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Second-harmonic scattering experiments of water and other bulk molecular liquids have long been assumed to be insensitive to interactions between the molecules. The measured intensity is generally thought to arise from incoherent scattering…
We use molecular simulation to compute the thermodynamic properties of 7 rigid models for water (SPC/E, TIP3P, TIP4P, TIP4P/2005, TIP4P/Ew, TIP5P, OPC) over a wide range of temperature and pressure. Carrying out Expanded Wang-Landau…
Biological processes like the sequestration of Superoxide Dismutase 1 (SOD1) into biomolecular condensates such as FUS and stress granules are essential to understanding disease mechanisms, including amyotrophic lateral sclerosis (ALS). Our…
Molecular dynamics simulations are indispensable for exploring the behavior of atoms and molecules. Grounded in quantum mechanical principles, quantum molecular dynamics provides high predictive power but its computational cost is dominated…
Results are presented from a time--dependent, numerical investigation of spherical accretion onto black holes, within the framework of relativistic radiation hydrodynamics. We have studied the stability of self--consistent, stationary…
We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal…
Measurements of local density fluctuations are crucial to characterizing the interfacial properties of equilibrium fluids. A specific case that has been well-explored involves the heightened compressibility of water near hydrophobic…
The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is…
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…
A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry…
We propose a numerical method to simulate electrohydrodynamic phenomena in charged colloidal dispersions. This method enables us to compute the time evolutions of colloidal particles, ions, and host fluids simultaneously by solving Newton,…
We present a maximum entropy approach to analyze the internal dynamics of a small system in contact with a large bath e.g. a solute-solvent system. For the small solute, the fluctuations around the mean values of observables are not…
Recent simulation and model system studies suggest that local structural excitations play an important role in the dynamics of liquids and glasses. Here, for the first time, we quantify excitation populations in real liquids, showing that…
We introduce a technique to solve numerically the relativistic Euler's equations in scenarios with spherical symmetry using the standard Smoothed Particles Hydrodynamics method in cartesian coordinates. This implementation allow us to…
In this paper we calculate the entropy of a thin spherical shell that contracts reversibly from infinity down to its event horizon. We find that, for a broad class of equations of state, the entropy of a non-extremal shell is one-quarter of…
Computational fluid dynamics is a crucial tool to theoretically explore the cosmos. In the last decade, we have seen a substantial methodological diversification with a number of cross-fertilizations between originally different methods.…
Smoothed particle hydrodynamics is a particle-based, fully Lagrangian, method for fluid-flow simulations. In this work, fundamental concepts of the method are first briefly recalled. Then, we present a thorough comparison of three different…
It is difficult to calculate the energy levels and eigenstates of a large physical system on a classical computer because of the exponentially growing size of the Hilbert space. In this work, we experimentally demonstrate a quantum…
We present a new methodology to analyze complicated multi-physics simulations by introducing a fictitious parameter. Using the method, we study quantum mechanical aspects of an organic molecule in water. The simulation is variationally…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…