Computational statistical mechanics leans heavily on the class of Markov Chain Monte Carlo Algorithms. Many such algorithms exist, and simulations can run for several weeks, making the selection of algorithms a difficult, but critical task. In this work, we introduce a benchmark system of two quadratic wells with an analytical...
The motor protein dynein is responsible for cellular processes such as axonal transport and cell division by delivering vital information along the microtubule track. A failed delivery can cause severe damage to the cell’s functionality and lead to neurological diseases. Despite dynein’s rich history in cellular research, the mechanism of...
The equation of state for a fluid described by the Weeks-Chandler-Andersen (WCA) potential was solved to determine at what pressures and temperatures the fluid will theoretically freeze. A Monte Carlo (MC) algorithm was used to sample a system of 256 spheres for a set of thermodynamic averages to locate and...
This dissertation reports on the computational physics research in the area of
inhomogeneous fluids. I first discuss the theory background for this work beginning
with water, which is important for the two published articles that are presented in
this work (Chapters 5 and 6). Next, I give a brief overview...
This thesis reports on computational research in two different areas. I first discuss the Min-protein system found within Escherichia coli. Following this I discuss an extended investigation into improving free energy functionals that are used within Classical Density Functional Theory in order to model water. Chapter 2 examines the dynamics...
We developed a model to investigate the dielectric properties of the
BaTiO₃ − Bi(Zn₁/₂Ti₁/₂)O₃ (BT-BZT) solid solution, which is a relaxor ferroelectric and exhibits long range disorder. The model uses ab initio methods
to determine all polarization states for every atomic configuration of 2 x 2 x 2
supercells of...
Metal organic frameworks(MOFs) are a class of crystalline materials utilized in gas storage, chemicalsensing, and other engineering applications. Recently chemists have begun synthesizing MOFs withmoving parts in order to further these applications. A wide array of dynamic MOFs have been created andtheorized. Among them is the interlocking of a ring...
We present a classical density functional to model the soft, repulsive potential of a Weeks-Chandler-Andersen (WCA) fluid using Soft Fundamental Measure Theory (SFMT) with temperature-dependent parameters inspired by the Barker-Henderson method. Our functional uses soft spheres to model the soft-sphere WCA potential, and gives results that are in good agreement...
We use Classical Density Functional Theory (cDFT) to predict the freezing of a Weeks-Chandler-Anderson (WCA) fluid, and construct pressure-temperature and temperature-density phase diagrams. A WCA fluid consists of soft spheres that exhibit the repulsive portion of the Lennard-Jones potential widely used to model the interaction of two neutral atoms. Our...
This work introduces the novel flat-histogram Monte Carlo (MC) method stochastic approximation with a dynamic update factor (SAD) and explores the convergence properties of a variety of related weight-based MC methods. The new method is applied to a number of physical `test’ systems including the 2D Ising model, a square-well...