相关论文: Enhanced solvation force extrapolation for speedin…
The phase separation of oppositely-charged polyelectrolytes in solution is of current interest . In this work we study the driving force for polyelectrolyte complexation using molecular dynamics simulations. We calculate the potential of…
A crucial aspect in the simulation of electrochemical interfaces consists in treating the distribution of electronic charge of electrode materials that are put in contact with an electrolyte solution. Recently, it has been shown how a…
Nonnegative tensors arise very naturally in many applications that involve large and complex data flows. Due to the relatively small requirement in terms of memory storage and number of operations per step, the (shifted) higher-order power…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
We derive a new formulation to calculate the excess chemical potential of a fraction of $N_1$ particles interacting with $N_2$ particles of a different species. The excess chemical potential is calculated numerically from first principles…
An extended first-principles molecular dynamics (FPMD) method based on Kohn-Sham scheme is proposed to elevate the temperature limit of the FPMD method in the calculation of dense plasmas. The extended method treats the wave functions of…
We study multivariate numerical integration of smooth functions in weighted Sobolev spaces with dominating mixed smoothness $\alpha\geq 2$ defined over the $s$-dimensional unit cube. We propose a new quasi-Monte Carlo (QMC)-based quadrature…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
Smoothed particle hydrodynamics (SPH) discretization techniques are generalized to develop a method, smoothed particle interpolation (SPI), for solving initial value problems of systems of non-hydrodynamical nature. Under this approach, SPH…
Hybrid particle-field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. Here, we introduce a…
A new algorithm is introduced to integrate the equations of rotational motion. The algorithm is derived within a leapfrog framework and the quantities involved into the integration are mid-step angular momenta and on-step orientational…
The accurate prediction of solvation free energy is of significant importance as it governs the behavior of solutes in solution. In this work, we apply a variety of machine learning techniques to predict and analyze the alchemical free…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Theory of solutions in energy representation (ER method) developed by Matubayasi and Nakahara provides with an approximate way of calculating solvation free energies (or, identically, the excess chemical potentials) from atomistic…
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics…
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Magnetic field in the solar corona is usually extrapolated from photospheric vector magnetogram using a nonlinear force-free field (NLFFF) model. NLFFF extrapolation needs a considerable effort to be devoted for its numerical realization.…