相关论文: Enhanced solvation force extrapolation for speedin…

Simulating physical problems involving multi-time scale coupling is challenging due to the need of solving these multi-time scale processes simultaneously. In response to this challenge, this paper proposed an explicit multi-time step…

The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and…

The modeling of solute chemistry at low-symmetry defects in materials is historically challenging, due to the computation cost required to evaluate thermodynamic properties from first principles. Here, we offer a hybrid multiscale approach…

Gaussian process regression has recently emerged as a powerful, system-agnostic tool for building global potential energy surfaces (PES) of polyatomic molecules. While the accuracy of GP models of PES increases with the number of potential…

RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…

Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…

Recently, we introduced Relative Resolution as a hybrid formalism for fluid mixtures [1]. The essence of this approach is that it switches molecular resolution in terms or relative separation: While nearest neighbors are characterized by a…

Simulations of water near extended hydrophobic spherical solutes have revealed the presence of a region of depleted density and accompanying enhanced density fluctuations.The physical origin of both phenomena has remained somewhat obscure.…

A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation…

Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…

Yeh and Hummer's simplified estimation method has often been adopted to obtain diffusion coefficients for solute molecules using molecular dynamic simulation. However, the simplified formula is not necessarily valid when a small basic cell…

Extrapolation is a generic problem in physics and mathematics: how to use asymptotic data in one parametric regime to learn about the behavior of a function in another parametric regime. For example: extending weak coupling expansions to…

We propose an ab-initio molecular dynamics method, capable to reduce dramatically the autocorrelation time required for the simulation of classical and quantum particles at finite temperature. The method is based on an efficient…

We present an approach to the estimate of the potential of mean force along a generic reaction coordinate based on maximum likelihood methods and path-ensemble averages in systems driven far from equilibrium. Following similar arguments,…

We propose an accelerated block proximal linear framework with adaptive momentum (ABPL$^+$) for nonconvex and nonsmooth optimization. We analyze the potential causes of the extrapolation step failing in some algorithms, and resolve this…

For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…

Aitken extrapolation normally applied to convergent fixed point iteration is extended to extrapolate the solution of a divergent iteration. In addition, higher order Aitken extrapolation is introduced that enables successive decomposition…

Direct numerical simulations (DNS) are accurate but computationally expensive for predicting materials evolution across timescales, due to the complexity of the underlying evolution equations, the nature of multiscale spatio-temporal…

In molecular simulations, machine-learning force fields can achieve ab initio accuracy at a lower cost but remain limited in the explicit modeling of electrons. In this work, we develop an electron-aware machine-learning force field, in…

Most recently, some substitutional solute atoms in {\alpha}-Ti have been predicted to occupy unexpectedly the low-symmetry (LS) positions away from the high-symmetry (HS) lattice site, which was speculated to result in enhanced solid…