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Hydrophobic interactions are central to biological self-assembly and soft matter organization, yet their microscopic origins remain debated. A key hallmark is the strengthening of attraction between hydrophobic solutes with increasing…
In this work, we investigate entropy solutions for a class of systems of nonlocal {balance laws in which the convective flux and the source involves terms where the state variable convolved with kernels} in both spatial and temporal…
In computational fluid dynamics, the demand for increasingly multidisciplinary reliable simulations, for both analysis and design optimization purposes, requires transformational advances in individual components of future solvers. At the…
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…
In this paper we propose an accurate, and computationally efficient method for incorporating adaptive spatial resolution into weakly-compressible Smoothed Particle Hydrodynamics (SPH) schemes. Particles are adaptively split and merged in an…
Despite increasing demands for the thermodynamic data of liquids in a wide range of science and engineering fields, there is a still a considerable lack of reliable data over a wide range of temperature ($T$) and pressure conditions. The…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
On a basis of a two-length scale description of hydrophobic interactions we develop a continuous self-consistent theory of solute-water interactions which allows to determine a hydrophobic layer of a solute molecules of any geometry with…
Computation of entropy in liquids and liquid crystal phases is a big challenge in statistical physics. In this work, we extend the two-phase thermodynamic model (2PT) to shape anisotropic soft repulsive spherocylinders (SRSs) and report the…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
We develop a new numerical scheme for solving the radiative transfer equation in a spherically symmetric system. This scheme does not rely on any kind of diffusion approximation and it is accurate for optically thin, thick, and intermediate…
Motivated by the necessity to UV-regularise entanglement entropy, we present a spectral method for calculating the entropy of quasifree states, for both bosonic and fermionic field theories. This construction is defined in spacetime rather…
We explore the relationship between a machine-learned structural quantity (softness) and excess entropy in simulations of supercooled liquids. Excess entropy is known to scale well the dynamical properties of liquids, but this…
Hydrodynamic simulations have become irreplaceable in modern cosmology for exploring complex systems and making predictions to steer future observations. In Chapter 1, we begin with a philosophical discussion on the role of simulations in…
We model the thermodynamics of local structures within the hard sphere liquid at arbitrary volume fractions through the \textit{morphometric} calculation of $n$-body correlations. We calculate absolute free energies of local geometric…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
In transitions between different environmental settings, a molecular system inevitably undergoes a range of detectable changes, and the ability to accurately simulate such responses, e.g., in the form of shifts to molecular energies,…
The smoothed-particle hydrodynamics (SPH) technique is a numerical method for solving gas-dynamical problems. It has been applied to simulate the evolution of a wide variety of astrophysical systems. The method has a second-order accuracy,…
We investigate the curvature-dependence of water dynamics in the vicinity of hydrophobic spherical solutes using molecular dynamics simulations. For both, the lateral and perpendicular diffusivity as well as for H-bond kinetics of water in…
Smoothed particle hydrodynamics (SPH) is typically used for barotropic fluids, where the pressure depends only on the local mass density. Here, we show how to incorporate the entropy into the SPH, so that the pressure can also depend on the…