Related papers: A continuum solvent model: the DISOLV program - al…
The gradient descent approach is the key ingredient in variational quantum algorithms and machine learning tasks, which is an optimization algorithm for finding a local minimum of an objective function. The quantum versions of gradient…
In this paper, we propose to use the HLL finite volume scheme combined with implicit techniques for modelling the coupled surface and subsurface water flows. In our approach, we used the shallow water equations modelling surface water flow…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
Accuracy in neural PDE solvers often breaks down not because of limited expressivity, but due to poor optimisation caused by ill-conditioning, especially in multi-fidelity and stiff problems. We study this issue in Physics-Informed Extreme…
We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in…
We consider a class of one dimensional compressible systems with degenerate diffusion coefficients. We establish the fact that the solutions remain smooth as long as the diffusion coefficients do not vanish, and give local and global…
To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…
Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach,…
This is the second article in a series where we succeed in enlarging the class of solvable problems in one and three dimensions. We do that by working in a complete square integrable basis that carries a tridiagonal matrix representation of…
This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief…
We employ a fast and accurate algorithm to treat dielectric interfaces within molecular dynamics simulations and demonstrate the importance of dielectric boundary forces (DBFs) in two systems of interests in soft-condensed matter science.…
We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and inter-molecular potentials obtained at zero density. We show how this model is able to accurately…
Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent…
An algorithm for the computation of global discrete conformal parametrizations with prescribed global holonomy signatures for triangle meshes was recently described in [Campen and Zorin 2017]. In this paper we provide a detailed analysis of…
A previously-developed hybrid particle-continuum method [J. B. Bell, A. Garcia and S. A. Williams, SIAM Multiscale Modeling and Simulation, 6:1256-1280, 2008] is generalized to dense fluids and two and three dimensional flows. The scheme…
We propose an efficient algorithm for the immersed boundary method on distributed-memory architectures, with the computational complexity of a completely explicit method and excellent parallel scaling. The algorithm utilizes the…
Understanding and predicting polymer solubility in various solvents is critical for applications ranging from recycling to pharmaceutical formulation. This work presents a deep learning framework that predicts polymer solubility, expressed…
The electromagnetic behavior of plasmonic structures can be predicted after discretizing and solving a linear system of equations, derived from a continuous surface integral equation (SIE) and the appropriate boundary conditions, using a…
We derive and implement analytic nuclear gradients and derivative couplings for a constrained Complete Active Space Self-Consistent Field with a small active space designed to model electron or hole transfer. Using a Lagrangian formalism,…
Quantum chemical calculations on quantum computers have been focused mostly on simulating molecules in gas-phase. Molecules in liquid solution are however most relevant for Chemistry. Continuum solvation models represent a good compromise…