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Numerical Simulation Of Microflows And Nanoflows

Narayan R. Aluru and George Em Karniadakis

in Micro/Nano Technology Systems for Biomedical Applications: Microfluidics, Optics, and Surface Chemistry

Published in print:
2010
Published Online:
September 2010
ISBN:
9780199219698
eISBN:
9780191594229
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199219698.003.0003
Subject:
Mathematics, Mathematical Biology

In this chapter we review recent advances in numerical simulation of micro and nanoflows. For coarse-grained simulation of microfuidics, we present an overview of Lattice Boltzmann, Brownian ... More


Coarse-Grained Molecular Dynamics: Concurrent Multiscale Simulation at Finite Temperature Protect 1

Robert E. Rudd

in Multiscale Methods: Bridging the Scales in Science and Engineering

Published in print:
2009
Published Online:
February 2010
ISBN:
9780199233854
eISBN:
9780191715532
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199233854.003.0005
Subject:
Mathematics, Applied Mathematics

Coarse-grained molecular dynamics (CGMD) is a computer modeling technique that couples conventional molecular dynamics (MD) in some spatial regions of the simulation to a more coarse-grained ... More


The liquid state

ANGELO GAVEZZOTTI

in Molecular Aggregation: Structure analysis and molecular simulation of crystals and liquids

Published in print:
2006
Published Online:
January 2010
ISBN:
9780198570806
eISBN:
9780191718779
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198570806.003.0009
Subject:
Physics, Atomic, Laser, and Optical Physics

In the gaseous state, molecules are to a good approximation isolated entities traveling in space at high speed with sparse and near elastic collisions. At the other extreme, a perfect crystal has a ... More


MULTISCALE COMPUTER SIMULATION METHODS

Nasr M. Ghoniem and Daniel D. Walgraef

in Instabilities and Self-Organization in Materials: Volume I: Fundamentals of Nanoscience, Volume II: Applications in Materials Design and Nanotechnology

Published in print:
2008
Published Online:
May 2008
ISBN:
9780199298686
eISBN:
9780191720222
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199298686.003.0010
Subject:
Physics, Condensed Matter Physics / Materials

Computational modelling of materials behaviour is becoming a reliable tool of scientific investigation, complementary to traditional theory and experimentation. The Multiscale Materials Modelling ... More


OUTLOOK

Francesco Calogero

in Isochronous Systems

Published in print:
2008
Published Online:
May 2008
ISBN:
9780199535286
eISBN:
9780191715853
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199535286.003.0008
Subject:
Physics, Theoretical, Computational, and Statistical Physics

In Chapter 8 five directions of future research are tersely mentioned in order of increasing importance. The investigation of Diophantine relations, such as those reported in Appendix C. The ... More


Kinetic Theory of Granular Gases

Nikolai V. Brilliantov and Thorsten Pöschel

Published in print:
2004
Published Online:
January 2010
ISBN:
9780198530381
eISBN:
9780191713057
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198530381.001.0001
Subject:
Physics, Condensed Matter Physics / Materials

Kinetic Theory of Granular Gases provides an introduction to the rapidly developing theory of dissipative gas dynamics — a theory which has mainly evolved over the last decade. The book ... More


Non-Equilibrium Computer Simulation Algorithms

Phil Attard

in Non-equilibrium Thermodynamics and Statistical Mechanics: Foundations and Applications

Published in print:
2012
Published Online:
January 2013
ISBN:
9780199662760
eISBN:
9780191745287
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199662760.003.0011
Subject:
Physics, Condensed Matter Physics / Materials

Three non-equilibrium computer simulation algorithms are presented in detail: stochastic molecular dynamics, non-equilibrium Monte Carlo, and Brownian dynamics. Stochastic molecular dynamics is based ... More


Surface waves and patterns in periodically vibrated granular layers

Igor S. Aranson and Lev S. Tsimring

in Granular Patterns

Published in print:
2008
Published Online:
January 2009
ISBN:
9780199534418
eISBN:
9780191714665
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199534418.003.0005
Subject:
Physics, Condensed Matter Physics / Materials

This chapter examines pattern-forming phenomena in thin layers of granular materials subjected to low-frequency periodic vertical vibration above the acceleration of gravity. Compared to driven ... More


Main theoretical concepts and tools

Igor S. Aranson and Lev S. Tsimring

in Granular Patterns

Published in print:
2008
Published Online:
January 2009
ISBN:
9780199534418
eISBN:
9780191714665
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199534418.003.0003
Subject:
Physics, Condensed Matter Physics / Materials

This chapter introduces the main theoretical approaches and models employed in the physics of granular media, such as the kinetic theory of diluted granular gases, various methods of molecular ... More


Principles of systematic upscaling

Achi Brandt

in Multiscale Methods: Bridging the Scales in Science and Engineering

Published in print:
2009
Published Online:
February 2010
ISBN:
9780199233854
eISBN:
9780191715532
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199233854.003.0007
Subject:
Mathematics, Applied Mathematics

Building on the complementary advantages of Renormalization Group (RG) and multigrid (MG) methods, Systematic Upscaling (SU) comprises rigorous procedures for deriving suitable variables and ... More


High density expansions

Barry M. McCoy

in Advanced Statistical Mechanics

Published in print:
2009
Published Online:
February 2010
ISBN:
9780199556632
eISBN:
9780191723278
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199556632.003.0008
Subject:
Physics, Theoretical, Computational, and Statistical Physics

This chapter sketches the basic principles of molecular dynamics computations. It presents the results of high density computations for hard spheres and discs. It provides data for the freezing ... More


Refinement

Dennis Sherwood and Jon Cooper

in Crystals, X-rays and Proteins: Comprehensive Protein Crystallography

Published in print:
2010
Published Online:
January 2011
ISBN:
9780199559046
eISBN:
9780191595028
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199559046.003.0015
Subject:
Physics, Crystallography

This chapter begins by emphasizing that the initial electron density for a protein will be significantly affected by errors in the experimental phases and, subsequently, additional errors of ... More


Molecular dynamics

Michael P. Allen and Dominic J. Tildesley

in Computer Simulation of Liquids: Second Edition

Published in print:
2017
Published Online:
November 2017
ISBN:
9780198803195
eISBN:
9780191841439
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198803195.003.0003
Subject:
Physics, Theoretical, Computational, and Statistical Physics, Soft Matter / Biological Physics

This chapter introduces the classical equations of motion for a system of molecules, and describes their solution by stable, accurate, time-stepping algorithms. Simple atomic systems, rigid ... More


Ultrafast electron dynamics as a route to explore chemical processes

Alexander I. Kuleff

in Current Trends in Atomic Physics

Published in print:
2019
Published Online:
July 2019
ISBN:
9780198837190
eISBN:
9780191873973
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198837190.003.0009
Subject:
Physics, Atomic, Laser, and Optical Physics, Particle Physics / Astrophysics / Cosmology

These lecture notes give a concise overview of the problem of describing quantum-mechanically the correlated motion of electrons and nuclei in a molecule. The focus is put on the methodology allowing ... More


Nuclear motion

Carsten A. Ullrich

in Time-Dependent Density-Functional Theory: Concepts and Applications

Published in print:
2011
Published Online:
December 2013
ISBN:
9780199563029
eISBN:
9780191775130
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199563029.003.0017
Subject:
Physics, Condensed Matter Physics / Materials

This chapter focuses on the coupling of electron dynamics and nuclear motion. In principle, electronic and nuclear degrees of freedom both have to be treated quantum mechanically and on an equal ... More


Molecular simulation: a virtual microscope in the toolbox of integrated structural biology

François Dehez

in From Molecules to Living Organisms: An Interplay Between Biology and Physics: Lecture Notes of the Les Houches School of Physics: Volume 102, July 2014

Published in print:
2016
Published Online:
March 2016
ISBN:
9780198752950
eISBN:
9780191814426
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198752950.003.0013
Subject:
Physics, Soft Matter / Biological Physics

Accessing the full atomistic details of complex biological processes in near physiological conditions remains challenging at the experimental level. The development of molecular modeling approaches, ... More


The Scale of Life?

Anne Marcovich and Terry Shinn

in Toward a New Dimension: Exploring the Nanoscale

Published in print:
2014
Published Online:
November 2014
ISBN:
9780198714613
eISBN:
9780191782923
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198714613.003.0004
Subject:
Physics, History of Physics

Nanoscale research has deeply penetrated biological fields. A new light has been cast on the worlds of proteins and DNA, thanks to nano’s appreciation and mastery of single molecules and its ability ... More


Quantum simulations

Michael P. Allen and Dominic J. Tildesley

in Computer Simulation of Liquids: Second Edition

Published in print:
2017
Published Online:
November 2017
ISBN:
9780198803195
eISBN:
9780191841439
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198803195.003.0013
Subject:
Physics, Theoretical, Computational, and Statistical Physics, Soft Matter / Biological Physics

This chapter covers the introduction of quantum mechanics into computer simulation methods. The chapter begins by explaining how electronic degrees of freedom may be handled in an ab initio fashion ... More


Core Metabolism as a Self-Organized System

Eric Smith, Harold J. Morowitz, and Shelley D. Copley

in Protocells: Bridging Nonliving and Living Matter

Published in print:
2008
Published Online:
August 2013
ISBN:
9780262182683
eISBN:
9780262282093
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262182683.003.0020
Subject:
Biology, Microbiology

This chapter focuses on the numerical approaches for protocell simulation. It discusses the ab initio methods, semiempirical methods, molecular mechanics or molecular dynamics (MM or MD), quantum ... More


Theory and Experiment

Anthony J. Stone

in The Theory of Intermolecular Forces

Published in print:
2013
Published Online:
May 2013
ISBN:
9780199672394
eISBN:
9780191751417
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199672394.003.0013
Subject:
Physics, Atomic, Laser, and Optical Physics

The theory must always be validated by reference to experiment. It is rarely possible to obtain full details of an intermolecular potential from experiment alone, though some molecular properties ... More


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