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The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and…
Molecular discovery within the vast chemical space remains a significant challenge due to the immense number of possible molecules and limited scalability of conventional screening methods. To approach chemical space exploration more…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
A quantum thermodynamic system is described by a Hamiltonian and a list of conserved, non-commuting charges, and a fundamental goal is to determine the minimum energy of the system subject to constraints on the charges. Recently, [Liu et…
Embedding calculations that find approximate solutions to the Schr\"{o}dinger equation for large molecules and realistic solids are performed commonly in a three step procedure involving (i) construction of a model system with effective…
We perform simulations of giant impacts onto the young Uranus using smoothed particle hydrodynamics (SPH) with over 100 million particles. This 100--1000$\times$ improvement in particle number reveals that simulations with below 10^7…
The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the…
The smoothed particle hydrodynamics (SPH) method is a useful numerical tool for the study of a variety of astrophysical and planetlogical problems. However, it turned out that the standard SPH algorithm has problems in dealing with…
Smoothed particle hydrodynamics (SPH) discretization techniques are generalized to develop a method, smoothed particle interpolation (SPI), for solving initial value problems of systems of non-hydrodynamical nature. Under this approach, SPH…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
In this paper we test a special-relativistic formulation of Smoothed Particle Hydrodynamics (SPH) that has been derived from the Lagrangian of an ideal fluid. Apart from its symmetry in the particle indices, the new formulation differs from…
Smoothed Particle Hydrodynamics (SPH) is a Lagrangian method for solving the fluid equations that is commonplace in astrophysics, prized for its natural adaptivity and stability. The choice of variable to smooth in SPH has been the topic of…
We present an efficient, accurate, and robust method for simulation of dense suspensions of deformable and rigid particles immersed in Stokesian fluid in two dimensions. We use a well-established boundary integral formulation for the…
While the excess chemical potential is the key quantity in determining phase diagrams, its direct computation for high-density liquids of long polymer chains has posed a significant challenge. Computationally, the excess chemical potential…
Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in…
There are many interesting physical processes which involve the generation of high density plasmas in large volumes. However, when modeling these systems numerically, the large densities and volumes present a significant computational…
We present the results from a two-day study in which we discussed various implementations of Smooth Particle Hydrodynamics (SPH), one of the leading methods used across a variety of areas of large-scale astrophysical simulations. In…
We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonical-like version (GC-AdResS) [Wang et al. Phys.Rev.X 3, 011018 (2013)], to calculate the excess chemical potential, $\mu^{ex}$, of various liquids and…
Accurate mesh-free simulation of fluid flows involving complex boundaries requires that the boundaries be captured accurately in terms of particles. In the context of incompressible/weakly-compressible fluid flow, the SPH method is more…
Polymer chains in colloid-polymer mixtures can be coarse-grained by replacing them with single soft particles interacting via effective polymer-polymer and polymer-colloid pair potentials. Here we describe in detail how Ornstein-Zernike…