Applied Mathematics Commons^™

Sampling From The Hardcore Process, William C. Dodds

CMC Senior Theses

Partially Recursive Acceptance Rejection (PRAR) and bounding chains used in conjunction with coupling from the past (CFTP) are two perfect simulation protocols which can be used to sample from a variety of unnormalized target distributions. This paper first examines and then implements these two protocols to sample from the hardcore gas process. We empirically determine the subset of the hardcore process's parameters for which these two algorithms run in polynomial time. Comparing the efficiency of these two algorithms, we find that PRAR runs much faster for small values of the hardcore process's parameter whereas the bounding chain approach is vastly …

Constructing Phylogenetic Trees Using Maximum Likelihood, Anna Cho

Scripps Senior Theses

Maximum likelihood methods are used to estimate the phylogenetic trees for a set of species. The probabilities of DNA base substitutions are modeled by continuous-time Markov chains. We use these probabilities to estimate which DNA bases would produce the data that we observe. The topology of the tree is also determined using base substitution probabilities and conditional likelihoods. Felsenstein [2] introduced this method of finding an estimate for the maximum likelihood phylogenetic tree. We will explore this method in detail in this paper.

R₀ Analysis Of A Spatiotemporal Model For A Stream Population, H. W. Mckenzie, Y. Jin, Jon T. Jacobsen, M. A. Lewis

All HMC Faculty Publications and Research

Water resources worldwide require management to meet industrial, agricultural, and urban consumption needs. Management actions change the natural flow regime, which impacts the river ecosystem. Water managers are tasked with meeting water needs while mitigating ecosystem impacts. We develop process-oriented advection-diffusion-reaction equations that couple hydraulic flow to population growth, and we analyze them to assess the effect of water flow on population persistence. We present a new mathematical framework, based on the net reproductive rate R₀ for advection-diffusion-reaction equations and on related measures. We apply the measures to population persistence in rivers under various flow regimes. This work lays …

Two-Subspace Projection Method For Coherent Overdetermined Systems, Deanna Needell, Rachel Ward

CMC Faculty Publications and Research

We present a Projection onto Convex Sets (POCS) type algorithm for solving systems of linear equations. POCS methods have found many applications ranging from computer tomography to digital signal and image processing. The Kaczmarz method is one of the most popular solvers for overdetermined systems of linear equations due to its speed and simplicity. Here we introduce and analyze an extension of the Kaczmarz method which iteratively projects the estimate onto a solution space given from two randomly selected rows. We show that this projection algorithm provides exponential convergence to the solution in expectation. The convergence rate significantly improves upon …

A Fire Simulation Model For Heterogeneous Environments Using The Level Set Method, Shin-En Lo

CGU Theses & Dissertations

Wildfire hazard and its destructive consequences have become a growing issue around the world especially in the context of global warming. An effective and efficient fire simulation model will make it possible to predict the fire spread and assist firefighters in the process of controlling the damage and containing the fire area. Simulating wildfire spread remains challenging due to the complexity of fire behaviors. The raster-based method and the vector-based method are two major approaches that allow one to perform computerized fire spread simulation. In this thesis, we present a scheme we have developed that utilizes a level set method …

Discrete Event Simulation Of Elevator Systems, Sasi Bharath Desai

CMC Senior Theses

The intent of this paper is to present the reader with a simple comparison of two systems of vertical transportation. Vertical transportation is a a relatively new field and is the subject of much interest in today's world. As buildings get taller and real estate becomes more expensive, the need to find a quick, efficient system with a small footprint becomes important. By performing a simulation and subjecting the two systems under study to similar traffic conditions, one can determine the effectiveness of one system relative to the other. Additionally, we look at the effects of changing various system attributes …

Study Of Vortex Ring Dynamics In The Nonlinear Schrödinger Equation Utilizing Gpu-Accelerated High-Order Compact Numerical Integrators, Ronald Meyer Caplan

CGU Theses & Dissertations

We numerically study the dynamics and interactions of vortex rings in the nonlinear Schrödinger equation (NLSE). Single ring dynamics for both bright and dark vortex rings are explored including their traverse velocity, stability, and perturbations resulting in quadrupole oscillations. Multi-ring dynamics of dark vortex rings are investigated, including scattering and merging of two colliding rings, leapfrogging interactions of co-traveling rings, as well as co-moving steady-state multi-ring ensembles. Simulations of choreographed multi-ring setups are also performed, leading to intriguing interaction dynamics.

Due to the inherent lack of a close form solution for vortex rings and the dimensionality where they live, efficient …

Squaring, Cubing, And Cube Rooting, Arthur T. Benjamin

All HMC Faculty Publications and Research

We present mentally efficient algorithms for mentally squaring and cubing 2-digit and 3-digit numbers and for finding cube roots of numbers with 2-digit or 3-digit answers.

Finding The Beat In Music: Using Adaptive Oscillators, Kate M. Burgers

HMC Senior Theses

The task of finding the beat in music is simple for most people, but surprisingly difficult to replicate in a robot. Progress in this problem has been made using various preprocessing techniques (Hitz 2008; Tomic and Janata 2008). However, a real-time method is not yet available. Methods using a class of oscillators called relay relaxation oscillators are promising. In particular, systems of forced Hopf oscillators (Large 2000; Righetti et al. 2006) have been used with relative success. This work describes current methods of beat tracking and develops a new method that incorporates the best ideas from each existing method and …

Swarm Control Through Symmetry And Distribution Characterization, Georgi Dinolov

HMC Senior Theses

Two methods for control of swarms are described. The first of these methods, the Virtual Attractive-Repulsive (VARP) method, is based on potentials defined between swarm elements. The second control method, or the abstraction method, is based on controlling the macroscopic characteristics of a swarm. The derivation of a new control law based on the second method is described. Numerical simulation and analytical interpretation of the result is also presented.

Verification Of Solutions To The Sensor Location Problem, Chandler May

HMC Senior Theses

Traffic congestion is a serious problem with large economic and environmental impacts. To reduce congestion (as a city planner) or simply to avoid congested channels (as a road user), one might like to accurately know the flow on roads in the traffic network. This information can be obtained from traffic sensors, devices that can be installed on roads or intersections to measure traffic flow. The sensor location problem is the problem of efficiently locating traffic sensors on intersections such that the flow on the entire network can be extrapolated from the readings of those sensors. I build on current research …

Simulations Of Surfactant Spreading, Jeffrey Wong

HMC Senior Theses

Thin liquid films driven by surface tension gradients are studied in diverse applications, including the spreading of a droplet and fluid flow in the lung. The nonlinear partial differential equations that govern thin films are difficult to solve analytically, and must be approached through numerical simulations. We describe the development of a numerical solver designed to solve a variety of thin film problems in two dimensions. Validation of the solver includes grid refinement studies and comparison to previous results for thin film problems. In addition, we apply the solver to a model of surfactant spreading and make comparisons with theoretical …

Analytic And Numerical Studies Of A Simple Model Of Attractive-Repulsive Swarms, Andrew S. Ronan

HMC Senior Theses

We study the equilibrium solutions of an integrodifferential equation used to model one-dimensional biological swarms. We assume that the motion of the swarm is governed by pairwise interactions, or a convolution in the continuous setting, and derive a continuous model from conservation laws. The steady-state solution found for the model is compactly supported and is shown to be an attractive equilibrium solution via linear perturbation theory. Numerical simulations support that the steady-state solution is attractive for all initial swarm distributions. Some initial results for the model in higher dimensions are also presented.

Noise, Delays, And Resonance In A Neural Network, Austin Quan

HMC Senior Theses

A stochastic-delay differential equation (SDDE) model of a small neural network with recurrent inhibition is presented and analyzed. The model exhibits unexpected transient behavior: oscillations that occur at the boundary of the basins of attraction when the system is bistable. These are known as delay-induced transitory oscillations (DITOs). This behavior is analyzed in the context of stochastic resonance, an unintuitive, though widely researched phenomenon in physical bistable systems where noise can play in constructive role in strengthening an input signal. A method for modeling the dynamics using a probabilistic three-state model is proposed, and supported with numerical evidence. The potential …

Inter-Colony Comparison Of Diving Behavior Of An Arctic Top Predator: Implications For Warming In The Greenland Sea, Nina J. Karnovsky, Zachary W. Brown '07, Jorg Welcker, Ann M.A. Harding, Wojciech Walkusz, André Cavalcanti, Johanna S. Hardin, Alexander Kitaysky, Geir Gabrielsen, David Grémillet

Pomona Faculty Publications and Research

The goal of this study was to assess how diverse oceanographic conditions and prey communities affect the foraging behavior of little auks Alle alle. The Greenland Sea is characterized by 3 distinct water masses: (1) the East Greenland Current (EGC), which carries Arctic waters southward; (2) the Sørkapp Current (SC), which originates in the Arctic Ocean but flows north along the west coast of Spitsbergen; and (3) the West Spitsbergen Current (WSC), which carries warm Atlantic-derived water north. Each of these 3 water masses is characterized by a distinct mesozooplankton community. Little auks breeding adjacent to the EGC have …

Problems In Gps Accuracy, Michael Thomas Vodhanel

CGU Theses & Dissertations

Improving and predicting the accuracy of positioning estimates derived from the global positioning system (GPS) continues to be a problem of great interest. Dependable and accurate positioning is especially important for navigation applications such as the landing of commercial aircraft. This subject gives rise to many interesting and challenging mathematical problems. This dissertation investigates two such problems. The first problem involves the study of the relationship between positioning accuracy and satellite geometry configurations relative to a user's position. In this work, accuracy is measured by so-called dilution of precision (DOP) terms. The DOP terms arise from the linear regression model …

Engineering Flow States With Localized Forcing In A Thin, Marangoni-Driven Inclined Film, Rachel Levy, Stephen Rosenthal '09, Jeffrey Wong '11

All HMC Faculty Publications and Research

Numerical simulations of lubrication models provide clues for experimentalists about the development of wave structures in thin liquid films. We analyze numerical simulations of a lubrication model for an inclined thin liquid film modified by Marangoni forces due to a thermal gradient and additional localized forcing heating the substrate. Numerical results can be explained through connections to theory for hyperbolic conservation laws predicting wave fronts from Marangoni-driven thin films without forcing. We demonstrate how a variety of forcing profiles, such as Gaussian, rectangular, and triangular, affect the formation of downstream transient structures, including an N wave not commonly discussed in …

Existence Of Solutions For A Semilinear Wave Equation With Non-Monotone Nonlinearity, Alfonso Castro, Benjamin Preskill '09

All HMC Faculty Publications and Research

For double-periodic and Dirichlet-periodic boundary conditions, we prove the existence of solutions to a forced semilinear wave equation with asymptotically linear nonlinearity, no resonance, and non-monotone nonlinearity when the forcing term is not flat on characteristics. The solutions are in L^∞ when the forcing term is in L^∞ and continous when the forcing term is continuous. This is in contrast with the results in [4], where the non-enxistence of continuous solutions is established even when forcing term is of class C^∞ but is flat on a characteristic.

Voting In Agreeable Societies, Deborah E. Berg '06, Serguei Norine, Francis E. Su, Robin Thomas, Paul Wollan

All HMC Faculty Publications and Research

No abstract provided in this article.

An Amazing Mathematical Card Trick, Arthur T. Benjamin

All HMC Faculty Publications and Research

A magician gives a member of the audience 20 cards to shuffle. After the cards are thoroughly mixed, the magician goes through the deck two cards at a time, sometimes putting the two cards face to face, sometimes back to back, and sometimes in the same direction. Before dealing each pair of cards into a pile, he asks random members of the audience if the pair should be flipped over or not. He goes through the pile again four cards at a time and before each group of four is dealt to a pile, the audience gets to decide whether …

Sex, Mixability, And Modularity, Adi Livnat, Christos Papadimitriou, Nicholas Pippenger, Marcus W. Feldman

All HMC Faculty Publications and Research

The assumption that different genetic elements can make separate contributions to the same quantitative trait was originally made in order to reconcile biometry and Mendelism and ever since has been used in population genetics, specifically for the trait of fitness. Here we show that sex is responsible for the existence of separate genetic effects on fitness and, more generally, for the existence of a hierarchy of genetic evolutionary modules. Using the tools developed in the process, we also demonstrate that in terms of their fitness effects, separation and fusion of genes are associated with the increase and decrease of the …

A Semilinear Wave Equation With Smooth Data And No Resonance Having No Continuous Solution, Jose F. Caicedo, Alfonso Castro

All HMC Faculty Publications and Research

We prove that a boundary value problem for a semilinear wave equation with smooth nonlinearity, smooth forcing, and no resonance cannot have continuous solutions. Our proof shows that this is due to the non-monotonicity of the nonlinearity.

Sum Rules And Universality In Electron-Modulated Acoustic Phonon Interaction In A Free-Standing Semiconductor Plate, Shigeyasu Uno, Darryl H. Yong, Nobuya Mori

All HMC Faculty Publications and Research

Analysis of acoustic phonons modulated due to the surfaces of a free-standing semiconductor plate and their deformation-potential interaction with electrons are presented. The form factor for electron-modulated acoustic phonon interaction is formulated and analyzed in detail. The form factor at zero in-plane phonon wave vector satisfies sum rules regardless of electron wave function. The form factor is larger than that calculated using bulk phonons, leading to a higher scattering rate and lower electron mobility. When properly normalized, the form factors lie on a universal curve regardless of plate thickness and material.

Noisy Signal Recovery Via Iterative Reweighted L1-Minimization, Deanna Needell

CMC Faculty Publications and Research

Compressed sensing has shown that it is possible to reconstruct sparse high dimensional signals from few linear measurements. In many cases, the solution can be obtained by solving an L1-minimization problem, and this method is accurate even in the presence of noise. Recent a modified version of this method, reweighted L1-minimization, has been suggested. Although no provable results have yet been attained, empirical studies have suggested the reweighted version outperforms the standard method. Here we analyze the reweighted L1-minimization method in the noisy case, and provide provable results showing an improvement in the error bound over the standard bounds.

Stability Of Traveling Waves In Thin Liquid Films Driven By Gravity And Surfactant, Ellen Peterson, Michael Shearer, Thomas P. Witelski, Rachel Levy

All HMC Faculty Publications and Research

A thin layer of fluid flowing down a solid planar surface has a free surface height described by a nonlinear PDE derived via the lubrication approximation from the Navier Stokes equations. For thin films, surface tension plays an important role both in providing a significant driving force and in smoothing the free surface. Surfactant molecules on the free surface tend to reduce surface tension, setting up gradients that modify the shape of the free surface. In earlier work [12, 13J a traveling wave was found in which the free surface undergoes three sharp transitions, or internal layers, and the surfactant …

Mathematical Aids Epidemic Model: Preferential Anti-Retroviral Therapy Distribution In Resource Constrained Countries, Nadia Abuelezam

HMC Senior Theses

HIV/AIDS is one of the largest health problems the world is currently facing. Even with anti-retroviral therapies (ART), many resource-constrained countries are unable to meet the treatment needs of their infected populations. ART-distribution methods need to be created that prevent the largest number of future HIV infections. We have developed a compartment model that tracks the spread of HIV in multiple two-sex populations over time in the presence of limited treatment. The model has been fit to represent the HIV epidemic in rural and urban areas in Uganda. With the model we examine the spread of HIV among urban and …

Greedy Signal Recovery Review, Deanna Needell, Joel A. Tropp, Roman Vershynin

CMC Faculty Publications and Research

The two major approaches to sparse recovery are L1-minimization and greedy methods. Recently, Needell and Vershynin developed Regularized Orthogonal Matching Pursuit (ROMP) that has bridged the gap between these two approaches. ROMP is the first stable greedy algorithm providing uniform guarantees.

Even more recently, Needell and Tropp developed the stable greedy algorithm Compressive Sampling Matching Pursuit (CoSaMP). CoSaMP provides uniform guarantees and improves upon the stability bounds and RIC requirements of ROMP. CoSaMP offers rigorous bounds on computational cost and storage. In many cases, the running time is just O(NlogN), where N is the ambient dimension of the signal. This …

Uniform Uncertainty Principle And Signal Recovery Via Regularized Orthogonal Matching Pursuit, Deanna Needell, Roman Vershynin

CMC Faculty Publications and Research

This paper seeks to bridge the two major algorithmic approaches to sparse signal recovery from an incomplete set of linear measurements—L1-minimization methods and iterative methods (Matching Pursuits). We find a simple regularized version of Orthogonal Matching Pursuit (ROMP) which has advantages of both approaches: the speed and transparency of OMP and the strong uniform guarantees of L1-minimization. Our algorithm, ROMP, reconstructs a sparse signal in a number of iterations linear in the sparsity, and the reconstruction is exact provided the linear measurements satisfy the uniform uncertainty principle.

Traveling Waves And Shocks In A Viscoelastic Generalization Of Burgers' Equation, Victor Camacho '07, Robert D. Guy, Jon T. Jacobsen

All HMC Faculty Publications and Research

We consider traveling wave phenomena for a viscoelastic generalization of Burgers' equation. For asymptotically constant velocity profiles we find three classes of solutions corresponding to smooth traveling waves, piecewise smooth waves, and piecewise constant (shock) solutions. Each solution type is possible for a given pair of asymptotic limits, and we characterize the dynamics in terms of the relaxation time and viscosity.

Gravity-Driven Thin Liquid Films With Insoluble Surfactant: Smooth Traveling Waves, Rachel Levy, Michael Shearer, Thomas P. Witelski

All HMC Faculty Publications and Research

The flow of a thin layer of fluid down an inclined plane is modified by the presence of insoluble surfactant. For any finite surfactant mass, traveling waves are constructed for a system of lubrication equations describing the evolution of the free-surface fluid height and the surfactant concentration. The one-parameter family of solutions is investigated using perturbation theory with three small parameters: the coefficient of surface tension, the surfactant diffusivity, and the coefficient of the gravity-driven diffusive spreading of the fluid. When all three parameters are zero, the nonlinear PDE system is hyperbolic/degenerateparabolic, and admits traveling wave solutions in which the …