Molecular modeling and simulation. An interdisciplinary guide
From MaRDI portal
Publication:700877
zbMath1011.92019MaRDI QIDQ700877
Publication date: 10 October 2002
Published in: Interdisciplinary Applied Mathematics (Search for Journal in Brave)
Probabilistic models, generic numerical methods in probability and statistics (65C20) Biochemistry, molecular biology (92C40) Introductory exposition (textbooks, tutorial papers, etc.) pertaining to biology (92-01) Research exposition (monographs, survey articles) pertaining to biology (92-02)
Related Items
Linear response based parameter estimation in the presence of model error, Variable order revised binary treecode, Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules, An adhesive contact mechanics formulation based on atomistically induced surface traction, The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances, Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation, Multiple-time-stepping generalized hybrid Monte Carlo methods, A multiplicative weights update algorithm for MINLP, An incomplete Hessian Newton minimization method and its application in a chemical database problem, Image approximations to electrostatic potentials in layered electrolytes/dielectrics and an ion-channel model, Coarse grained normal mode analysis vs. refined Gaussian network model for protein residue-level structural fluctuations, Adaptive multi-stage integrators for optimal energy conservation in molecular simulations, Recent advances on the discretizable molecular distance geometry problem, A stochastic immersed boundary method for fluid-structure dynamics at microscopic length scales, Recent advances on the interval distance geometry problem, Method of molecular dynamics in mechanics of deformable solids, A three-dimensional atomistic-based process zone model simulation of fragmentation in polycrystalline solids, A three-dimensional surface stress tensor formulation for simulation of adhesive contact in finite deformation, A Branch‐and‐Prune algorithm for the Molecular Distance Geometry Problem, Hyperbolic smoothing and penalty techniques applied to molecular structure determination, SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973--1977, Palindromic 3-stage splitting integrators, a roadmap, On a Relationship Between Graph Realizability and Distance Matrix Completion, An embedded atom hyperelastic constitutive model and multiscale cohesive finite element method, Application of rigid body mechanics to theoretical description of rotation within F\(_0\)F\(_1\)-ATP synthase, Coarse-graining Langevin dynamics using reduced-order techniques, Mechanistic modeling of swarms, Molecular dynamics multidimensional scaling, On the number of realizations of certain Henneberg graphs arising in protein conformation, Accelerated Cartesian expansions -- a fast method for computing of potentials of the form \(R^{ - \nu }\) for all real \(\nu \), Discretization orders for protein side chains, Robust estimation of nonlinear constitutive law from static equilibrium data for modeling the mechanics of DNA, Discretization vertex orders in distance geometry, Extending the fast multipole method for charges inside a dielectric sphere in an ionic solvent: high-order image approximations for reaction fields, Balanced model reduction of partially observed Langevin equations: an averaging principle, Error analysis of a stochastic immersed boundary method incorporating thermal fluctuations, A stochastic phase-field model determined from molecular dynamics, On the estimation and correction of discretization error in molecular dynamics averages, The discretizable molecular distance geometry problem, Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization, On the computation of protein backbones by using artificial backbones of hydrogens, A contact mechanics model for quasi-continua, An asymptotic comparative analysis of the thermodynamics of non-covalent association, Polyspherical coordinate systems on orbit spaces with applications to biomolecular shape, Global optimization in protein docking using clustering, underestimation and semidefinite programming, Theoretical and numerical comparison of some sampling methods for molecular dynamics, Moduli spaces and macromolecules, On the foundations of the stochastic immersed boundary method, On ergodicity for multidimensional harmonic oscillator systems with Nosé-Hoover-type thermostat, On progressive blast envelope evolution of charged particles in electromagnetic fields, A Cartesian treecode for screened Coulomb interactions, Geometric integrators and the Hamiltonian Monte Carlo method, Calculating the possible conformations arising from uncertainty in the molecular distance geometry problem using constraint interval analysis, Stochastic theory of the classical molecular dynamics method, WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinates, Temperature–energy-space sampling molecular dynamics: deterministic and single-replica method utilizing continuous temperature system
