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. ^

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.^

An exergy based engineering and economic analysis of sustainable building

To achieve the goal of sustainable development, the building energy system was evaluated from both the first and second law of thermodynamics point of view. The relationship between exergy destruction and sustainable development were discussed at first, followed by the description of the resource abundance model, the life cycle analysis model and the economic investment effectiveness model. By combining the forgoing models, a new sustainable index was proposed. Several green building case studies in U.S. and China were presented. The influences of building function, geographic location, climate pattern, the regional energy structure, and the technology improvement potential of renewable energy in the future were discussed. The building’s envelope, HVAC system, on-site renewable energy system life cycle analysis from energy, exergy, environmental and economic perspective were compared. It was found that climate pattern had a dramatic influence on the life cycle investment effectiveness of the building envelope. The building HVAC system energy performance was much better than its exergy performance. To further increase the exergy efficiency, renewable energy rather than fossil fuel should be used as the primary energy. A building life cycle cost and exergy consumption regression model was set up. The optimal building insulation level could be affected by either cost minimization or exergy consumption minimization approach. The exergy approach would cause better insulation than cost approach. The influence of energy price on the system selection strategy was discussed. Two photovoltaics (PV) systems—stand alone and grid tied system were compared by the life cycle assessment method. The superiority of the latter one was quite obvious. The analysis also showed that during its life span PV technology was less attractive economically because the electricity price in U.S. and China did not fully reflect the environmental burden associated with it. However if future energy price surges and PV system cost reductions were considered, the technology could be very promising for sustainable buildings in the future.

Structural Characterization of Metal Hydrides for Energy Applications

Hydrogen can be an unlimited source of clean energy for future because of its very high energy density compared to the conventional fuels like gasoline. An efficient and safer way of storing hydrogen is in metals and alloys as hydrides. Light metal hydrides, alanates and borohydrides have very good hydrogen storage capacity, but high operation temperatures hinder their application. Improvement of thermodynamic properties of these hydrides is important for their commercial use as a source of energy. Application of pressure on materials can have influence on their properties favoring hydrogen storage. Hydrogen desorption in many complex hydrides occurs above the transition temperature. Therefore, it is important to study the physical properties of the hydride compounds at ambient and high pressure and/or high temperature conditions, which can assist in the design of suitable storage materials with desired thermodynamic properties. ^ The high pressure-temperature phase diagram, thermal expansion and compressibility have only been evaluated for a limited number of hydrides so far. This situation serves as a main motivation for studying such properties of a number of technologically important hydrides. Focus of this dissertation was on X-ray diffraction and Raman spectroscopy studies of Mg2FeH6, Ca(BH4) 2, Mg(BH4)2, NaBH4, NaAlH4, LiAlH4, LiNH2BH3 and mixture of MgH 2 with AlH3 or Si, at different conditions of pressure and temperature, to obtain their bulk modulus and thermal expansion coefficient. These data are potential source of information regarding inter-atomic forces and also serve as a basis for developing theoretical models. Some high pressure phases were identified for the complex hydrides in this study which may have better hydrogen storage properties than the ambient phase. The results showed that the highly compressible B-H or Al-H bonds and the associated bond disordering under pressure is responsible for phase transitions observed in brorohydrides or alanates. Complex hydrides exhibited very high compressibility suggesting possibility to destabilize them with pressure. With high capacity and favorable thermodynamics, complex hydrides are suitable for reversible storage. Further studies are required to overcome the kinetic barriers in complex hydrides by catalytic addition. A comparative study of the hydride properties with that of the constituting metal, and their inter relationships were carried out with many interesting features.^

An Exergy Based Engineering and Economic Analysis of Sustainable Building

To achieve the goal of sustainable development, the building energy system was evaluated from both the first and second law of thermodynamics point of view. The relationship between exergy destruction and sustainable development were discussed at first, followed by the description of the resource abundance model, the life cycle analysis model and the economic investment effectiveness model. By combining the forgoing models, a new sustainable index was proposed. Several green building case studies in U.S. and China were presented. The influences of building function, geographic location, climate pattern, the regional energy structure, and the technology improvement potential of renewable energy in the future were discussed. The building’s envelope, HVAC system, on-site renewable energy system life cycle analysis from energy, exergy, environmental and economic perspective were compared. It was found that climate pattern had a dramatic influence on the life cycle investment effectiveness of the building envelope. The building HVAC system energy performance was much better than its exergy performance. To further increase the exergy efficiency, renewable energy rather than fossil fuel should be used as the primary energy. A building life cycle cost and exergy consumption regression model was set up. The optimal building insulation level could be affected by either cost minimization or exergy consumption minimization approach. The exergy approach would cause better insulation than cost approach. The influence of energy price on the system selection strategy was discussed. Two photovoltaics (PV) systems – stand alone and grid tied system were compared by the life cycle assessment method. The superiority of the latter one was quite obvious. The analysis also showed that during its life span PV technology was less attractive economically because the electricity price in U.S. and China did not fully reflect the environmental burden associated with it. However if future energy price surges and PV system cost reductions were considered, the technology could be very promising for sustainable buildings in the future.