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Suspension of particles in a fluid solvent are ubiquitous in nature, for example, water mixed with sugar or bacteria self-propelling through mucus. Particles create local flow perturbations that can modify drastically the effective…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Research on conjugated polymers for thermoelectric applications has made tremendous progress in recent years, which is accompanied by surging interest in molecular doping as a means to achieve the high electrical conductivities that are…
Capillary electrophoresis has long been been recognized as a powerful analytic tool. Here it is demonstrated that the same capillary electrophoretic experiments also reveal dynamic properties of the polymer solutions being used as the…
The separation of liquid mixture has been studied for a long time. Separation proceeds based on the difference in physical properties including pore size and electrostatic interaction. Therefore, there are many difficulties in separation of…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
The process of diagnosing a disease from the 2D gel electrophoresis image is a challenging problem. This is due to technical difficulties of generating reproducible images with a normalized form and the effect of negative stain. In this…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
The extraction of inhomogeneous 3-dimensional densities around tagged solutes from molecular simulations is known to have a very high computational cost because this is traditionally performed by collecting histograms, with each discrete…
The influence of thiol blocking on the resolution of basic proteins by two-dimensional electrophoresis was investigated. Cysteine blocking greatly increased resolution and decreased streaking, especially in the basic region of the gels. Two…
It is well known that the efficiency of a good thermoelectric material should be optimized with respect to doping concentration. However, much less attention has been paid to the optimization of the dopant's energy level. Thermoelectric…
Considering the density-density correlation function of a concentrated polymer solution with multicomponent solvent we find a phase transition due to the heterogeneity of excluded volume constant. This new phase transition implies a strong…
Implicit electron-density solvation models based on joint density-functional theory offer a computationally efficient solution to the problem of calculating thermodynamic quantities of solvated systems from firstprinciples quantum…
Filters whose porosity decreases with depth are often more efficient at removing solute from a fluid than filters with a uniform porosity. We investigate this phenomenon via an extension of homogenization theory that accounts for a…
In this thesis we investigate high throughput computational methods for processing large quantities of data collected from synchrotrons and their application to spectral analysis of powder diffraction data. We also present the main product…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
One-atom-thick crystals are impermeable to atoms and molecules, but hydrogen ions (thermal protons) penetrate through them. We show that monolayers of graphene and boron nitride can be used to separate hydrogen ion isotopes. Employing…
A general method of separating isotopes by centrifuging dissolved chemical compounds in a liquid solution is introduced. This technique can be applied to almost all elements and leads to large separation factors. The method has been…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…