Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

THERMAL CHARACTERIZATION OF A GASOLINE TURBOCHARGED DIRECT INJECTION (GTDI) ENGINE UTILIZING LEAN OPERATION AND EXHAUST GAS RECIRCULATION (EGR)

The push for improved fuel economy and reduced emissions has led to great achievements in engine performance and control. These achievements have increased the efficiency and power density of gasoline engines dramatically in the last two decades. With the added power density, thermal management of the engine has become increasingly important. Therefore it is critical to have accurate temperature and heat transfer models as well as data to validate them. With the recent adoption of the 2025 Corporate Average Fuel Economy(CAFE) standard, there has been a push to improve the thermal efficiency of internal combustion engines even further. Lean and dilute combustion regimes along with waste heat recovery systems are being explored as options for improving efficiency. In order to understand how these technologies will impact engine performance and each other, this research sought to analyze the engine from both a 1st law energy balance perspective, as well as from a 2nd law exergy analysis. This research also provided insights into the effects of various parameters on in-cylinder temperatures and heat transfer as well as provides data for validation of other models. It was found that the engine load was the dominant factor for the energy distribution, with higher loads resulting in lower coolant heat transfer and higher brake work and exhaust energy. From an exergy perspective, the exhaust system provided the best waste heat recovery potential due to its significantly higher temperatures compared to the cooling circuit. EGR and lean combustion both resulted in lower combustion chamber and exhaust temperatures; however, in most cases the increased flow rates resulted in a net increase in the energy in the exhaust. The exhaust exergy, on the other hand, was either increased or decreased depending on the location in the exhaust system and the other operating conditions. The effects of dilution from lean operation and EGR were compared using a dilution ratio, and the results showed that lean operation resulted in a larger increase in efficiency than the same amount of dilution with EGR. Finally, a method for identifying fuel spray impingement from piston surface temperature measurements was found. Note: The material contained in this section is planned for submission as part of a journal article and/or conference paper in the future.

Selective Mercury Sequestration from a Silver/Mercury Cyanide Solution

Silver and mercury are both dissolved in cyanide leaching and the mercury co-precipitates with silver during metal recovery. Mercury must then be removed from the silver/mercury amalgam by vaporizing the mercury in a retort, leading to environmental and health hazards. The need for retorting silver can be greatly reduced if mercury is selectively removed from leaching solutions. Theoretical calculations were carried out based on the thermodynamics of the Ag/Hg/CN- system in order to determine possible approaches to either preventing mercury dissolution, or selectively precipitating it without silver loss. Preliminary experiments were then carried out based on these calculations to determine if the reaction would be spontaneous with reasonably fast kinetics. In an attempt to stop mercury from dissolving and leaching the heap leach, the first set of experiments were to determine if selenium and mercury would form a mercury selenide under leaching conditions, lowering the amount of mercury in solution while forming a stable compound. From the results of the synthetic ore experiments with selenium, it was determined that another effect was already suppressing mercury dissolution and the effect of the selenium could not be well analyzed on the small amount of change. The effect dominating the reactions led to the second set of experiments in using silver sulfide as a selective precipitant of mercury. The next experiments were to determine if adding solutions containing mercury cyanide to un-leached silver sulfide would facilitate a precipitation reaction, putting silver in solution and precipitating mercury as mercury sulfide. Counter current flow experiments using the high selenium ore showed a 99.8% removal of mercury from solution. As compared to leaching with only cyanide, about 60% of the silver was removed per pass for the high selenium ore, and around 90% for the high mercury ore. Since silver sulfide is rather expensive to use solely as a mercury precipitant, another compound was sought which could selectively precipitate mercury and leave silver in solution. In looking for a more inexpensive selective precipitant, zinc sulfide was tested. The third set of experiments did show that zinc sulfide (as sphalerite) could be used to selectively precipitate mercury while leaving silver cyanide in solution. Parameters such as particle size, reduction potential, and amount of oxidation of the sphalerite were tested. Batch experiments worked well, showing 99.8% mercury removal with only ≈1% silver loss (starting with 930 ppb mercury, 300 ppb silver) at one hour. A continual flow process would work better for industrial applications, which was demonstrated with the filter funnel set up. Funnels with filter paper and sphalerite tested showed good mercury removal (from 31 ppb mercury and 333 ppb silver with a 87% mercury removal and 7% silver loss through one funnel). A counter current flow set up showed 100% mercury removal and under 0.1% silver loss starting with 704 ppb silver and 922 ppb mercury. The resulting sphalerite coated with mercury sulfide was also shown to be stable (not releasing mercury) under leaching tests. Use of sphalerite could be easily implemented through such means as sphalerite impregnated filter paper placed in currently existing processes. In summary, this work focuses on preventing mercury from following silver through the leaching circuit. Currently the only possible means of removing mercury is by retort, creating possible health hazards in the distillation process and in transportation and storage of the final mercury waste product. Preventing mercury from following silver in the earlier stages of the leaching process will greatly reduce the risk of mercury spills, human exposure to mercury, and possible environmental disasters. This will save mining companies millions of dollars from mercury handling and storage, projects to clean up spilled mercury, and will result in better health for those living near and working in the mines.