相关论文: Enhanced solvation force extrapolation for speedin…

We introduce a novel extrapolation algorithm inspired by quantum mechanics and evaluate its performance against linear prediction. Our method involves mapping function values onto a quantum state and estimating future function values by…

Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…

Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…

In this paper, we derive an asymptotic error expansion for the eigenvalue approximations by the lowest order Raviart-Thomas mixed finite element method for the general second order elliptic eigenvalue problems. Extrapolation based on such…

All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…

The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the…

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn,…

Although aqueous electrolytes are among the most important solutions, the molecular simulation of their intertwined properties of chemical potentials, solubility and activity coefficients has remained a challenging problem, and has…

In molecular simulations, neural network force fields aim at achieving \emph{ab initio} accuracy with reduced computational cost. This work introduces enhancements to the Deep Potential network architecture, integrating a message-passing…

Computational multi-scale methods capitalize on a large time-scale separation to efficiently simulate slow dynamics over long time intervals. For stochastic systems, one often aims at resolving the statistics of the slowest dynamics. This…

Simulating charged many-body systems has been a computational demanding task due to the long-range nature of electrostatic interaction. For the multi-scale model of electrolytes which combines the strengths of atomistic/continuum…

The problem of extrapolation and interpolation of asymptotic series is considered. Several new variants of improving the accuracy of the self-similar approximants are suggested. The methods are illustrated by examples typical of chemical…

In this paper, we consider an unconstrained stochastic optimization problem where the objective function exhibits high-order smoothness. Specifically, we propose a new stochastic first-order method (SFOM) with multi-extrapolated momentum,…

We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethane<->methanol transformation. The results suggest that extrapolation can greatly reduce the systematic…

We present an efficient method to mix well converged ab initio forces with simpler and faster ones in molecular dynamics. While the cheap forces are evaluated every time step, the converged ones correct the trajectory only every n time…

We extend the insertion approach for calculating depletion potentials to the case of non-spherical solutes. Instead of a brute-force calculation we suggest to employ the recently developed curvature expansion of density profiles close to…

Born-Oppenheimer Molecular Dynamics (BOMD) is a powerful but expensive technique. The main bottleneck in a density functional theory bomd calculation is the solution to the Kohn-Sham (KS) equations, that requires an iterative procedure that…

The method of regularised stokeslets is widely used in microscale biological fluid dynamics due to its ease of implementation, natural treatment of complex moving geometries, and removal of singular functions to integrate. The standard…

The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm…

We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory…