The Art of Molecular Dynamics Simulation
From MaRDI portal
The book describes the extremely powerful techniques of molecular-dynamics (MD) simulation. It contains recipes in the form of complete computer-simulation codes for a wide variety of classical atomistic models, along with clear explanations of the statistical mechanics, applied mathematics, and programming needed to understand and implement them. The volume is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. Case studies are backed up by extensive references to the literature. The book begins with the simplest case of basic molecular dynamics, a soft-disk fluid. Later chapters extend the basic model in various directions, deal with various types of measurements, improve the computational methods, and introduce new models for more complex problems. These chapters also discuss the methodology for simulating monatomic systems and focus on measuring the thermodynamic and structural properties of systems in equilibrium. Consideration is given to the dynamical properties of equilibrium systems, including transport coefficients and the correlation functions that characterize space- and time-dependent properties. Chapters are devoted to the study of systems under constant temperature and pressure and the dynamics of rigid systems; flexible molecules are also discussed, including the use of angle and torsion forces and the application of bond-length constraints. The next chapters cover the Ewald sum (applied to dipolar systems); three-body forces; and hard-sphere simulations. Finally there are two chapters which contain the atomistic approach to fluid dynamics and algorithms for parallel and vector supercomputers. This second edition has been extensively revised and enlarged. It contains a substantial amount of new material and the software used in the case studies has been completely rewritten. The book will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner.
Recommendations
Cited in
(only showing first 100 items - show all)- Transport properties of liquid argon in krypton nanochannels: Anisotropy and non-homogeneity introduced by the solid walls
- An XFEM/level set approach to modelling surface/interface effects and to computing the size-dependent effective properties of nanocomposites
- A phenomenological and extended continuum approach for modelling non-equilibrium flows
- Collision detection for complicated polyhedra using the fast multipole method or ray crossing
- Influence of travelling surface waves on nanofluidic viscosity
- The study on interface characteristics near the metal wall by a molecular dynamics method
- Elastoplastic model of rocks with a linear structural parameter
- Local effective viscosity of gas in nano-scale channels
- On the dynamics of axonal membrane: ion channel as the basic unit of a deterministic model
- Shock propagation in the hard sphere gas in two dimensions: comparison between simulations and hydrodynamics
- Quasi-stationary distribution for the Langevin process in cylindrical domains. I: Existence, uniqueness and long-time convergence
- Transfer operators from optimal transport plans for coherent set detection
- Modern methods and software systems of molecular modeling and application of behavior algebra
- A minimalistic approach to physics-informed machine learning using neighbour lists as physics-optimized convolutions for inverse problems involving particle systems
- Tunable rheological behaviour of magnetized complex plasma
- Spectral estimation from simulations via sketching
- Effects of the long-range cohesive forces in binary particle packing dynamics
- Mathematical methods of diagonalization of quadratic forms applied to the study of stability of thermodynamic systems
- Nonlinear stability and vibration of imperfect CNTs by doublet mechanics
- A smooth dissipative particle dynamics method for nonisothermal liquid and gas flows in bounded domains
- Influence of the long-range forces in non-Gaussian random-packing dynamics
- Coarse-grained modeling with hierarchical deformable and rigid assemblages (HiDRA)
- Developing of multiscale approach to HPC-simulation of multiphase fluid flows
- Energy-momentum conserving integration schemes for molecular dynamics
- Genesis of the multiscale approach for materials with microstructure
- Atomistic modeling of metal nanocluster motion caused by gas flow impact
- On progressive blast envelope evolution of charged particles in electromagnetic fields
- Laser-induced heating of dynamic particulate depositions in additive manufacturing
- Treatment of long-range interactions arising in the Enskog-Vlasov description of dense fluids
- Quantum information in the Posner model of quantum cognition
- Molecular dynamics. With deterministic and stochastic numerical methods
- Quantification of sampling uncertainty for molecular dynamics simulation: time-dependent diffusion coefficient in simple fluids
- A semi-analytical approach to molecular dynamics
- Electrodynamic machine-learning-enhanced fault-tolerance of robotic free-form printing of complex mixtures
- SPARC: accurate and efficient finite-difference formulation and parallel implementation of density functional theory: extended systems
- A comparative study on poiseuille flow of simple fluids through cylindrical and slit-like nanochannels
- A concurrent multiscale method based on the alternating Schwarz scheme for coupling atomic and continuum scales with first-order compatibility
- Derivation of microstructured continua from lattice systems via principle of virtual works: the case of masonry-like materials as micropolar, second gradient and classical continua
- A Laplacian-based algorithm for non-isothermal atomistic-continuum hybrid simulation of micro and nano-flows
- A coupled discrete element lattice Boltzmann method for the simulation of fluid-solid interaction with particles of general shapes
- A cohesive law for carbon nanotube/polymer interfaces based on the van der Waals force
- A master equation for a spatial population model with pair interactions
- Simulation of instabilities in thin nanostructures by a perturbation approach
- Complexities in modeling of heterogeneous catalytic reactions
- An improved smoothed molecular dynamics method by alternating with molecular dynamics
- A mesoscopic simulation approach for modeling intracellular reactions
- Shock propagation following an intense explosion: comparison between hydrodynamics and simulations
- Interfacing finite elements with deep neural operators for fast multiscale modeling of mechanics problems
- Bulk viscosity of dilute monatomic gases revisited
- Intelligent dissipative particle dynamics: bridging mesoscopic models from microscopic simulations via deep neural networks
- Moduli spaces and macromolecules
- Some remarks on applying homogenization theory to modeling the constitutive response of carbon nanotubes
- Stochastic theory of the classical molecular dynamics method
- Roughness effect on flow and thermal boundaries in microchannel/nanochannel flow using molecular dynamics-continuum hybrid simulation
- Coupling of nonlocal and local continuum models by the Arlequin approach
- Introduction to molecular dynamics simulation
- Computational methods to study the structure and dynamics of biomolecules and biomolecular processes. From bioinformatics to molecular quantum mechanics
- Selective damping method for the weak-Arlequin coupling of molecular dynamics and finite element method
- The atomistic-continuum hybrid taxonomy and the hybrid-hybrid approach
- Continuum shell model for buckling of single-walled carbon nanotubes with different chiral angles
- A numerical investigation of the jamming transition in traffic flow on diluted planar networks
- Flexible dissipative particle dynamics
- Computer simulations of molecules and condensed matter. From electronic structures to molecular dynamics
- Hard sphere simulation by event-driven molecular dynamics: breakthrough, numerical difficulty, and overcoming the issues
- Hybrid molecular-continuum methods: from prototypes to coupling software
- Dissipative particle dynamics (DPD): an overview and recent developments
- From Molecular Dynamics and Particle Simulations towards Constitutive Relations for Continuum Theory
- Recent developments in the molecular modeling of diffusion in nanoporous materials
- Homogeneous non-equilibrium molecular dynamics simulations of viscous flow: techniques and applications
- A smooth dissipative particle dynamics method for domains with arbitrary-geometry solid boundaries
- Heat flux expressions that satisfy the conservation laws in atomistic system involving multibody potentials
- Molecular dynamics in arbitrary geometries: Parallel evaluation of pair forces
- Dissipative particle dynamics simulation of multiphase fluid flow in microchannels and microchannel networks
- Scale effect on flow and thermal boundaries in micro-/nano-channel flow using molecular dynamics-continuum hybrid simulation method
- Energy nonequipartition, rheology, and microstructure in sheared bidisperse granular mixtures
- Interfacial separation between elastic solids with randomly rough surfaces: comparison between theory and numerical techniques
- Voigt and Poincaré's mechanistic-energetic approaches to linear elasticity and suggestions for multiscale modelling
- Analysis of rheological properties of fibre suspensions in a Newtonian fluid by direct fibre simulation. I: Rigid fibre suspensions
- Analysis of rheological properties of fibre suspensions in a Newtonian fluid by direct fibre simulation. II: Flexible fibre suspensions
- scientific article; zbMATH DE number 46777 (Why is no real title available?)
- Parallel hybrid particle/finite volume algorithm for transported PDF methods employing sub-time stepping
- Molecular dynamics beyonds the limits: Massive scaling on 72 racks of a BlueGene/P and supercooled glass dynamics of a 1 billion particles system
- Off-lattice pattern recognition scheme for kinetic Monte Carlo simulations
- Multiresolution representation of operators with boundary conditions on simple domains
- scientific article; zbMATH DE number 1082719 (Why is no real title available?)
- scientific article; zbMATH DE number 1959567 (Why is no real title available?)
- Numerical simulation in the dynamics of molecules. Numerics, algorithms, parallelization, applications
- Study for the particle's scale effect on some thermophysical properties of nanofluids by a simplified molecular dynamics method
- A New Leapfrog Integrator of Rotational Motion. The Revised Angular-Momentum Approach
- A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure
- Introduction to first-principle simulation of molecular systems
- Motion planning algorithms for molecular simulations: a survey
- An overview on smoothed particle hydrodynamics
- Approximating the dynamical evolution of systems of strongly interacting overdamped particles
- Molecular dynamics simulation of a two-dimensional Heisenberg fluid
- Atomistic computer simulations. A practical guide
- Simulating flow of DNA suspension using dissipative particle dynamics
- GPU-accelerated molecular dynamics simulation of solid covalent crystals
- Passing from discrete to continuum models of electrostatic energy
- Long-time convergence of an adaptive biasing force method: variance reduction by Helmholtz projection
This page was built for publication: The Art of Molecular Dynamics Simulation
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5713306)
