Related papers: Computing spatially resolved rotational hydration …
We study ``draining bathtub'' as an acoustic analogue of a three-dimensional rotating black hole. Rotating fluid near the sonic horizon necessarily gives rise to the superradiant modes, which are partially responsible for the thermodynamic…
We introduce and test a new and highly efficient method for treating the thermal and radiative effects influencing the energy equation in SPH simulations of star formation. The method uses the density, temperature and gravitational…
We describe a systematic development of kinetic entropy as a diagnostic in fully kinetic particle-in-cell (PIC) simulations and use it to interpret plasma physics processes in heliospheric, planetary, and astrophysical systems. First, we…
Stochastic hydrodynamics provides a dynamical framework for the evolution of fluctuations in heavy-ion collisions, but poses significant challenges in numerical simulations. We present an algorithm for the simulation of non-relativistic…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
A numerical method based on smoothed particle hydrodynamics with adaptive spatial resolution (SPH-ASR) was developed for simulating free surface flows. This method can reduce the computational demands while maintaining the numerical…
When a hydrophilic solute in water is suddenly turned into a hydrophobic species, for instance, by photoionization, a layer of hydrated water molecules forms around the solute on a time scale of a few picoseconds. We study the dynamic…
We describe and demonstrate a method for increasing the resolution locally in a Smoothed Particle Hydrodynamic (SPH) simulation, by splitting particles. We show that in simulations of self-gravitating collapse (of the sort which are…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
We study dynamics of a locally conserved energy in ergodic, local many-body quantum systems on a lattice with no additional symmetry. The resulting dynamics is well approximated by a coarse grained, classical linear functional diffusion…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
The entropic lattice Boltzmann framework proposed the construction of the discrete equilibrium by taking into consideration minimization of a discrete entropy functional. The effect of this form of the discrete equilibrium on properties of…
A theoretical model for the effect of water hydrogen bonding on the thermodynamics of hydrophobic hydration is proposed as a combination of the classical density functional theory with the recently developed probabilistic approach to water…
To make relevant predictions about observable emission, hydrodynamical simulation codes must employ schemes that account for radiative losses, but the large dimensionality of accurate radiative transfer schemes is often prohibitive.…
Atmospheric systems incorporating thermal dynamics must be stable with respect to both energy and entropy. While energy conservation can be enforced via the preservation of the skew-symmetric structure of the Hamiltonian form of the…
We propose a mixed quantum-classical hydrodynamic framework to model short-time inertial effects in the non-adiabatic evolution of a quantum solute coupled to a classical polar solvent. Drawing upon the work of Burghardt and Bagchi [Chem.…
We present an overview of the recent progress that has been made in understanding the origin of hydrophobic interactions. We discuss the different character of the solvation behavior of apolar solutes at small and large length scales. We…
We demonstrate pre-transition effects in space-time in trajectories of systems in which the dynamics displays a first-order phase transition between distinct dynamical phases. These effects are analogous to those observed for thermodynamic…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
In this work we propose a novel method to ensure important entropy inequalities are satisfied semi-discretely when constructing reduced order models (ROMs) on nonlinear reduced manifolds. We are in particular interested in ROMs of systems…