Related papers: Integral equation models for solvent in macromolec…
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…
The new predictive electrolyte model COSMO-RS-ES is evaluated and refined for the calculation of solubilities of salts in mixed solvent systems. It is demonstrated that the model is capable of predicting solid-liquid equilibria at 25…
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-…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
Many astrophysical systems can only be accurately modelled when the behaviour of their baryonic gas components is well understood. The residual distribution (RD) family of partial differential equation (PDE) solvers produce approximate…
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…
The predictive electrolyte model COSMO-RS-ES is refined to improve the description of systems at 25{\deg}C in which strong ion pairing is expected due to a low static permittivity of the liquid phase. Furthermore, the short-range ion energy…
Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
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…
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,…
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…
Machine learning (ML) potentials are a powerful tool in molecular modeling, enabling ab initio accuracy for comparably small computational costs. Nevertheless, all-atom simulations employing best-performing graph neural network…
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.…
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…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
Semi-implicit time-stepping schemes for atmosphere and ocean models require elliptic solvers that work efficiently on modern supercomputers. This paper reports our study of the potential computational savings when using mixed precision…
We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The…
We study a fluid-fluid phase transition of the explicit solvent model represented as a mixture of the restricted primitive model (RPM) of ionic fluid and neutral hard spherocylinders (HSC). To this end, we combine two theoretical…