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Equilibrium And Active Self-Assembly And Collective Properties Of Network-Based Biomaterials, Lauren Melcher
Equilibrium And Active Self-Assembly And Collective Properties Of Network-Based Biomaterials, Lauren Melcher
Theses
Biological systems have the unique ability to self-organize, respond to environmental stimuli, and generate autonomous motion and work. The fields of biomaterials and synthetic biology seek to recapitulate these remarkable properties of biological systems in in-vitro reconstitutions of biological systems, and in abiotic or biotic-abiotic hybrid materials to better understand the underlying rules of life and to predict the design principles of biomimetic smart materials. Motivated by this, we create bottom-up mathematical models, rooted in experiments, of network-based synthetic and biological materials. These encompass two-dimensional colloidal networks connected by rhythmic crosslinkers, and three-dimensional biopolymer networks assembled via depletion interactions, physical …
Functional Evolutionary Adaptation Of Binding Dynamics In The Sars-Cov-2/Ace2 Interface From Bats To Humans, Madhusudan Rajendran
Functional Evolutionary Adaptation Of Binding Dynamics In The Sars-Cov-2/Ace2 Interface From Bats To Humans, Madhusudan Rajendran
Theses
The COVID-19 pandemic highlights the substantial public health, economic, and societal consequences of virus spillover from a wildlife reservoir. Widespread human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also presents a new set of challenges when considering viral spillover from people to naïve wildlife and other animal populations. Here, we used molecular dynamic (MD) simulations to understand the transmission of the SARS-CoV-2 virus from bats to humans and investigate the evolution of the various human variants. More specifically, we used MD simulations to understand the atomic fluctuation dampening at the receptor-binding domain (RBD)/ angiotensin-converting enzyme 2 (ACE2) interface …
Designing Fenicr(Cocu) High Entropy Alloys Using Molecular Dynamics: A Study Of The Enhanced Mechanical Properties Of A Novel Group Of Composites, Leander I. Held
Designing Fenicr(Cocu) High Entropy Alloys Using Molecular Dynamics: A Study Of The Enhanced Mechanical Properties Of A Novel Group Of Composites, Leander I. Held
Theses
High-Entropy Alloys (HEAs) are an emergent class of crystalline materials have exhibited unique mechanical properties and high-temperature functionality. Their unusual composition, having multiple principal elements in contrast to common alloys that use one principal element, results in a variety of useful, and in many cases unexpected characteristics. This project, in partnership with experimentalists at the Idaho National Laboratory and machine learning scientists at the University of Utah, explores these characteristics and composition-property relationships in HEAs. Utilizing Molecular Dynamics (MD) simulations, three HEAs, namely FeNiCr, FeNiCrCo, and FeNiCrCoCu, are studied in detail. The radial distribution function (RDF) and tensile strength (TS) …
Effect Of Turbostratic Orientations And Confined Fluid On Mechanical Strength Of Bi-Layer Graphene: A Molecular Dynamics Study, Nil B. Dhankecha
Effect Of Turbostratic Orientations And Confined Fluid On Mechanical Strength Of Bi-Layer Graphene: A Molecular Dynamics Study, Nil B. Dhankecha
Theses
The rise of graphene as a reinforcement material in the last decade has been exponential owing to its superior mechanical properties. This one atom thick 2D material is applicable in many industries related to nanomechanical, nanoelectronics and optical devices. Despite its strength and superior properties, single-layer graphene tends to be unstable in a free-standing form. This led to active use of bi-layer and multilayered graphene in many of the above-stated applications. Though properties of single-layer graphene have been extensively investigated both computationally as well as experimentally for over a decade, bilayer graphene and its turbostratic form are still under research. …
Event-Driven Molecular Dynamics Simulations Of Protein Mixtures, Marek Cyran
Event-Driven Molecular Dynamics Simulations Of Protein Mixtures, Marek Cyran
Theses
The structure of liquids is central to their thermodynamic properties and is described in a probabilistic manner. The structure is a consequence of the forces between the molecules and may be investigated with the use of many techniques. One of these techniques is the use of computer simulation, and in particular the techniques are called Monte Carlo Statistical Thermodynamic simulation, and Molecular Dynamics. In this thesis we construct a program that is capable of carrying out Event-Driven Molecular Dynamics simulation of mixtures of particles that have stepwise constant pair potential energies. We have implemented our simulation for the case of …
Quantitative Evaluation Of Substituent Effects On Stabilization Energies Of Strained And Unsaturated Molecules, Tyler Arthur Stevenson
Quantitative Evaluation Of Substituent Effects On Stabilization Energies Of Strained And Unsaturated Molecules, Tyler Arthur Stevenson
Theses
Thermodynamic stabilization energies are presented for a series of monosubstituted vinyl, cyclopropyl, ethynyl, and phenyl compounds. The energies are calculated using ab initio molecular orbital calculations at the 4-31G level, and also with published experimental heat of formation data. Correlation analyses are then attempted with the dual substituent parameter approach with the stabilization energies. The analyses are also attempted with a triple-parameter approach using Topsom's theoretically calculated X, F, and Ro constants. Among the findings are the facts that π-donating substituents correlate well, while π-accepting substituents do not. Indications of the relative sensitivities of hydrocarbon frameworks to substituent electrostatic and …