相关论文: Enhanced solvation force extrapolation for speedin…

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…

In this work a new finite element based Method of Relaxed Streamline Upwinding is proposed to solve hyperbolic conservation laws. Formulation of the proposed scheme is based on relaxation system which replaces hyperbolic conservation laws…

This paper introduces a simple variant of the power method. It is shown analytically and numerically to accelerate convergence to the dominant eigenvalue/eigenvector pair; and, it is particularly effective for problems featuring a small…

Cosimulation methods allow combination of simulation tools of physical systems running in parallel to act as a single simulation environment for a big system. As data is passed across subsystem boundaries instead of solving the system as…

A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular…

We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…

The immersed boundary method is a mathematical formulation and numerical method for solving fluid-structure interaction problems. For many biological problems, such as models that include the cell membrane, the immersed structure is a…

The constant potential molecular dynamics simulation method proposed by Siepmann and Sprik and reformulated later by Reed (SR-CPM) has been widely employed to investigate the metallic electrolyte/electrode interfaces, especially for…

Applications of 3D-RISM-KH molecular solvation theory range from solvation energy of small molecules to phase behavior of polymers and biomolecules. It predicts the molecular mechanisms of chemical and biomolecular systems. Replica…

We demonstrate a new, hybrid symbolic-numerical method for the automatic synthesis of all families of translation operators required for the execution of the Fast Multipole Method (FMM). Our method is applicable in any dimensionality and to…

Mechanochemically active enzymes change their shapes within every turnover cycle. Therefore, they induce circulating flows in the solvent around them and behave as oscillating hydrodynamic force dipoles. Because of non-equilibrium…

Active gel theory has recently been very successful in describing biologically active materials such as actin filaments or moving bacteria in temporally fixed and simple geometries such as cubes or spheres. Here we develop a computational…

We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…

In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics.…

In solution-processing of thin films, the material layer is deposited from a solution composed of several solutes and solvents. The final morphology and hence the properties of the film often depend on the time needed for the evaporation of…

A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…

This paper deals with speeding up the convergence of a class of two-step iterative methods for solving linear systems of equations. To implement the acceleration technique, the residual norm associated with computed approximations for each…

Traditional force fields commonly use a combination of bonded torsional terms and empirically scaled non-bonded interactions to capture 1-4 energies and forces of atoms separated by three bonds in a molecule. While this approach can yield…

The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…

We introduce a theoretical approach to study the quantum-dissipative dynamics of electronic excitations in macromolecules, which enables to perform calculations in large systems and cover long time intervals. All the parameters of the…