Related papers: Computing spatially resolved rotational hydration …
We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure.…
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…
We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory…
We formulate theoretical modeling approaches and develop practical computational simulation methods for investigating the non-equilibrium statistical mechanics of fluid interfaces with passive and active immersed particles. Our approaches…
We show that a geometrical notion of entropy, definable in flat space, governs the first quantum correction to the Bekenstein-Hawking black hole entropy. We describe two methods for calculating this entropy -- a straightforward Hamiltonian…
Hypothesis: A broad range of phenomena, such as emulsification and emulsion stability, foam formation or liquid evaporation, are closely related to the dynamics of adsorbing colloidal particles. Elucidation of the mechanisms implied is key…
The use of adaptive spatial resolution to simulate flows of practical interest using Smoothed Particle Hydrodynamics (SPH) is of considerable importance. Recently, Muta and Ramachandran [1] have proposed an efficient adaptive SPH method…
A three-dimensional model is presented for the prediction of solidification behavior using a nonlinear transformation of the enthalpy equation in a Smoothed Particle Hydrodynamics (SPH) discretization. The effect of phase change in the form…
The similarity of local atomic environments is an important concept in many machine-learning techniques which find applications in computational chemistry and material science. Here, we present and discuss a connection between the…
We define the entropy S and uncertainty function of a squeezed system interacting with a thermal bath, and study how they change in time by following the evolution of the reduced density matrix in the influence functional formalism. As…
We build a comprehensive methodology for the fast computation of entropy across both solid and liquid phases. The proposed method utilizes a single trajectory of molecular dynamics (MD) to facilitate the calculation of entropy, which is…
We have used non-equilibrium molecular dynamics to simulate the flow of water molecules around a charged nanoparticle described at the atomic scale. These non-equilibrium simulations allowed us to compute the friction coefficient of the…
We use molecular dynamics simulations of the SPC-E model of liquid water to derive probability distributions for water density fluctuations in probe volumes of different shapes and sizes, both in the bulk as well as near hydrophobic and…
The efficiency of soft particles to stabilize emulsions is examined by measuring their desorption free energy, i.e., the mechanical work required to detach the particle from a fluid interface. Here, we consider rubber-like elastic as well…
We connect the configurational entropy of a liquid to the geometrical properties of its local energy landscape, using a high-temperature expansion. It is proposed that correlations between local structures arises from their overlap and,…
We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of…
We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a…
Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing in particular the importance of interfaces that emerge in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of…
In our recent works, based on the structural studies on water and interfacial water (topmost water layer at the solute/water interface), hydration free energy is derived and utilized to investigate the physical origin of hydrophobic…
Abridged: We simulate a massive galaxy cluster in a LCDM Universe using three different approaches to solving the equations of non-radiative hydrodynamics: `classic' Smoothed Particle Hydrodynamics (SPH); a novel SPH with a higher order…