : importance sampling r 1 r 2 r n Understanding Molecular Simulation Molecular

618 views • 38 slides

Molecular Simulation Introduction Understanding Molecular Simulation Introduction Why to use

Molecular Simulation Introduction Understanding Molecular Simulation Introduction Why to use a simulation Some examples of questions we can address Understanding Molecular Simulation Molecular Simulations MD Molecular dynamics :

707 views • 32 slides

2. Thermodynamics Introduction Understanding Molecular Simulation Molecular Simulations

2. Thermodynamics Introduction Understanding Molecular Simulation Molecular Simulations Molecular dynamics : solve equations of motion r 1 r 2 r n Monte Carlo : importance sampling r 1 r 2 r n Understanding Molecular Simulation How do

1.02k views • 87 slides

2. Thermodynamics Introduction Understanding Molecular Simulation Molecular Simulations

1.19k views • 88 slides

Molecular Dynamics Simulation A Short Introduction Michel Cuendet 1 Molecular Dynamics

Molecular Dynamics Simulation A Short Introduction Michel Cuendet 1 Molecular Dynamics Simulation - Michel Cuendet - EMBL 2008 Plan Introduction The classical force field Setting up a simulation Connection to statistical

1.28k views • 67 slides

3. Monte Carlo Simulations Understanding Molecular Simulation Molecular Simulations Molecular

3. Monte Carlo Simulations Understanding Molecular Simulation Molecular Simulations Molecular dynamics : solve equations of motion r 1 r 2 r n Monte Carlo : importance sampling r 1 r 2 r n Understanding Molecular Simulation Monte Carlo

1.02k views • 50 slides

BCNucleation-Aggregation Workshop Grand canonical molecular dynamics simulation Grand canonical

D EPARTMENT OF M ECHANICAL E NGINEERING BCNucleation-Aggregation Workshop Grand canonical molecular dynamics simulation Grand canonical molecular dynamics simulation of homogeneous nucleation Universitat de Barcelona, Departament de Fsica

513 views • 18 slides

Molecular Simulation Methods with Gromacs CSC 2016 Alex de Vries with special thanks to Tsjerk

Molecular Simulation Methods with Gromacs CSC 2016 Alex de Vries with special thanks to Tsjerk Wassenaar Hands-on tutorial Multiscaling Simulation and Back-mapping 1 2 Aim Demonstrate how to combine different Classical Mechanical level

769 views • 28 slides

Introduction Introduction Why to use a simulation Some examples of questions we can

Introduction Introduction Why to use a simulation Some examples of questions we can address Molecular Simulations MD Molecular dynamics : solve equations of motion r 1 Monte Carlo : r 2 importance sampling r n Calculate

1.13k views • 81 slides

Activities in electrolyte solutions by molecular simulation of the osmotic pressure M. T.

Activities in electrolyte solutions by molecular simulation of the osmotic pressure M. T. Horsch, M. Kohns, S. Reiser, M. Schappals, and H. Hasse Laboratory of Engineering Thermodynamics University of Kaiserslautern, Germany 2016 AIChE Annual

351 views • 14 slides

Molecular Dynamics simulation of glass structures J.-M. Delaye 1 with the contributions of T.

Molecular Dynamics simulation of glass structures J.-M. Delaye 1 with the contributions of T. Charpentier 2 , L.-H. Kieu 1 , F. Pacaud 1 , M. Salanne 3 1 Service dEtudes de Vitrification et procds hautes Tempratures (SEVT), CEA Marcoule,

4.64k views • 31 slides

High-throughput molecular dynamics simulation and Markov modeling Frank No (FU Berlin)

High-throughput molecular dynamics simulation and Markov modeling Frank No (FU Berlin) frank.noe@fu-berlin.de Molecular dynamics Molecular dynamics are stochastic Single trajectories are usually not representative

398 views • 29 slides

History, Development and Basics of Molecular Dynamics Simulation Technique A way to do

History, Development and Basics of Molecular Dynamics Simulation Technique A way to do experiments in computers (Odourless) Creating virtual matter and then studying them in computers S. Yashonath Solid State and Structural Chemistry Unit

931 views • 51 slides

Molecular simulation of aqueous and non-aqueous electrolyte solutions M. T. Horsch, 1 S. Reiser,

Laboratory of Engineering Thermodynamics Prof. Dr.-Ing. H. Hasse AIChE Annual Meeting, San Francisco, 4 th November 13 Molecular simulation of aqueous and non-aqueous electrolyte solutions M. T. Horsch, 1 S. Reiser, 1 S. Deublein, 1 J. Vrabec,

432 views • 16 slides

Molecular dynamics simulation of entanglement growth in generalized hydrodynamics M arton

Molecular dynamics simulation of entanglement growth in generalized hydrodynamics M arton Mesty an SISSA Based on 1905.03206 Joint work with Vincenzo Alba M arton Mesty an (SISSA) Molecular dynamics of GHD & entanglement

485 views • 20 slides

Molecular dynamics simulation of the melting of Na nanoclusters Yoon Tiem Leong Talk given at

Molecular dynamics simulation of the melting of Na nanoclusters Yoon Tiem Leong Talk given at Theoretical and Computational Group seminar, School of Physics, Universiti Sains Malaysia Friday, 29 March 2013 ABSTRACT The paper by Aguado et al.,

613 views • 34 slides

MOLECULAR DYNAMIC SIMULATION OF THE STRESS IN METALLIC ALLOYS BY: SARAH BARTLEY RESEARCH

MOLECULAR DYNAMIC SIMULATION OF THE STRESS IN METALLIC ALLOYS BY: SARAH BARTLEY RESEARCH MENTOR: DR. JUANA MORENO REU TEAM MEMBERS: DR. KA MING TAM CIMM REU 2016 LOUISIANA STATE UNIVERSITY , DEPARTMENT OF PHYSICS & ASTRONOMY NICHOLSON

107 views • 9 slides

Homogeneous nucleation of carbon dioxide by molecular simulation Martin Horsch, Kai Langenbach,

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Homogeneous nucleation of carbon dioxide by molecular simulation Martin Horsch, Kai Langenbach, Katrin Stbener, Stephan Werth, Zengyong Lin, Thorsten Windmann, Jadran

305 views • 16 slides

Multicriteria optimization of force field models for molecular simulation of interfacial and bulk

Multicriteria optimization of force field models for molecular simulation of interfacial and bulk properties Martin Thomas Horsch, 1, 2 Stephan Werth, 1 Katrin Stbener, 1, 3 Peter Klein, 3 Karl-Heinz Kfer, 3 and Hans Hasse 1 1 Laboratory of

440 views • 17 slides

Using Molecular Simulation to Trace the Role of Conformational Dynamics in Enzyme Evolution

Virtual CECAM-ITCP School 2020 Using Molecular Simulation to Trace the Role of Conformational Dynamics in Enzyme Evolution Caroline Lynn Kamerlin Department of Chemistry - BMC Uppsala University The Role of Conformational Diversity Tawfiks

775 views • 29 slides

Molecular simulation of curved vapour-liquid interfaces M. T. Horsch, 1 S. Werth, 1 S. V.

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Molecular simulation of curved vapour-liquid interfaces M. T. Horsch, 1 S. Werth, 1 S. V. Lishchuk, 2 J. Vrabec, 3 and H. Hasse 1 TU Kaiserslautern, 1 U. of Leicester, 2 and

726 views • 13 slides

USING NSIGHT TOOLS TO OPTIMIZE THE NAMD MOLECULAR DYNAMICS SIMULATION PROGRAM Robert (Bob) Knight

USING NSIGHT TOOLS TO OPTIMIZE THE NAMD MOLECULAR DYNAMICS SIMULATION PROGRAM Robert (Bob) Knight Software Engineer, NVIDIA David Hardy Senior Research Programmer, U. Illinois at Urbana Champaign March 19, 2019 Its Time to Rebalance

648 views • 54 slides

Macro-Scale Molecular Communications D. T. McGuiness, A. Marshall, S. Taylor, S. Giannoukos

Macro-Scale Molecular Communications D. T. McGuiness, A. Marshall, S. Taylor, S. Giannoukos Dynamic Modelling and Simulation for Molecular Communication Networks Introduction v Molecular Communication (MC) is the act of transmitting information

395 views • 22 slides

Introduction Monday, January 5, 15 1 Introduction Why to use a simulation Some examples

Introduction Monday, January 5, 15 1 Introduction Why to use a simulation Some examples of questions we can address Monday, January 5, 15 2 Molecular Simulations MD Molecular dynamics : solve equations of motion r 1

534 views • 31 slides