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We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…
We present new linear energy-stable numerical schemes for numerical simulation of complex polymer-solvent mixtures. The mathematical model proposed by Zhou, Zhang and E (Physical Review E 73, 2006) consists of the Cahn-Hilliard equation…
Molecular dynamics simulations are indispensable for exploring the behavior of atoms and molecules. Grounded in quantum mechanical principles, quantum molecular dynamics provides high predictive power but its computational cost is dominated…
The solvation free energy (SFE) of molecules and ions is a fundamental property governing their solvation behavior and solubility. Molecular simulations offer a route to compute SFEs using alchemical free energy methods, such as…
We present an energy-stable scheme for numerically approximating the governing equations for incompressible two-phase flows with different densities and dynamic viscosities for the two fluids. The proposed scheme employs a scalar-valued…
Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model…
Approximate molecular calculations via standard Kohn-Sham Density Functional Theory are exactly reproduced by performing self-consistent calculations on isolated fragments via Partition Density Functional Theory [Phys. Rev. A 82, 024501…
The determination of thermal and vibrational relaxation rates of triatomic systems suitable for application in hypersonic model calculations is discussed. For this, potential energy surfaces for ground and electronically excited state…
Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in…
One-dimensional ideal diatomic gas is simulated through possible types of motion of a molecule. Energy of each type of its motion is calculated from theory and numerical method. Calculation of kinetic energy of an atom in…
Employing a classical density-functional description of liquid environments, we introduce a rigorous method for the diffusion quantum Monte Carlo calculation of free energies and thermodynamic averages of solvated systems that requires…
The Bethe-Salpeter equation (BSE) is a reliable model for estimating the absorption spectra in molecules and solids on the basis of accurate calculation of the excited states from first principles. This challenging task includes calculation…
For a first principles understanding of macromolecular processes, a quantitative understanding of the underlying free energy landscape and in particular its entropy contribution is crucial. The stability of biomolecules, such as proteins,…
We construct a new phase-field model for the solvation of charged molecules with a variational implicit solvent. Our phase-field free-energy functional includes the surface energy, solute-solvent van der Waals dispersion energy, and…
Near-term quantum computers are expected to facilitate material and chemical research through accurate molecular simulations. Several developments have already shown that accurate ground-state energies for small molecules can be evaluated…
The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent…
Solid-On-Solid (SOS) computer simulations are employed to investigate the sublimation of surfaces. We distinguish three sublimation regimes: layer-by-layer sublimation, free step flow and hindered step flow. The sublimation regime is…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
The oscillator representation method is presented and used to calculate the energy spectra for a superposition of Coulomb and power-law potentials and for Coulomb and Yukawa potentials. The method provides an efficient way to obtain…