Browsing by Subject "Biophysics"
Now showing items 1-20 of 83
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Accelerating self-consistent field convergence with the augmented Roothaan-Hall energy function.
(J Chem Phys, 2010-02-07)Based on Pulay's direct inversion iterative subspace (DIIS) approach, we present a method to accelerate self-consistent field (SCF) convergence. In this method, the quadratic augmented Roothaan-Hall (ARH) energy function, ... -
An Asymptotic Model of Electroporation-Mediated Molecular Delivery in Skeletal Muscle Tissue
(2014)Electroporation is a biological cell's natural reaction to strong electric fields, where transient pores are created in the cell membrane. While electroporation holds promise of being a safe and effective tool for enhancing ... -
Analysis and Redesign of Protein-Protein Interactions: A Hotspot-Centric View
(2010)<p>One of the most significant discoveries from mutational analysis of protein interfaces is that often a large percentage of interface residues negligibly perturb the binding energy upon mutation, while residues in a few ... -
Applications of Photoemission Electron Microscopy to Melanin and Melanosomes
(2011)Melanin is a biological pigment that is ubiquitous in nature and generally produced within melanosomes, specialized organelles. Typically, melanin is categorized into two distinct classes, based on color and molecular precursor: ... -
Aqueous Desolvation and Molecular Recognition: Experimental and Computational Studies of a Novel Host-Guest System Based on Cucurbit[7]uril
(2012)Molecular recognition is arguably the most elementary physical process essential for life that arises at the molecular scale. Molecular recognition drives events across virtually all length scales, from the folding of proteins ... -
Atomic Basis of Coordination, Force Generation, and Translocation in Ring ATPases
(2021)Many vital biological tasks, such as protein degradation, DNA strand separation, and viral DNA packaging are performed by ring NTPase assemblies. These assemblies harvest energy from NTP binding and hydrolysis in order to ... -
B-cyclin/CDK Regulation of Mitotic Spindle Assembly through Phosphorylation of Kinesin-5 Motors in the Budding Yeast, <italic>Saccharomyces cerevisiae</italic>
(2012)Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle and entry into mitosis, the full complement of relevant CDK targets has not been identified. It has previously ... -
Biological Charge Transfer in Redox Regulation and Signaling
(2020)Biological signaling via DNA-mediated charge transfer between high-potential [4Fe4S]2+/3+ clusters is widely discussed in the literature. Recently, it was proposed that for DNA replication on the lagging strand, primer handover ... -
Biophysical Investigation of Cell Oscillations and Cell Ingression in Tissue Dynamics
(2011)Embryonic development involves a precisely orchestrated interplay between gene expression, tissue movement and cell-shape changes. Using time-lapsed <italic>in vivo</italic> confocal microscopy we investigate the time-dependence ... -
Clearly Camouflaged Crustaceans: The Physical Basis of Transparency in Hyperiid Amphipods and Anemone Shrimp
(2017)This dissertation research focused on the ways in which clear crustaceans with complex bodies (i.e. with hard cuticles, thick muscles, and other internal organs) maintain transparency across their entire body volume. I ... -
Combined Computational, Experimental, and Assay-Development Studies of Protein:Protein and Protein:Small Molecule Complexes, with Applications to the Inhibition of Enzymes and Protein:Protein Interactions
(2019)Despite the best efforts of both academia and the pharma industry, most non-resectable cancers remain uncurable and lethal. The world health organization (WHO) believes cancer to be the second leading cause of death worldwide, ... -
Computational Protein Design with Ensembles, Flexibility and Mathematical Guarantees, and its Application to Drug Resistance Prediction, and Antibody Design
(2015-01-01)Proteins are involved in all of life's processes and are also responsible for many diseases. Thus, engineering proteins to perform new tasks could revolutionize many areas of biomedical research. One promising technique ... -
Describing the Statistical Conformation of Highly Flexible Proteins by Small-Angle X-ray Scattering
(2014)Small-angle X-ray scattering (SAXS) is a biophysical technique that allows one to study the statistical conformation of a biopolymer in solution. The two-dimensional data obtained from SAXS is a low-resolution probe of the ... -
Design and Characterization of Protein-Based Building Blocks for Self-Assembled Nano-Structured Biomaterials
(2011)This study is focused on designing and characterizing protein-based building blocks in order to construct self-assembled nano-structured biomaterials. In detail, this research aims to: (1) investigate a new class of proteins ... -
Design Principles and Coupling of Biological Oscillators
(2015)One of the main challenges that biological oscillators face at the cellular level is maintaining coherence in the presence of molecular noise. Mechanisms of noise resistance have been proposed, however the findings are sometimes ... -
Determination of Biomolecular Interdomain Motions using Nuclear Magnetic Resonance
(2016)Biological macromolecules can rearrange interdomain orientations when binding to various partners. Interdomain dynamics serve as a molecular mechanism to guide the transitions between orientations. However, our understanding ... -
Developing Hybrid Material Interfaces for Microcontact Printing and Molecular Recognition
(2012)Monomolecular hybrid organic-inorganic interfaces provide opportunities for applications in fields ranging from sensors to electronics. In this thesis, we report our efforts towards (1) developing a universal method for ... -
Development and Application of a quantitative Mass spectrometry based Platform for Thermodynamic Analysis of Protein interaction Networks
(2013)The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions ... -
Development of Tunable Molecular Tension Sensors to Visualize Vinculin Loading and Detect Mechanosensitive Protein Recruitment to Focal Adhesions
(2018)Mechanical forces are potent drivers of many biological processes. The form and function of many tissues depends on cells receiving the proper mechanical signals either from neighboring cells or from the underlying matrix. ... -
DNA Conformational Equilibria in Replication Fidelity
(2019)All organisms must accurately replicate their genomic DNA in order to transmit genetic information from generation to generation. The cognate Watson-Crick base pairs (dA•dT, dG•dC) adopt near identical ‘Watson-Crick geometry’ ...
