Numerical Analysis and Computation Commons^™

Utilizing Non-Negative Least Squares For Data-Driven Discovery Of Dynamics, Tracey G. Oellerich

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling The Communication Dynamics In Human-Autonomy Teams: Insights From Search And Rescue Scenarios, Carlos E. Bustamante Orellana, Lucero Rodriguez Rodriguez, Yun Kang

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Complex Biosystems Program: Dissertations and Student Research

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Rigid Body Constrained Motion Optimization And Control On Lie Groups And Their Tangent Bundles, Brennan S. Mccann

Doctoral Dissertations and Master's Theses

Rigid body motion requires formulations where rotational and translational motion are accounted for appropriately. Two Lie groups, the special orthogonal group SO(3) and the space of quaternions H, are commonly used to represent attitude. When considering rigid body pose, that is spacecraft position and attitude, the special Euclidean group SE(3) and the space of dual quaternions DH are frequently utilized. All these groups are Lie groups and Riemannian manifolds, and these identifications have profound implications for dynamics and controls. The trajectory optimization and optimal control problem on Riemannian manifolds presents significant opportunities for theoretical development. Riemannian optimization is an attractive …

Modeling Nonsegmented Negative-Strand Rna Virus (Nnsv) Transcription With Ejective Polymerase Collisions And Biased Diffusion, Felipe-Andres Piedra

Research Symposium

Background: The textbook model of NNSV transcription predicts a gene expression gradient. However, multiple studies show non-gradient gene expression patterns or data inconsistent with a simple gradient. Regarding the latter, several studies show a dramatic decrease in gene expression over the last two genes of the respiratory syncytial virus (RSV) genome (a highly studied NNSV). The textbook model cannot explain these phenomena.

Methods: Computational models of RSV and vesicular stomatitis virus (VSV – another highly studied NNSV) transcription were written in the Python programming language using the Scientific Python Development Environment. The model code is freely available on GitHub: …

An Implementation Of The Method Of Moments On Chemical Systems With Constant And Time-Dependent Rates, Emmanuel O. Adara, Roger B. Sidje

Northeast Journal of Complex Systems (NEJCS)

Among numerical techniques used to facilitate the analysis of biochemical reactions, we can use the method of moments to directly approximate statistics such as the mean numbers of molecules. The method is computationally viable in time and memory, compared to solving the chemical master equation (CME) which is notoriously expensive. In this study, we apply the method of moments to a chemical system with a constant rate representing a vascular endothelial growth factor (VEGF) model, as well as another system with time-dependent propensities representing the susceptible, infected, and recovered (SIR) model with periodic contact rate. We assess the accuracy of …

Flow Dynamics In Cardiovascular Devices: A Comprehensive Review, Venant Niyonkuru, Bosco Jean Ndayishimiye Dr, Anicet Barthélemy Sibomana

Digital Journal of Clinical Medicine

This review explores flow dynamics in cardiovascular devices, focusing on fundamental fluid mechanics principles and normal blood flow patterns. It discusses the role of different structures in maintaining flow dynamics and the importance of stents, heart valves, artificial hearts, and ventricular assist devices in cardiovascular interventions. The review emphasizes the need for optimized designs and further research to enhance knowledge of flow dynamics in cardiovascular devices, advancing the field and improving patient care in cardiovascular interventions.

Temporality-Induced Chaos In The Kuramoto Model, Keanu Mason Rock, Hamza Dirie, Sean P. Cornelius

Northeast Journal of Complex Systems (NEJCS)

Switched dynamical systems have been extensively studied in engineering literature in the context of system control. In these systems, the dynamical laws change between different subsystems depending on the environment, a process that is known to produce emergent behaviors---notably chaos. These dynamics are analogous to those of temporal networks, in which the network topology changes over time, thereby altering the dynamics on the network. It stands to reason that temporal networks may therefore produce emergent chaos and other exotic behaviors unanticipated in static networks, yet concrete examples remain elusive. Here, we present a minimal example of a networked system in …

Modeling, Simulation And Control Of Microrobots For The Microfactory., Zhong Yang

Electronic Theses and Dissertations

Future assembly technologies will involve higher levels of automation in order to satisfy increased microscale or nanoscale precision requirements. Traditionally, assembly using a top-down robotic approach has been well-studied and applied to the microelectronics and MEMS industries, but less so in nanotechnology. With the boom of nanotechnology since the 1990s, newly designed products with new materials, coatings, and nanoparticles are gradually entering everyone’s lives, while the industry has grown into a billion-dollar volume worldwide. Traditionally, nanotechnology products are assembled using bottom-up methods, such as self-assembly, rather than top-down robotic assembly. This is due to considerations of volume handling of large …

Dynamical Aspects In (4+1)-Body Problems, Ryan Gauthier

Theses and Dissertations (Comprehensive)

The n-body problem models a system of n-point masses that attract each other via some binary interaction. The (n + 1)-body problem assumes that one of the masses is located at the origin of the coordinate system. For example, an (n+1)-body problem is an ideal model for Saturn, seen as the central mass, and one of its outer rings. A relative equilibrium (RE) is a special solution of the (n+1)-body problem where the non-central bodies rotate rigidly about the centre of mass. In rotating coordinates, these solutions become equilibria.

In this thesis we study dynamical aspects of planar (4 + …

Dynamic Function Learning Through Control Of Ensemble Systems, Wei Zhang, Vignesh Narayanan, Jr-Shin Li

Publications

Learning tasks involving function approximation are preva- lent in numerous domains of science and engineering. The underlying idea is to design a learning algorithm that gener- ates a sequence of functions converging to the desired target function with arbitrary accuracy by using the available data samples. In this paper, we present a novel interpretation of iterative function learning through the lens of ensemble dy- namical systems, with an emphasis on establishing the equiv- alence between convergence of function learning algorithms and asymptotic behavior of ensemble systems. In particular, given a set of observation data in a function learning task, we …

On Analysis Of Effectiveness Controlling Covid-19 With Quarantine And Vaccination Compartments In Indonesia, Prihantini Prihantini

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Novel Method For Sensitivity Analysis Of Time-Averaged Chaotic System Solutions, Christian A. Spencer-Coker

Theses and Dissertations

The direct and adjoint methods are to linearize the time-averaged solution of bounded dynamical systems about one or more design parameters. Hence, such methods are one way to obtain the gradient necessary in locally optimizing a dynamical system’s time-averaged behavior over those design parameters. However, when analyzing nonlinear systems whose solutions exhibit chaos, standard direct and adjoint sensitivity methods yield meaningless results due to time-local instability of the system. The present work proposes a new method of solving the direct and adjoint linear systems in time, then tests that method’s ability to solve instances of the Lorenz system that exhibit …

Role Of Inhibition And Spiking Variability In Ortho- And Retronasal Olfactory Processing, Michelle F. Craft

Theses and Dissertations

Odor perception is the impetus for important animal behaviors, most pertinently for feeding, but also for mating and communication. There are two predominate modes of odor processing: odors pass through the front of nose (ortho) while inhaling and sniffing, or through the rear (retro) during exhalation and while eating and drinking. Despite the importance of olfaction for an animal’s well-being and specifically that ortho and retro naturally occur, it is unknown whether the modality (ortho versus retro) is transmitted to cortical brain regions, which could significantly instruct how odors are processed. Prior imaging studies show different …

Contributions To The Teaching And Learning Of Fluid Mechanics, Ashwin Vaidya

Department of Mathematics Faculty Scholarship and Creative Works

This issue showcases a compilation of papers on fluid mechanics (FM) education, covering different sub topics of the subject. The success of the first volume [1] prompted us to consider another follow-up special issue on the topic, which has also been very successful in garnering an impressive variety of submissions.

As a classical branch of science, the beauty and complexity of fluid dynamics cannot be overemphasized. This is an extremely well-studied subject which has now become a significant component of several major scientific disciplines ranging from aerospace engineering, astrophysics, atmospheric science (including climate modeling), biological and biomedical science …

Dynamic Parameter Estimation From Partial Observations Of The Lorenz System, Eunice Ng

Theses and Dissertations

Recent numerical work of Carlson-Hudson-Larios leverages a nudging-based algorithm for data assimilation to asymptotically recover viscosity in the 2D Navier-Stokes equations as partial observations on the velocity are received continuously-in-time. This "on-the-fly" algorithm is studied both analytically and numerically for the Lorenz equations in this thesis.

An Examination Of Fontan Circulation Using Differential Equation Models And Numerical Methods, Vanessa Maybruck

Honors Student Research

Certain congenital heart defects can lead to the development of only a single pumping chamber, or ventricle, in the heart instead of the usual two ventricles. Individuals with this defect undergo a corrective, three-part surgery, the third step of which is the Fontan procedure, but as the patients age, their cardiovascular health will likely deteriorate. Using computational fluid dynamics and differential equations, Fontan circulation can be modeled to investigate why the procedure fails and how Fontan failure can be maximally prevented. Borrowing from well-established literature on RC circuits, the differential equation models simulate systemic blood flow in a piecewise, switch-like …

Lecture 07: Nonlinear Preconditioning Methods And Applications, Xiao-Chuan Cai

Mathematical Sciences Spring Lecture Series

We consider solving system of nonlinear algebraic equations arising from the discretization of partial differential equations. Inexact Newton is a popular technique for such problems. When the nonlinearities in the system are well-balanced, Newton's method works well, but when a small number of nonlinear functions in the system are much more nonlinear than the others, Newton may converge slowly or even stagnate. In such a situation, we introduce some nonlinear preconditioners to balance the nonlinearities in the system. The preconditioners are often constructed using a combination of some domain decomposition methods and nonlinear elimination methods. For the nonlinearly preconditioned problem, …

Fractals, Fractional Derivatives, And Newton-Like Methods, Eleanor Byrnes

HMC Senior Theses

Inspired by the fractals generated by the discretizations of the Continuous Newton Method and the notion of a fractional derivative, we ask what it would mean if such a fractional derivative were to replace the derivatives in Newton's Method. This work, largely experimental in nature, examines these new iterative methods by generating their Julia sets, computing their fractal dimension, and in certain tractable cases examining the behaviors using tools from dynamical systems.

Modelling The Transition From Homogeneous To Columnar States In Locust Hopper Bands, Miguel Velez

HMC Senior Theses

Many biological systems form structured swarms, for instance in locusts, whose swarms are known as hopper bands. There is growing interest in applying mathematical models to understand the emergence and dynamics of these biological and social systems. We model the locusts of a hopper band as point particles interacting through repulsive and attractive social "forces" on a one dimensional periodic domain. The primary goal of this work is to modify this well studied modelling framework to be more biological by restricting repulsion to act locally between near neighbors, while attraction acts globally between all individuals. This is a biologically motivated …

The Revised Nim For Solving The Non-Linear System Variant Boussinesq Equations And Comparison With Nim, Oday Ahmed Jasim

Karbala International Journal of Modern Science

This research aims to guide researchers to use a new method, and it is the Revised New Iterative Method (RNIM) to solve partial differential equation systems and apply them to solve problems in various disciplines such as chemistry, physics, engineering and medicine. In this paper, the numerical solutions of the nonlinear Variable Boussinesq Equation System (VBE) were obtained using a new modified iterative method (RNIM); this was planned by (Bhaleker and Datterder-Gejj). A numerical solution to the Variable Boussinesq Equation System (VBE) was also found using a widely known method, a new iterative method (NIM). By comparing the numerical solutions …

Sum Of Cubes Of The First N Integers, Obiamaka L. Agu

Electronic Theses, Projects, and Dissertations

In Calculus we learned that 􏰅Sum^{n}_{k=1} k = [n(n+1)]/2 , that Sum^{􏰅n}_{k=1} k^2 = [n(n+1)(2n+1)]/6 , and that Sum^{n}_{k=1} k^{3} = (n(n+1)/2)^{2}. These formulas are useful when solving for the area below quadratic or cubic function over an interval [a, b]. This tedious process, solving for areas under a quadratic or a cubic, served as motivation for the introduction of Riemman integrals. For the overzealous math student, these steps were replaced by a simpler method of evaluating antiderivatives at the endpoints a and b. From my recollection, a former instructor informed us to do the value of memorizing these formulas. …

Asymptotic Analysis Of Radial Point Rupture Solutions For Elliptic Equations, Attou Miloua

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Numerical Computations Of Vortex Formation Length In Flow Past An Elliptical Cylinder, Matthew Karlson, Bogdan Nita, Ashwin Vaidya

Department of Mathematics Faculty Scholarship and Creative Works

We examine two dimensional properties of vortex shedding past elliptical cylinders through numerical simulations. Specifically, we investigate the vortex formation length in the Reynolds number regime 10 to 100 for elliptical bodies of aspect ratio in the range 0.4 to 1.4. Our computations reveal that in the steady flow regime, the change in the vortex length follows a linear profile with respect to the Reynolds number, while in the unsteady regime, the time averaged vortex length decreases in an exponential manner with increasing Reynolds number. The transition in profile is used to identify the critical Reynolds number which marks the …

Teaching And Learning Of Fluid Mechanics, Ashwin Vaidya

Department of Mathematics Faculty Scholarship and Creative Works

Fluid mechanics occupies a privileged position in the sciences; it is taught in various science departments including physics, mathematics, environmental sciences and mechanical, chemical and civil engineering, with each highlighting a different aspect or interpretation of the foundation and applications of fluids. Doll’s fluid analogy [5] for this idea is especially relevant to this issue: “Emergence of creativity from complex flow of knowledge—example of Benard convection pattern as an analogy—dissipation or dispersal of knowledge (complex knowledge) results in emergent structures, i.e., creativity which in the context of education should be thought of as a unique way to arrange information so …

The Potentials Of Faecal Sludge Treatment Using Local Conditioners In Tanzania: A Review, Doglas Benjamin1

Tanzania Journal of Engineering and Technology (TJET)

Worldwide, every day human beings generate millions of tons of Faecal Sludge (FS), which is rich in water, nutrients, energy, and organic compounds. Yet FS is not being managed in a way that permits us to derive value from its reuse, while at the same time, millions of farmers struggle with depleted soils and lack of water. In most of the developing countries, energy for cooking is mainly derived from cutting of trees, either as wood or charcoal. Resource recovery and reuse from FS can create livelihoods, enhance food security, support green economies, reduce waste and contribute to cost recovery …

Transient Dynamics Of Infection Transmission In An Intensive Care Unit, Christopher Short, Matthew S. Mietchen, Eric T. Lofgren

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Discrete-Time Disease Model With Population Motion Under The Kolmogorov Equation View And Application, Ye Li

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Mathematical Modeling, Analysis, Simulation Of The Opioid Crisis With Prescription And Social Drug Addiction Models, Kirthi Kumar

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

School Policy Evaluated With Time-Reversible Markov Chain, Trajan Murphy, Iddo Ben-Ari

Honors Scholar Theses

In this work we propose a reversible Markov chain scheme to model for the mobility of students affected by a grade school leveling policy. This model provides unified and mathematically tractable framework in which transition functions are sampled uniformly from the set of {\bf reversible} transition functions. The results from the study appear to confirm the disadvantageous effects of this school policy, on par with the of a previous model on the same policy.