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COMPUTER SIMULATIONS OF PROTEIN FOLDING
(2013)
Understanding how proteins fold and interact with each other is key to understanding virtually all biological processes. Recent advances in computer power and modeling techniques make it possible to study proteins and other ...
Simulations of nonuniform fluids with long-ranged and short-ranged interactions
(2012)
The study of nonuniform fluids is of great importance in many areas of chemistry, biophysics,and materials science. Computer simulations of model systems have provided great insight into fundamental physical issues. We ...
Exploring Equilibrium Systems with Nonequilibrium Simulations
(2012)
Equilibrium sampling is at the core of computational thermodynamics, aiding our understanding of various phenomena in the natural sciences including phase coexistence, molecular solvation, and protein folding. Despite the ...
Nanofabrication on engineered silicon (100) surfaces using scanning probe microscopy
(2011)
Fabricating and measuring sub-5 nanometer features brings to light several pressing issues in future semiconductor industry manufacturing and dimensional metrology. This dissertation presents a feasible process to create ...
Using Energy Landscape Theory to Uncover the Organization of Conformational Space of Proteins in Their Native States.
(2011)
The functional motions of proteins navigate on rugged energy landscapes. Hence, mapping of these multidimensional landscapes into lower dimensional manifolds is imperative for gaining deeper insights into the functional ...
Cellular contact guidance through dynamic sensing of nanotopographies via actin polymerization waves
(2015)
Many biological and physiological processes depend upon directed migration of cells, which is typically mediated by chemical or physical gradients. However, conventional chemical or physical gradients have finite dynamic ...
STUDYING LIQUID DYNAMICS WITH OPTICAL KERR EFFECT SPECTROSCOPY
(2015)
Time-resolved optical Kerr effect (OKE) spectroscopy is an established tech-nique for studying the orientational dynamics of liquids. The reduced spectral density (RSD) obtained from transforming the OKE spectrum into the ...
Experimental, Computational and, Theoretical Analysis of the GroEL/GroES Catalytic Cycle
(2014)
The GroEL/GroES system is among the best characterized molecular chaperonins, having been the focus of numerous studies since its discovery just over 40 years ago. There are several aspects of the chaperonin's catalytic ...
Equilibrium free energies from nonequilibrium simulations: Improving convergence by reducing dissipation
(2011)
The estimation of equilibrium free energy differences is an important problem in computational thermodynamics, with applications to studies of ligand binding, phase coexistence and phase equilibrium, solvation of small ...
Jamming effects in glasses and biopolymers
(2014)
In this dissertation, jamming effects in highly packed systems are studied in two specific materials: glasses and biopolymers in cellular environments. Suspensions consisting of highly charged colloids, which are well-known ...