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.