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Full-Text Articles in Computational Chemistry
Deciphering Chemomechanical Couplings In Proteins Using Molecular Dynamics And Enhanced Sampling Techniques, Matthew Brownd
Deciphering Chemomechanical Couplings In Proteins Using Molecular Dynamics And Enhanced Sampling Techniques, Matthew Brownd
Graduate Theses and Dissertations
Proteins function through a complex interplay between chemical interactions and mechanical motions across multiple spatial and temporal scales. Understanding how ligand binding, conformational dynamics, and structural flexibility collectively regulate protein function remains one of the central challenges in molecular biophysics. This dissertation presents a computational investigation into chemomechanical coupling in three distinct classes of biomolecular systems using all-atom molecular dynamics (MD) simulations and enhanced sampling methods, with particular emphasis on free-energy calculations and long-timescale conformational analysis. The first part of this work focuses on ligand binding in hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which regulate rhythmic electrical activity in the heart …
First-Principles Study Of Doping Effects On Ferroelectricity And On Rashba Spin Splitting, Zegnet Yimer Muhammed
First-Principles Study Of Doping Effects On Ferroelectricity And On Rashba Spin Splitting, Zegnet Yimer Muhammed
Graduate Theses and Dissertations
In this dissertation, we have thoroughly studied the effect of chemical and charge dopingon ferroelectrics (PbTiO3 and BaTiO3) and Rashba type semiconductor (BiTeI). In the first project, We investigate the polar instability and soft modes in electron-doped PbTiO3 using linear-response density functional calculations. Because, metallicity and ferroelectric-like polar distortion are mutually non-compatible, and their coexistence in the same system is an intriguing subject of fundamental interest in the field of structure phase transition. However, it is unclear what mechanism may extend the limit of metallicity that allows polar distortion. We find that ferroelectric instability can remarkably sustain up to an …
Using Molecular Dynamics Simulations To Decipher Mechanistic Details Of Biomolecular Processes Of Biology And Biotechnology Oriented Applications, Adithya Polasa
Graduate Theses and Dissertations
Researchers in chemistry and biology often utilize computer simulations, in conjunction with experimental data, to model and predict the structures, energies, kinetics, processes, and functions of the systems that are their focus of study, ranging from single molecules to whole viruses. Here, we use molecular dynamics (MD) techniques to gain a deeper understanding of biomolecular processes in biology and biotechnology-oriented applications. Using a mixture of equilibrium and non-equilibrium MD simulations, this work describes the insertion process of YidC at the atomic level. In order to better comprehend the insertion process, several docking models of YidC-Pf3 in the lipid bilayer were …
Understanding Interfacial Reactions Initiating On Electrode Materials For Energy Storage Technologies, Jingnan Li
Understanding Interfacial Reactions Initiating On Electrode Materials For Energy Storage Technologies, Jingnan Li
Graduate Theses and Dissertations
Since the first generation of lithium-ion batteries featured lithium cobalt oxide cathode and carbon anode commercialized in the 1990s, the high-capacity materials with lower cost are in demand to further increase the battery energy density. Lithium metal and silicon anode are promising high-capacity anode materials to achieve next-generation lithium batteries. However, both the materials actively react in electrolytes and suffer from dramatic volume change. Therefore, a reliable passivation layer at the electrolyte/electrode interphase (i.e., solid electrolyte interphase, or “SEI”) is required to support the long-term cycling of both materials. Cetrimonium hydro fluoride (CTAHF2) has been proposed and synthesized as an …