Biological and Chemical Physics Commons^™

Developing An Unfolding-Incorporated Coarse-Grained Polymer Model For Fibrinogen To Study The Mechanical Behaviour, Vivek Sharma, Poulomi Sadhukhan

Northeast Journal of Complex Systems (NEJCS)

Fibrinogen is a protein found in blood that forms Fibrin polymer network to build a clot during wound healing process when there is a cut in the blood vessel. The fibrin fiber is highly stretchable and shows a complex mechanical properties. The fibrin monomer, Fibrinogen, has a very complex structure which is responsible for its unusual elastic behaviour. In this work, we focus on mechanism of unfolding of D-domain of Fibrinogen, and study its effect in the mechanical behaviour. We develop a coarse-grained (CG) bead-spring model for Fibrinogen which captures the unfolding of folded D-domains along with other necessary structural …

Influence Of Oil Density On Self-Propelled Motion Of Belousov-Zhabotinsky Reaction Droplet, Vivek Bharat Meshram, Anupama Sebastian, Puthiyapurayil Sibeesh, T K Shajahan

Northeast Journal of Complex Systems (NEJCS)

Belousov-Zhabotinsky reaction serves as an example of the nonlinear chemical oscillator in which the reacting substance undergoes sequential oxidation and reduction. A droplet containing the BZ reaction, when placed within the oily environment, can self-propel. In this experimental work, we explore the effect of oil medium density on the BZ reaction droplet dynamics. In an oil medium with lower density, the BZ droplet exhibits higher speed and effective diffusivity but a shorter lifetime. Both the distance and speed of the droplet initially increase with droplet volume. However, beyond a critical volume, the distance decreases while the speed stays constant. Interestingly, …

Predicting Biomolecular Properties And Interactions Using Numerical, Statistical And Machine Learning Methods, Elyssa Sliheet

Mathematics Theses and Dissertations

We investigate machine learning and electrostatic methods to predict biophysical properties of proteins, such as solvation energy and protein ligand binding affinity, for the purpose of drug discovery/development. We focus on the Poisson-Boltzmann model and various high performance computing considerations such as parallelization schemes.

Mathematical Analysis Of Eukaryotic Pericentromere, Puranjan Ghimire

Theses and Dissertations

The centromere is crucial for chromosomal stability and their proper segregation during cell division in eukaryotes. Surrounding the centromere are pericentromeres, made of repetitive DNA elements called pericentromeric repeats, varying from 10 in fission yeast to thousands in humans. These repeats form densely packed heterochromatin, where genes are usually silenced. The silencing mechanism across different pericentromeric repeats remains unclear.

Despite variations in sequence and length, pericentromeric repeats are conserved across eukaryotes, indicating their functional importance. This dissertation presents mathematical models to quantify gene silencing in fission yeast and humans. In fission yeast, my model predicts that silencing occurs only with …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

Emergence, Mechanics, And Development: How Behavior And Geometry Underlie Cowrie Seashell Form, Michael G. Levy, Michael R. Deweese

Biology and Medicine Through Mathematics Conference

No abstract provided.

A Framework Of Multi-Dimensional And Multi-Scale Modeling With Applications, Zilong Li

Doctoral Dissertations

In this dissertation, a framework for multi-dimensional and multi-scale modeling is proposed. The essential idea is based on oriented space curves, which can be represented as a 3D slender object or 1D step parameters. SMILES and Masks provide functionalities that extend slender objects into branched and other objects. We treat the conversion between 1D, 2D, 3D, and 4D representations as data unification. A mathematical analysis of different methods applied to helices (a special type of space curves) is also provided. Computational implementation utilizes Model-ViewController design principles to integrate data unification with graphical visualizations to create a dashboard. Applications of multi-dimensional …

Analog Implementation Of The Hodgkin-Huxley Model Neuron, Zachary D. Mobille, George H. Rutherford, Jordan Brandt-Trainer, Rosangela Follmann, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Period Drift In A Neutrally Stable Stochastic Oscillator, Kevin Sanft

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Quantifying Complex Systems Via Computational Fly Swarms, Troy Taylor

Senior Theses

Complexity is prevalent both in natural and in human-made systems, yet is not well understood quantitatively. Qualitatively, complexity describes a phenomena in which a system composed of individual pieces, each having simple interactions with one another, results in interesting bulk properties that would otherwise not exist. One example of a complex biological system is the bird flock, in particular, a starling murmuration. Starlings are known to move in the direction of their neighbors and avoid collisions with fellow starlings, but as a result of these simple movement choices, the flock as a whole tends to exhibit fluid-like movements and form …

The Computational Study Of Fly Swarms & Complexity, Austin Bebee

Senior Theses

A system is considered complex if it is composed of individual parts that abide by their own set of rules, while the system, as a whole, will produce non-deterministic properties. This prevents the behavior of such systems from being accurately predicted. The motivation for studying complexity spurs from the fact that it is a fundamental aspect of innumerable systems. Among complex systems, fly swarms are relatively simple, but even so they are still not well understood. In this research, several computational models were developed to assist with the understanding of fly swarms. These models were primarily analyzed by using the …

An Application Of M-Matrices To Preserve Bounded Positive Solutions To The Evolution Equations Of Biofilm Models, Richard S. Landry Jr.

LSU New Orleans Theses and Dissertations

In this work, we design a linear, two step implicit finite difference method to approximate the solutions of a biological system that describes the interaction between a microbial colony and a surrounding substrate. Three separate models are analyzed, all of which can be described as systems of partial differential equations (PDE)s with nonlinear diffusion and reaction, where the biological colony grows and decays based on the substrate bioavailability. The systems under investigation are all complex models describing the dynamics of biological films. In view of the difficulties to calculate analytical solutions of the models, we design here a numerical technique …

A Critical Firing Rate In Synchronous Transitions Of Coupled Neurons, Annabelle Shaffer, Epaminondas Rosa, Rosangela Follmann

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Building And Validating A Model For Investigating The Dynamics Of Isolated Water Molecules, Grant Cates

Senior Theses

Understanding how water molecules behave in isolation is vital to understand many fundamental processes in nature. To that end, scientists have begun studying crystals in which single water molecules become trapped in regularly occurring cavities in the crystal structure. As part of that investigation, numerical models used to investigate the dynamics of isolated water molecules are sought to help bolster our fundamental understanding of how these systems behave. To that end, the efficacy of three computational methods—the Euler Method, the Euler-Aspel Method and the Beeman Method—is compared using a newly defined parameter, called the predictive stability coefficient ρ. This …

Modeling Of Bacillus Spores: Inactivation And Outgrowth, Alexis X. Hurst

Theses and Dissertations

This research models and analyzes the thermochemical damage produced in Bacillus spores by short, high-temperature exposures as well the repair process within damaged Bacillus spores. Thermochemical damage in spores is significantly due to reaction with water, hydrolysis reactions. Applying heat to the spore causes absorbed and chemically bound water molecules become mobile within the spore. These mobile water molecules react by hydrolysis reactions to degrade DNA and enzyme molecules in the spore. In order to survive the thermal inactivation, the spore must repair the damaged DNA during spore germination. The DNA repair process, as well as other germination functions, is …

Scroll Waves In The Presence Of Slowly Varying Anisotropy With Application To The Heart, S. Setayeshgar, Andrew J. Bernoff

All HMC Faculty Publications and Research

We consider the dynamics of scroll waves in the presence of rotating anisotropy, a model of the left ventricle of the heart in which the orientation of fibers in successive layers of tissue rotates. By choosing a coordinate system aligned with the fiber rotation and studying the phase dynamics of a straight but twisted scroll wave, we derive a Burgers’ equation with forcing associated with the fiber rotation rate. We present asymptotic solutions for scroll twist, verified by numerics, using a realistic fiber distribution profile. We make connection with earlier numerical and analytical work on scroll dynamics.