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. ^

Development of surface flaw thresholds for pre-cured fiber reinforced polymer and groove size tolerance for near surface mounted fiber reinforced polymer retrofit systems

Since the introduction of fiber reinforced polymers (FRP) for the repair and retrofit of concrete structures in the 1980’s, considerable research has been devoted to the feasibility of their application and predictive modeling of their performance. However, the effects of flaws present in the constitutive components and the practices in substrate preparation and treatment have not yet been thoroughly studied. This research aims at investigating the effect of surface preparation and treatment for the pre-cured FRP systems and the groove size tolerance for near surface mounted (NSM) FRP systems; and to set thresholds for guaranteed system performance. This study was conducted as part of the National Cooperative Highway Research Program (NCHRP) Project 10-59B to develop construction specifications and process control manual for repair and retrofit of concrete structures using bonded FRP systems. The research included both analytical and experimental components. The experimental program for the pre-cured FRP systems consisted of a total of twenty-four (24) reinforced concrete (RC) T-beams with various surface preparation parameters and surface flaws, including roughness, flatness, voids and cracks (cuts). For the NSM FRP systems, a total of twelve (12) additional RC T-beams were tested with different grooves sizes for FRP bars and strips. The analytical program included developing an elaborate nonlinear finite element model using the general purpose software ANSYS. The bond interface between FRP and concrete was modeled by a series of nonlinear springs. The model was validated against test data from the present study as well as those available from the literature. The model was subsequently used to extend the experimental range of parameters for surface flatness in pre-cured FRP systems and for groove size study in the NSM FRP systems. Test results, confirmed by further analyses, indicated that contrary to the general belief in the industry, the impact of surface roughness on the global performance of pre-cured FRP systems was negligible. The study also verified that threshold limits set for wet lay-up FRP systems can be extended to pre-cured systems. The study showed that larger surface voids and cracks (cuts) can adversely impact both the strength and ductility of pre-cured FRP systems. On the other hand, frequency (or spacing) of surface cracks (cuts) may only affect system ductility rather than its strength. Finally, within the range studied, groove size tolerance of ±1/8 in. does not appear to have an adverse effect on the performance of NSM FRP systems.

Customization of the design of antenna using genetic algorithm and finite-difference time-domain technique

Antenna design is an iterative process in which structures are analyzed and changed to comply with certain performance parameters required. The classic approach starts with analyzing a "known" structure, obtaining the value of its performance parameter and changing this structure until the "target" value is achieved. This process relies on having an initial structure, which follows some known or "intuitive" patterns already familiar to the designer. The purpose of this research was to develop a method of designing UWB antennas. What is new in this proposal is that the design process is reversed: the designer will start with the target performance parameter and obtain a structure as the result of the design process. This method provided a new way to replicate and optimize existing performance parameters. The base of the method was the use of a Genetic Algorithm (GA) adapted to the format of the chromosome that will be evaluated by the Electromagnetic (EM) solver. For the electromagnetic study we used XFDTD™ program, based in the Finite-Difference Time-Domain technique. The programming portion of the method was created under the MatLab environment, which serves as the interface for converting chromosomes, file formats and transferring of data between the XFDTD™ and GA. A high level of customization had to be written into the code to work with the specific files generated by the XFDTD™ program. Two types of cost functions were evaluated; the first one seeking broadband performance within the UWB band, and the second one searching for curve replication of a reference geometry. The performance of the method was evaluated considering the speed provided by the computer resources used. Balance between accuracy, data file size and speed of execution was achieved by defining parameters in the GA code as well as changing the internal parameters of the XFDTD™ projects. The results showed that the GA produced geometries that were analyzed by the XFDTD™ program and changed following the search criteria until reaching the target value of the cost function. Results also showed how the parameters can change the search criteria and influence the running of the code to provide a variety of geometries.

Regional processes in mangrove ecosystems: spatial scaling relationships, biomass, and turnover rates following catastrophic disturbance

Physiological processes and local-scale structural dynamics of mangroves are relatively well studied. Regional-scale processes, however, are not as well understood. Here we provide long-term data on trends in structure and forest turnover at a large scale, following hurricane damage in mangrove ecosystems of South Florida, U.S.A. Twelve mangrove vegetation plots were monitored at periodic intervals, between October 1992 and March 2005. Mangrove forests of this region are defined by a −1.5 scaling relationship between mean stem diameter and stem density, mirroring self-thinning theory for mono-specific stands. This relationship is reflected in tree size frequency scaling exponents which, through time, have exhibited trends toward a community average that is indicative of full spatial resource utilization. These trends, together with an asymptotic standing biomass accumulation, indicate that coastal mangrove ecosystems do adhere to size-structured organizing principles as described for upland tree communities. Regenerative dynamics are different between areas inside and outside of the primary wind-path of Hurricane Andrew which occurred in 1992. Forest dynamic turnover rates, however, are steady through time. This suggests that ecological, more-so than structural factors, control forest productivity. In agreement, the relative mean rate of biomass growth exhibits an inverse relationship with the seasonal range of porewater salinities. The ecosystem average in forest scaling relationships may provide a useful investigative tool of mangrove community biomass relationships, as well as offer a robust indicator of general ecosystem health for use in mangrove forest ecosystem management and restoration.

Ontogenetic Scaling of Poison Glands in Dendrobates Pumilio

The relationship between granular (poison) gland size and density was examined in an ontogenetic series of the strawberry dart-poison frog, Dendrobates pumilio. Specimens used in this study were collected from the La Selva Biological Station in northeastern Costa Rica. Patches of skin from the dorsal surface of seven frogs, ranging in size from 11 to 23 mm snout-vent length (SVL), were fixed and embedded in paraffin for histological sectioning. Poison gland size and density were quantified microscopically in these sections. Poison glands are uniformly distributed across the skin and mean poison gland diameter increases at a rate faster than snout-vent length from 42.5 at SVL 11mm to 120.0 at SVL 23 mm. Conversely, gland density decreases with body size from 71.9 glands/mm2 to 33.2 glands/mm2 • Due to the positive allometric growth of the poison glands, the percentage of skin surface occupied by poison glands increases from 10.1-22.1% in small frogs (SVL<18 >mm) to 50.0-65.2% in large frogs (SVL>19MM), resulting in more toxin per mm2 in the larger animals. The largest increase in toxicity is correlated temporally with the onset of sexual maturity rather than with changes in aposematic coloring.

Development of Surface Flaw Thresholds for Pre-Cured Fiber Reinforced Polymer and Groove Size Tolerance for Near Surface Mounted Fiber Reinforced Polymer Retrofit Systems

Since the introduction of fiber reinforced polymers (FRP) for the repair and retrofit of concrete structures in the 1980’s, considerable research has been devoted to the feasibility of their application and predictive modeling of their performance. However, the effects of flaws present in the constitutive components and the practices in substrate preparation and treatment have not yet been thoroughly studied. This research aims at investigating the effect of surface preparation and treatment for the pre-cured FRP systems and the groove size tolerance for near surface mounted (NSM) FRP systems; and to set thresholds for guaranteed system performance. The research included both analytical and experimental components. The experimental program for the pre-cured FRP systems consisted of a total of twenty-four (24) reinforced concrete (RC) T-beams with various surface preparation parameters and surface flaws, including roughness, flatness, voids and cracks (cuts). For the NSM FRP systems, a total of twelve (12) additional RC T-beams were tested with different grooves sizes for FRP bars and strips. The analytical program included developing an elaborate nonlinear finite element model using the general purpose software ANSYS. The model was subsequently used to extend the experimental range of parameters for surface flatness in pre-cured FRP systems, and for groove size study in the NSM FRP systems. Test results, confirmed by further analyses, indicated that contrary to the general belief in the industry, the impact of surface roughness on the global performance of pre-cured FRP systems was negligible. The study also verified that threshold limits set for wet lay-up FRP systems can be extended to pre-cured systems. The study showed that larger surface voids and cracks (cuts) can adversely impact both the strength and ductility of pre-cured FRP systems. On the other hand, frequency (or spacing) of surface cracks (cuts) may only affect system ductility rather than its strength. Finally, within the range studied, groove size tolerance of +1/8 in. does not appear to have an adverse effect on the performance of NSM FRP systems.

Meshfree Method for Prediction of Thermal Properties of Porous Ceramic Materials

In the presented thesis work, meshfree method with distance fields is applied to create a novel computational approach which enables inclusion of the realistic geometric models of the microstructure and liberates Finite Element Analysis(FEA) from thedependance on and limitations of meshing of fine microstructural feature such as splats and porosity.Manufacturing processes of ceramics produce materials with complex porosity microstructure.Geometry of pores, their size and location substantially affect macro scale physical properties of the material. Complex structure and geometry of the pores severely limit application of modern Finite Element Analysis methods because they require construction of spatial grids (meshes) that conform to the geometric shape of the structure. As a result, there are virtually no effective tools available for predicting overall mechanical and thermal properties of porous materials based on their microstructure. This thesis is a separate handling and controls of geometric and physical computational models that are seamlessly combined at solution run time. Using the proposedapproach we will determine the effective thermal conductivity tensor of real porous ceramic materials featuring both isotropic and anisotropic thermal properties. This work involved development and implementation of numerical algorithms, data structure, and software.