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Molecular representation pretraining is critical in various applications for drug and material discovery due to the limited number of labeled molecules, and most existing work focuses on pretraining on 2D molecular graphs. However, the…
We propose a generalisation of molecular density functional theory to describe inhomogeneous solvent mixture, with the objective of modelling electrolytic solutions. Two electrolytic models are presented, both within the HNC approximation.…
The article provides a brief general introduction into the concepts of scaling, universality, and crossover scaling, plus the blob concept that provides an intuitive picture of crossover phenomena. We present the most important static and…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
The state-of-the-art researches indicate that analytic algorithms are promising in handling complex floorplanning scenarios. However, it is challenging to generate compact floorplans with excellent wirelength optimization effect due to the…
A substantial number of algorithms exists for the simulation of moving particles suspended in fluids. However, finding the best method to address a particular physical problem is often highly non-trivial and depends on the properties of the…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
We report a multiscale modeling study for charged cylindrical nanopores using three modeling levels that include (1) an all-atom explicit-water model studied with molecular dynamics (MD), and reduced models with implicit water containing…
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 develop a unified continuum modeling framework for viscous fluids and hyperelastic solids using the Gibbs free energy as the thermodynamic potential. This framework naturally leads to a pressure primitive variable formulation for the…
Ab initio modeling of electrochemical systems is becoming a key tool for understanding and predicting electrochemical behavior. Development and careful benchmarking of computational electrochemical methods are essential to ensure their…
We present a multiwavelet-based implementation of a quantum/classical polarizable continuum model. The solvent model uses a diffuse solute-solvent boundary and a position-dependent permittivity, lifting the sharp-boundary assumption…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
We present a novel deep learning approach to approximate the solution of large, sparse, symmetric, positive-definite linear systems of equations. These systems arise from many problems in applied science, e.g., in numerical methods for…
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…
We propose a new deflation strategy to accelerate the convergence of the preconditioned conjugate gradient(PCG) method for solving parametric large-scale linear systems of equations. Unlike traditional deflation techniques that rely on…
Despite decades of advancements, the simulation of fluids remains one of the most challenging areas of in scientific computing. Supported by the necessity of gradient information in deep learning, differentiable simulators have emerged as…
We discuss the development, verification, and performance of a GPU accelerated discontinuous Galerkin method for the solutions of two dimensional nonlinear shallow water equations. The shallow water equations are hyperbolic partial…
Integral equation theory of molecular liquids based on statistical mechanics is quite promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. Beginning with a molecular interaction…