Molecular modeling and simulation. An interdisciplinary guide

zbMATH Open1011.92019MaRDI QIDQ700877FDOQ700877

Publication date: 10 October 2002

Published in: Interdisciplinary Applied Mathematics (Search for Journal in Brave)

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Publication:3032115
scientific article; zbMATH DE number 1082719

simulations molecular structure molecular dynamics Monte Carlo techniques

Biochemistry, molecular biology (92C40) Probabilistic models, generic numerical methods in probability and statistics (65C20) Introductory exposition (textbooks, tutorial papers, etc.) pertaining to biology (92-01) Research exposition (monographs, survey articles) pertaining to biology (92-02)

Cited In (61)

Polyspherical coordinate systems on orbit spaces with applications to biomolecular shape
SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973--1977
Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules
The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances
Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization
Stochastic theory of the classical molecular dynamics method
WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinates
Recent advances on the interval distance geometry problem
Theoretical and numerical comparison of some sampling methods for molecular dynamics
Hyperbolic smoothing and penalty techniques applied to molecular structure determination
Extending the fast multipole method for charges inside a dielectric sphere in an ionic solvent: high-order image approximations for reaction fields
On the foundations of the stochastic immersed boundary method
An embedded atom hyperelastic constitutive model and multiscale cohesive finite element method
The discretizable molecular distance geometry problem
Computational methods for protein structure prediction and modeling. Volume 1: Basic characterization.
On the number of realizations of certain Henneberg graphs arising in protein conformation
Variable order revised binary treecode
On the computation of protein backbones by using artificial backbones of hydrogens
Molecular modeling and simulation. An interdisciplinary guide.
Temperature–energy-space sampling molecular dynamics: deterministic and single-replica method utilizing continuous temperature system
Robust estimation of nonlinear constitutive law from static equilibrium data for modeling the mechanics of DNA
A multiplicative weights update algorithm for MINLP
On the estimation and correction of discretization error in molecular dynamics averages
Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation
Moduli spaces and macromolecules
An asymptotic comparative analysis of the thermodynamics of non-covalent association
On a Relationship Between Graph Realizability and Distance Matrix Completion
Global optimization in protein docking using clustering, underestimation and semidefinite programming
Molecular dynamics multidimensional scaling
A three-dimensional surface stress tensor formulation for simulation of adhesive contact in finite deformation
An incomplete Hessian Newton minimization method and its application in a chemical database problem
On ergodicity for multidimensional harmonic oscillator systems with Nosé-Hoover-type thermostat
Method of molecular dynamics in mechanics of deformable solids
Discretization vertex orders in distance geometry
A three-dimensional atomistic-based process zone model simulation of fragmentation in polycrystalline solids
A Cartesian treecode for screened Coulomb interactions
Discretization orders for protein side chains
Coarse-graining Langevin dynamics using reduced-order techniques
Calculating the possible conformations arising from uncertainty in the molecular distance geometry problem using constraint interval analysis
Multiple-time-stepping generalized hybrid Monte Carlo methods
Image approximations to electrostatic potentials in layered electrolytes/dielectrics and an ion-channel model
A stochastic phase-field model determined from molecular dynamics
Adaptive multi-stage integrators for optimal energy conservation in molecular simulations
Geometric integrators and the Hamiltonian Monte Carlo method
Palindromic 3-stage splitting integrators, a roadmap
Balanced model reduction of partially observed Langevin equations: an averaging principle
A Branch‐and‐Prune algorithm for the Molecular Distance Geometry Problem
Recent advances on the discretizable molecular distance geometry problem
An adhesive contact mechanics formulation based on atomistically induced surface traction
A stochastic immersed boundary method for fluid-structure dynamics at microscopic length scales
Error analysis of a stochastic immersed boundary method incorporating thermal fluctuations
Coarse grained normal mode analysis vs. refined Gaussian network model for protein residue-level structural fluctuations
Mechanistic modeling of swarms
Title not available (Why is that?)
Linear response based parameter estimation in the presence of model error
Accelerated Cartesian expansions -- a fast method for computing of potentials of the form \(R^{ - \nu }\) for all real \(\nu \)
Title not available (Why is that?)
Application of rigid body mechanics to theoretical description of rotation within F\(_0\)F\(_1\)-ATP synthase
A contact mechanics model for quasi-continua
On progressive blast envelope evolution of charged particles in electromagnetic fields
Methods for macromolecular modeling \((M^3)\): assessment of progress and future perspectives

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