Related papers: Hydration of a B-DNA Fragment in the Method of Ato…
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…
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…
We introduce quantum algorithms able to sample equilibrium water solvent molecules configurations within proteins thanks to analog quantum computing. To do so, we combine a quantum placement strategy to the 3D Reference Interaction Site…
Solvent can occupy up to ~70% of macromolecular crystals and hence having models that predict solvent distributions in periodic systems could improve in the interpretation of crystallographic data. Yet there are few implicit solvent models…
Accurate modeling of aqueous monovalent ions is essential for understanding the function of biomolecules, such as nucleic acid stability and binding of charged drugs to protein targets. The 1D and 3D reference interaction site models (1D-…
The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However,…
The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the…
We have developed a one-dimensional code to solve ultra-relativistic hydrodynamic problems, using the Glimm method for an accurate treatment of shocks and contact discontinuities. The implementation of the Glimm method is based on an exact…
We study fluid structure and water-like anomalies of a system constituted by dimeric particles interacting via a purely repulsive core-softened potential by means of integral equation theories. In our model, dimers interact through a…
A simple "trick" is proposed, which allows to perform exactly the site-averaging procedure required when developing integral equation theories of interaction site models of macromolecular fluids. It shows that no approximation is involved…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
This paper presents an improved immersed moving boundary model (IBM) for solving complex fluid-particle interactions in a coupled lattice Boltzmann method (LBM) and an adhesive discrete element method (DEM), using the "partially saturated…
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…
An implementation of a complex solver for the solution of the response equations required to compute the complex response functions of damped response theory is presented for the resolution-of-identity (RI) coupled-cluster singles and…
We propose an algorithm that combines the inchworm method and the frozen Gaussian approximation to simulate the Caldeira-Leggett model in which a quantum particle is coupled with thermal harmonic baths. In particular, we are interested in…
The recently developed Doubles Connected Moments (DCM) expansion offers a tractable approach for computing correlation energy, exhibiting an noniterative O(N^6) scaling with system size N. Benchmark calculations on a set of molecules…
Solvation is a notoriously difficult and nagging problem for the rigorous theoretical description of chemistry in the liquid phase. Successes and failures of various approaches ranging from implicit solvation modeling through dielectric…
Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific…
Coupled nonlinear system of reaction-diffusion equations describing multi-component (species) interactions with heterogeneous coefficients is considered. Finite volume method based approximation for the space is used to construct…
We consider the efficient solution of strongly elliptic partial differential equations with random load based on the finite element method. The solution's two-point correlation can efficiently be approximated by means of an…