Search results | J. Murrey Atkins Library

Title: DO DYNAMIC ALLOSTERIC EFFECTS OCCUR IN IGG4 ANTIBODIES?
Author: Baker, Lonnie
Date Created: 2020
Subjects--Topical: Bioinformatics, Biophysics
Description: Antibodies are large, multi-chain proteins which play a critical roll in the func-tioning of vertebrate immune systems. Immune effector cells which are responsiblefor the destruction of foreign antigens do not randomly target molecules but rely on...

Title: ELUCIDATING FUNCTIONAL MECHANISMS IN PROTEINS USING THE DISTANCE CONSTRAINT MODEL
Author: Singer, Christopher
Date Created: 2019
Subjects--Topical: Bioinformatics, Biophysics, Physics
Description: Protein thermodynamics has been shown to be insightful and illuminating to the functional mechanisms behind biological function. By characterizing proteins and protein families according to their enthalpy and entropy we can make inferences to the ...

Title: ESSENTIAL DYNAMICS OF PROTEINS USING GEOMETRICAL SIMULATIONS AND SUBSPACE ANALYSIS
Author: David, Charles
Date Created: 2012
Subjects--Topical: Physics, Bioinformatics, Biophysics
Description: Essential dynamics is the application of principal component analysis to a dynamic trajectory derived from a simulation protocol in order to extract biologically relevant information contained in the high dimensional data. In this work, we apply t...

Title: Elucidating Dynamic Mechanisms for Extended Spectrum Antibiotic Resistance in Class A Beta-Lactamase through Machine Learning on Molecular Dynamics Simulations
Author: Avery, Christopher
Date Created: 2019
Subjects--Topical: Biophysics, Physics
Description: Beta-lactamase is a protein which is produced in bacteria and is a primary cause of antibiotic resistance to Beta Lactam antibiotics. Beta Lactams are among the most common types of antibiotics (including penicillin) and thus understanding the res...

Title: Hybrid solvation models for electrostatic interactions in molecular dynamics simulations of ionic solvent
Author: Xiang, Ming
Date Created: 2012
Subjects--Topical: Mathematics, Biochemistry, Biophysics
Description: In this dissertation, we mainly discuss the image approximation methods to the reaction field and their applications to electrostatic interactions in molecular dynamics simulations. The Poisson-Boltzman (PB) equation, a three-dimensional second or...

Title: MODELING, SIMULATION AND ANALYSIS OF THE REACTION FIELD FOR ELECTROSTATIC INTERACTIONS IN AQUEOUS SOLUTION
Author: SONG, WEI
Date Created: 2013
Subjects--Topical: Computer science, Bioinformatics, Biophysics
Description: How to deal with the long-range electrostatic interactions theoretically and computationally has been well studied due to their importance in biological processes and time consuming summations in computer simulations. The main focus of our researc...

Title: New Algorithms for Protein Structure Analysis: From Nonparametric Density Estimation to Characterization of Molecular Volume Spatial Distributions
Author: Farmer, Jenny
Date Created: 2018
Subjects--Topical: Bioinformatics, Biophysics, Physics
Description: The Flexibility and Stability Test (FAST) is a C++ class library designed in the early 2000’s to execute free energy decomposition and reconstitution operations applied to protein structures. The library has been substantially expanded to include ...

Title: PREPARATION AND VISUALIZATION OF INDIVIDUAL ACTIN FILAMENTS USING ATOMIC FORCE MICROSCOPY FOR THE STUDY OF ACTIN/DNA HYDROGEL COMPLEXES
Author: Kennedy, Joshua
Date Created: 2019
Subjects--Topical: Physics, Biophysics, Biomedical engineering
Description: A protocol of sample preparation for the visualization of single actin filaments at the nanoscale using atomic force microscopy for use in studies of engineered actin/DNA conjugated hydrogel complexes was developed. Hydrogels are cross-linked netw...

Title: PROTEIN-PROTEIN INTERACTION OF PAI-H19Y MUTANT OF THE SLEEPING BEAUTY TRANSPOSASE
Author: Yan, Chenbo
Date Created: 2020
Subjects--Topical: Biophysics, DNA
Description: Due to the substantial interest in developing transposon technology for gene delivery and gene therapy, the Sleeping Beauty (SB) transposon system, the most active transposon in the vertebrate species, has been extensively studied. The SB transpos...

Title: REGULATION OF ACTOMYOSIN ATPASE
Author: Ge, Jinghua
Date Created: 2016
Subjects--Topical: Optics, Physics, Biophysics
Description: Myosin is a molecular motor that converts chemical energy to mechanical energy, thus generating force and movement in muscles and cells. Myosin interacts with two ligands, ATP (fuel) and actin filaments (motor’s tracks). Actomyosin interaction is ...

Title: Role of Intramolecular Electrostatic Interactions on the Kinetics of Human Cardiac Myosin β-Isoform
Author: Gargey, Akhil
Date Created: 2021
Subjects--Topical: Molecular biology, Biochemistry, Biophysics
Description: Human cardiac myosin has two isoforms, α and β, sharing significant sequence similarity, but different in kinetics. Small differences in the sequence are responsible for distinct local inter-residue interactions within α and β isoforms, leading to...

Title: STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE H19Y MUTATED PRIMARY DNA RECOGNITION SUBDOMAIN OF SLEEPING BEAUTY TRANSPOSASE
Author: Leighton, Gage
Date Created: 2017
Subjects--Topical: Physics, Chemistry, Physical and theoretical, Biophysics
Description: The Sleeping Beauty transposon system, consisting of the transposon DNA and the transposase enzyme, is a member of the Tc1/mariner family of DNA transposons. Although it is an important tool in genetic applications and has been adapted for human g...

Title: SUBSURFACE THERMAL COAGULATION OF TISSUES USING NEAR INFRARED LASERS
Author: Chang, Chun-Hung
Date Created: 2017
Subjects--Topical: Optics, Biophysics, Biomedical engineering
Description: Noninvasive laser therapy is currently limited primarily to cosmetic dermatological applications such as skin resurfacing, hair removal, tattoo removal and treatment of vascular birthmarks. In order to expand applications of noninvasive laser ther...

Title: THE EFFECT OF TARGET SECONDARY STRUCTURE ON MICROARRAY DATA QUALITY
Author: Ratushna, Vladyslava
Date Created: 2010
Subjects--Topical: Bioinformatics, Biophysics
Description: DNA microarrays have become an invaluable high throughput biotechnology method, which allows a parallel investigation of thousands of cellular events in a single experiment. The principle behind the technology is very simple: fluorescently labeled...

Title: THERMODYNAMIC AND MECHANICAL EFFECTS OF DISULFIDE BONDS IN CXCL7 CHEMOKINE
Author: Singer, Christopher
Date Created: 2015
Subjects--Topical: Physics, Bioinformatics, Biophysics
Description: Chemokines are a family of signaling proteins mainly responsible for the chemotaxis of leukocytes, where their biological activity is modulated by their oligomerization state. Here, the dynamics and thermodynamic stability are characterized in mon...

Title: UNDERSTANDING BIAS IN NEXT-GENERATION SEQUENCING TECHNOLOGIES AND ANALYSES
Author: Price, Adam
Date Created: 2017
Subjects--Topical: Biology, Bioinformatics, Biophysics
Description: The problem of bias resulting from biological and technological sources is one that must be consistently reexamined alongside the development of new technologies and methods of analysis. This dissertation addresses the complexities of bias identif...

Title: Volume Microenvironment Self-Consistent Constraint Theory Applied to Protein Stability Prediction
Author: Johannessen, Nicholas
Date Created: 2021
Subjects--Topical: Biophysics, Physics
Description: Controlling thermodynamic stability is a challenge in protein engineering. Engineering a protein by introducing mutations into its sequence to increase efficacy can destabilize the protein thermodynamically, preventing it from functioning in its i...