Related papers: Computing spatially resolved rotational hydration …
According to excess-entropy scaling, dynamic properties of liquids like viscosity and diffusion coefficient are determined by the entropy. This link between dynamics and thermodynamics is increasingly studied and of interest also for…
Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The non-matching properties of…
We consider the computation of the entanglement entropy in curved backgrounds with event horizons. We use a Hamiltonian approach to the problem and perform numerical computations on a spherical lattice of spacing $a$. We study the…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
Molecular density functional theory is a powerful technique for efficiently computing the spatially and orientationally dependent equilibrium density of a molecular solvent around an arbitrary solute. This density encodes the detailed…
In this work, we design an entropy stable, finite volume approximation for the ideal magnetohydrodynamics (MHD) equations. The method is novel as we design an affordable analytical expression of the numerical interface flux function that…
Entanglement entropy for a spatial partition of a quantum system is studied in theories which admit a dual description in terms of the anti-de Sitter (AdS) gravity one dimension higher. A general proof of the holographic formula which…
We use molecular dynamics simulations to probe the rotational dynamics of the SPC/E model of water for a range of temperatures down to 200 K, 13 K above to the mode coupling temperature. We find that rotational dynamics is spatially…
We present three-dimensional solutions of the magnetohydrostatic equations in the co-rotating frame of reference outside a magnetized rigidly rotating cylinder. We make no symmetry assumption for the magnetic field, but to be able to make…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in…
We compute the low-temperature configurational entropy of a two-dimensional supercooled liquid. Our method, based on a higher-dimensional version of the Grassberger--Procaccia algorithm, can be implemented in a manner that is entirely…
Understanding concentrated electrolytes requires a theory that spans local hydration and mesoscale interfacial assembly. We present an integrated workflow-SCOPE-that combines (i) enhanced sampling focused on a single Li+ ion, (ii)…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
The characteristic decomposition for GRMHD is not known in a form useful for current numerical simulations. This prevents us from using the most accurate known computational methods, such as full-wave Riemann solvers. In this paper, we…
Stimulated by recent results by Meru and Bate (2010a,b), we revisit the issue of resolution requirements for simulating self-gravitating accretion discs with Smoothed Particle Hydrodynamics (SPH). We show that the results by Meru and Bate…
A weakly magnetized neutron star (NS) undergoing disk accretion should release about a half of its power in a compact region known as the accretion boundary layer. Latitudinal spread of the accreted matter and efficient radiative cooling…
We describe an energy-enstrophy conserving discretisation for the rotating shallow water equations with slip boundary conditions. This relaxes the assumption of boundary-free domains (periodic solutions or the surface of a sphere, for…
We modelled the aqueous solvation of a nonpolar solute as a function of the radius, temperature and pressure. In this study a simple two-dimensional Mercedes-Benz (MB) water model was used in NPT Monte Carlo simulations. This model has…
Colloidal gels are out-of-equilibrium structures, made up of a rarefied network of colloidal particles. Comparing experiments to numerical simulations, with hydrodynamic interactions switched off, we demonstrate the crucial role of the…