Biological and Chemical Physics Commons^™

A Causal Inference Approach For Spike Train Interactions, Zach Saccomano

Dissertations, Theses, and Capstone Projects

Since the 1960s, neuroscientists have worked on the problem of estimating synaptic properties, such as connectivity and strength, from simultaneously recorded spike trains. Recent years have seen renewed interest in the problem coinciding with rapid advances in experimental technologies, including an approximate exponential increase in the number of neurons that can be recorded in parallel and perturbation techniques such as optogenetics that can be used to calibrate and validate causal hypotheses about functional connectivity. This thesis presents a mathematical examination of synaptic inference from two perspectives: (1) using in vivo data and biophysical models, we ask in what cases the …

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 …

Langevin Dynamic Models For Smfret Dynamic Shift, David Frost, Keisha Cook Dr, Hugo Sanabria Dr

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Fluid-Structure Interaction Modelling Of Neighboring Tubes With Primary Cilium Analysis, Nerion Zekaj, Shawn D. Ryan, Andrew Resnick

Mathematics and Statistics Faculty Publications

We have developed a numerical model of two osculating cylindrical elastic renal tubules to investigate the impact of neighboring tubules on the stress applied to a primary cilium. We hypothesize that the stress at the base of the primary cilium will depend on the mechanical coupling of the tubules due to local constrained motion of the tubule wall. The objective of this work was to determine the in-plane stresses of a primary cilium attached to the inner wall of one renal tubule subject to the applied pulsatile flow, with a neighboring renal tube filled with stagnant fluid in close proximity …

Mathematics For Biomedical Physics, Jogindra M. Wadehra

Open Textbooks

Mathematics for Biomedical Physics is an open access peer-reviewed textbook geared to introduce several mathematical topics at the rudimentary level so that students can appreciate the applications of mathematics to the interdisciplinary field of biomedical physics. Most of the topics are presented in their simplest but rigorous form so that students can easily understand the advanced form of these topics when the need arises. Several end-of-chapter problems and chapter examples relate the applications of mathematics to biomedical physics. After mastering the topics of this book, students would be ready to embark on quantitative thinking in various topics of biology and …

Modeling And Analysis Of Fractional Tb Model With Atangana-Baleanu Derivative, Aatif Ali, Saeed Islam, Quaid Iqbal, Huma Gul, Muhammad Nafees

International Journal of Emerging Multidisciplinaries: Mathematics

In recent years Atangana and Baleanu proposed a new fractional derivative with non-singular and non-local kernel, this paper formulate a fragmentary request numerical TB model with AtanganaBaleanu derivative (AB derivative). We figured the basic reproduction number ( R0 ) and assessment of boundary dependent on genuine information of Khyber Pakhtunkhwa Pakistan, Initially we present the fundamental properties of the model, the existence and uniqueness of the model is proved using fixed point theory. At last, the model is tackled mathematically through Adams-Bashforth Moulton technique. The mathematical results for the extended model of the elements of Tuberculosis is shown graphically to …

Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei

Mathematics Faculty Publications

While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …

Numerical Simulations Of Capsule Deformation Using A Dual Time-Stepping Lattice Boltzmann Method, Charles Armstrong, Yan Peng

Mathematics & Statistics Faculty Publications

In this work a quasisteady, dual time-stepping lattice Boltzmann method is proposed for simulation of capsule deformation. At each time step the steady-state lattice Boltzmann equation is solved using the full approximation storage multigrid scheme for nonlinear equations. The capsule membrane is modeled as an infinitely thin shell suspended in an ambient fluid domain with the fluid structure interaction computed using the immersed boundary method. A finite element method is used to compute the elastic forces exerted by the capsule membrane. Results for a wide range of parameters and initial configurations are presented. The proposed method is found to reduce …

Period Estimation And Noise In A Neutrally Stable Stochastic Oscillator, Kevin R. Sanft, Ben F. M. Intoy

Spora: A Journal of Biomathematics

The periods of the orbits for the well-mixed cyclic three-species Lotka-Volterra model far away from the fixed point are studied. For finite system sizes, a discrete stochastic approach is employed and periods are found via wavelet analysis. As the system size is increased, a hierarchy of approximations ranging from Poisson noise to Gaussian noise to deterministic models are utilized. Based on the deterministic equations, a mathematical relationship between a conserved quantity of the model and the period of the population oscillations is found. Exploiting this property we then study the deterministic conserved quantity and period noise in finite size systems.

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.

Effective Statistical Energy Function Based Protein Un/Structure Prediction, Avdesh Mishra

University of New Orleans Theses and Dissertations

Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on …

Call For Abstracts - Resrb 2019, July 8-9, Wrocław, Poland, Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Mathematical Modeling Of Inhibitory Effects On Chemically Coupled Neurons, Nathhaniel Harraman, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Temperature Effects On Neuronal Tonic-To-Bursting Transitions, Manuela Burek, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Brief History Of Neuroscience, Zachary Mobille, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

C.V. - Wojciech Budzianowski, Wojciech M. Budzianowski

Wojciech Budzianowski

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Renewable Energy And Sustainable Development (Resd) Group, Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Procesy Cieplne I Aparaty (Lab), Wojciech M. Budzianowski

Wojciech Budzianowski

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Inżynieria Chemiczna Lab., Wojciech M. Budzianowski

Wojciech Budzianowski

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Inżynieria Chemiczna Ćw., Wojciech M. Budzianowski

Wojciech Budzianowski

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Tematyka Prac Doktorskich, Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Zespół Energii Odnawialnej I Zrównoważonego Rozwoju (Eozr), Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Termodynamika Procesowa I Techniczna Lab., Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Tematyka Prac Dyplomowych Dla Studentów Wydziału Mechaniczno-Energetycznego Pwr., Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Tematyka Prac Dyplomowych Dla Studentów Wydziału Chemicznego Pwr., Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Mechanika Płynów Lab., Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Dynamics Of The Fitzhugh-Nagumo Neuron Model, Zechariah Thurman

Physics

In this paper, the dynamical behavior of the Fitzhugh-Nagumo model is examined. The relationship between neuron input current and the firing frequency of the neuron is characterized. Various coupling schemes are also examined, and their effects on the dynamics of the system is discussed. The phenomenon of stochastic resonance is studied for a single uncoupled Fitzhugh-Nagumo neuron.

Tourbillion In The Phase Space Of The Bray-Liebhafsky Nonlinear Oscillatory Reaction And Related Multiple-Time-Scale Model, Zeljko D. Cupic

Zeljko D Cupic

The mixed-mode dynamical states found experimentally in the concentration phase space of the iodate catalyzed hydrogen peroxide decomposition (The Bray-Liebhafsky oscillatory reaction) are discussed theoretically in a related multiple-time-scale model, from the viewpoint of tourbillion. With aim to explain the mixed-mode oscillations obtained by numerical simulations of the various dynamical states of a model for the Bray-Liebhafsky reaction under CSTR conditions, the folded singularity points on the critical manifold of the full system and Andronov-Hopf bifurcation of the fast subsystem are calculated. The interaction between those singularities causes occurrence of tourbillion structure.

Mechaniczny Rozdział Faz Proj., Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.