The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

Crack tip stress study for elastic-perfectly plastic materials with some applications

The problems of plasticity and non-linear fracture mechanics have been generally recognized as the most difficult problems of solid mechanics. The present dissertation is devoted to some problems on the intersection of both plasticity and non-linear fracture mechanics. The crack tip is responsible for the crack growth and therefore is the focus of fracture science. The problem of crack has been studied by an army of outstanding scholars and engineers in this century, but has not, as yet, been solved for many important practical situations. The aim of this investigation is to provide an analytical solution to the problem of plasticity at the crack tip for elastic-perfectly plastic materials and to apply the solution to a classical problem of the mechanics of composite materials.^ In this work, the stresses inside the plastic region near the crack tip in a composite material made of two different elastic-perfectly plastic materials are studied. The problems of an interface crack, a crack impinging an interface at the right angle and at arbitrary angles are examined. The constituent materials are assumed to obey the Huber-Mises yielding condition criterion. The theory of slip lines for plane strain is utilized. For the particular homogeneous case these problems have two solutions: the continuous solution found earlier by Prandtl and modified by Hill and Sokolovsky, and the discontinuous solution found later by Cherepanov. The same type of solutions were discovered in the inhomogeneous problems of the present study. Some reasons to prefer the discontinuous solution are provided. The method is also applied to the analysis of a contact problem and a push-in/pull-out problem to determine the critical load for plasticity in these classical problems of the mechanics of composite materials.^ The results of this dissertation published in three journal articles (two of which are under revision) will also be presented in the Invited Lecture at the 7$\rm\sp{th}$ International Conference on Plasticity (Cancun, Mexico, January 1999). ^

Quantifying protein folding pathways

A deep understanding of the proteins folding dynamics can be get quantifying folding landscape by calculating how the number of microscopic configurations (entropy) varies with the energy of the chain, Ω=Ω(E). Because of the incredibly large number of microstates available to a protein, direct enumeration of Ω(E) is not possible on realistic computer simulations. An estimate of Ω(E) can be obtained by use of a combination of statistical mechanics and thermodynamics. By combining different definitions of entropy that are valid for a system whose probability for occupying a state is given by the canonical Boltzmann probability, computers allow the determination of Ω(E). ^ The energy landscapes of two similar, but not identical model proteins were studied. One protein contains no kinetic tracks. Results show a smooth funnel for the folding landscape. That allows the contour determination of the folding funnel. Also it was presented results for the folding landscape for a modified protein with kinetic traps. Final results show that the computational approach is able to distinguish and explore regions of the folding landscape that are due to kinetic traps from the native state folding funnel.^

Statistical analysis and optimal classification of blood cell populations using Gaussian distributions

This dissertation develops a new figure of merit to measure the similarity (or dissimilarity) of Gaussian distributions through a novel concept that relates the Fisher distance to the percentage of data overlap. The derivations are expanded to provide a generalized mathematical platform for determining an optimal separating boundary of Gaussian distributions in multiple dimensions. Real-world data used for implementation and in carrying out feasibility studies were provided by Beckman-Coulter. It is noted that although the data used is flow cytometric in nature, the mathematics are general in their derivation to include other types of data as long as their statistical behavior approximate Gaussian distributions. ^ Because this new figure of merit is heavily based on the statistical nature of the data, a new filtering technique is introduced to accommodate for the accumulation process involved with histogram data. When data is accumulated into a frequency histogram, the data is inherently smoothed in a linear fashion, since an averaging effect is taking place as the histogram is generated. This new filtering scheme addresses data that is accumulated in the uneven resolution of the channels of the frequency histogram. ^ The qualitative interpretation of flow cytometric data is currently a time consuming and imprecise method for evaluating histogram data. This method offers a broader spectrum of capabilities in the analysis of histograms, since the figure of merit derived in this dissertation integrates within its mathematics both a measure of similarity and the percentage of overlap between the distributions under analysis. ^