Related papers: Computing three-dimensional densities from force d…
Even though the computation of local properties, such as densities or radial distribution functions, remains one of the most standard goals of molecular simulation, it still largely relies on straighforward histogram-based strategies. Here…
We introduce and test an expression for calculating the variance of a physical field in three dimensions using only information contained in the two-dimensional projection of the field. The method is general but assumes statistical…
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 interstellar medium (ISM) exhibits complex, multi-scale structures that are challenging to study due to their projection into two-dimensional (2D) column density maps. We present the Volume Density Mapper, a novel algorithm based on…
A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation…
Three dimensional implementations of liquid state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical)…
Diffusion models have shown remarkable empirical success in sampling from rich multi-modal distributions. Their inference relies on numerically solving a certain differential equation. This differential equation cannot be solved in closed…
A recently proposed convolution technique for the calculation of local density of states is described more thouroughly and new results of its application are presented. For separable systems the exposed method allows to construct the ldos…
Computation of gas dispersal in urban places or hilly grounds requires a large amount of computer time when addressed with conventional multidimensional models. Those are usually based on two-phase flow or Navier-Stokes equations. Different…
Calculating one-body density profiles in equilibrium via particle-based simulation methods involves counting of events of particle occurrences at (histogram-resolved) space points. Here we investigate an alternative method based on a…
Dimensionless numbers and scaling laws provide elegant insights into the characteristic properties of physical systems. Classical dimensional analysis and similitude theory fail to identify a set of unique dimensionless numbers for a…
Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to…
Surface topography refers to the geometric micro-structure of a surface and defines its tactile characteristics (typically in the sub-millimeter range). High-resolution 3D scanning techniques developed recently enable the 3D reconstruction…
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,…
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…
The permeability of complex porous materials can be obtained via direct flow simulation, which provides the most accurate results, but is very computationally expensive. In particular, the simulation convergence time scales poorly as…
Fluid-structure simulations of slender inextensible filaments in a viscous fluid are often plagued by numerical stiffness. Recent coarse-graining studies have reduced the computational requirements of simulating such systems, though have…
Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions or local transport properties from molecular simulations, we show that the variance can be…
Patterns forming spontaneously in extended, three-dimensional, dissipative systems are likely to excite several homogeneous soft modes ($\approx$ hydrodynamic modes) of the underlying physical system, much more than quasi one- and…
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…