Recent PhD Theses - Applied Mathematics

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PhD Theses 2023

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Applied Mathematics Department

Applied Mathematics Theses and Dissertations

This collection contains theses and dissertations from the Department of Applied Mathematics, collected from the [email protected] Electronic Thesis and Dissertation Repository

Theses/Dissertations from 2023 2023

Spike-Time Neural Codes and their Implication for Memory , Alexandra Busch

Pythagorean Vectors and Rational Orthonormal Matrices , Aishat Olagunju

Theses/Dissertations from 2022 2022

A Molecular Dynamics Study Of Polymer Chains In Shear Flows and Nanocomposites , Venkat Bala

On the Spatial Modelling of Biological Invasions , Tedi Ramaj

Complete Hopf and Bogdanov-Takens Bifurcation Analysis on Two Epidemic Models , Yuzhu Ruan

A Theoretical Perspective on Parasite-Host Coevolution with Alternative Modes of Infection , George N. Shillcock

Theses/Dissertations from 2021 2021

Mathematical Modelling & Simulation of Large and Small Scale Structures in Star Formation , Gianfranco Bino

Mathematical Modelling of Ecological Systems in Patchy Environments , Ao Li

Credit Risk Measurement and Application based on BP Neural Networks , Jingshi Luo

Coevolution of Hosts and Pathogens in the Presence of Multiple Types of Hosts , Evan J. Mitchell

SymPhas: A modular API for phase-field modeling using compile-time symbolic algebra , Steven A. Silber

Population and Evolution Dynamics in Predator-prey Systems with Anti-predation Responses , Yang Wang

Theses/Dissertations from 2020 2020

The journey of a single polymer chain to a nanopore , Navid Afrasiabian

Exploration Of Stock Price Predictability In HFT With An Application In Spoofing Detection , Andrew Day

Multi-Scale Evolution of Virulence of HIV-1 , David W. Dick

Contraction Analysis of Functional Competitive Lotka-Volterra Systems: Understanding Competition Between Modified Bacteria and Plasmodium within Mosquitoes. , Nickolas Goncharenko

Phage-Bacteria Interaction and Prophage Sequences in Bacterial Genomes , Amjad Khan

The Effect of the Initial Structure on the System Relaxation Time in Langevin Dynamics , Omid Mozafar

Mathematical modelling of prophage dynamics , Tyler Pattenden

Hybrid Symbolic-Numeric Computing in Linear and Polynomial Algebra , Leili Rafiee Sevyeri

Abelian Integral Method and its Application , Xianbo Sun

Theses/Dissertations from 2019 2019

Algebraic Companions and Linearizations , Eunice Y. S. Chan

Algorithms for Mappings and Symmetries of Differential Equations , Zahra Mohammadi

Algorithms for Bohemian Matrices , Steven E. Thornton

A Survey Of Numerical Quadrature Methods For Highly Oscillatory Integrals , Jeet Trivedi

Theses/Dissertations from 2018 2018

Properties and Computation of the Inverse of the Gamma function , Folitse Komla Amenyou

Optimization Studies and Applications: in Retail Gasoline Market , Daero Kim

Models of conflict and voluntary cooperation between individuals in non-egalitarian social groups , Cody Koykka

Investigation of chaos in biological systems , Navaneeth Mohan

Bifurcation Analysis of Two Biological Systems: A Tritrophic Food Chain Model and An Oscillating Networks Model , Xiangyu Wang

Ecology and Evolution of Dispersal in Metapopulations , Jingjing Xu

Selected Topics in Quantization and Renormalization of Gauge Fields , Chenguang Zhao

Three Essays on Structural Models , Xinghua Zhou

Theses/Dissertations from 2017 2017

On Honey Bee Colony Dynamics and Disease Transmission , Matthew I. Betti

Simulation of driven elastic spheres in a Newtonian fluid , Shikhar M. Dwivedi

Feasible Computation in Symbolic and Numeric Integration , Robert H.C. Moir

Modelling Walleye Population and Its Cannibalism Effect , Quan Zhou

Theses/Dissertations from 2016 2016

Dynamics of Discs in a Nematic Liquid Crystal , Alena Antipova

Modelling the Impact of Climate Change on the Polar Bear Population in Western Hudson Bay , Nicole Bastow

A comparison of solution methods for Mandelbrot-like polynomials , Eunice Y. S. Chan

A model-based test of the efficacy of a simple rule for predicting adaptive sex allocation , Joshua D. Dunn

Universal Scaling Properties After Quantum Quenches , Damian Andres Galante

Modeling the Mass Function of Stellar Clusters Using the Modified Lognormal Power-Law Probability Distribution Function , Deepakshi Madaan

Bacteria-Phage Models with a Focus on Prophage as a Genetic Reservoir , Alina Nadeem

A Sequence of Symmetric Bézout Matrix Polynomials , Leili Rafiee Sevyeri

Study of Infectious Diseases by Mathematical Models: Predictions and Controls , SM Ashrafur Rahman

The survival probability of beneficial de novo mutations in budding viruses, with an emphasis on influenza A viral dynamics , Jennifer NS Reid

Essays in Market Structure and Liquidity , Adrian J. Walton

Computation of Real Radical Ideals by Semidefinite Programming and Iterative Methods , Fei Wang

Studying Both Direct and Indirect Effects in Predator-Prey Interaction , Xiaoying Wang

Theses/Dissertations from 2015 2015

The Effect of Diversification on the Dynamics of Mobile Genetic Elements in Prokaryotes: The Birth-Death-Diversification Model , Nicole E. Drakos

Algorithms to Compute Characteristic Classes , Martin Helmer

Studies of Contingent Capital Bonds , Jingya Li

Determination of Lie superalgebras of supersymmetries of super differential equations , Xuan Liu

Edge states and quantum Hall phases in graphene , Pavlo Piatkovskyi

Evolution of Mobile Promoters in Prokaryotic Genomes. , Mahnaz Rabbani

Extensions of the Cross-Entropy Method with Applications to Diffusion Processes and Portfolio Losses , Alexandre Scott

Theses/Dissertations from 2014 2014

A Molecular Simulation Study on Micelle Fragmentation and Wetting in Nano-Confined Channels , Mona Habibi

Study of Virus Dynamics by Mathematical Models , Xiulan Lai

Applications of Stochastic Control in Energy Real Options and Market Illiquidity , Christian Maxwell

Options Pricing and Hedging in a Regime-Switching Volatility Model , Melissa A. Mielkie

Optimal Contract Design for Co-development of Companion Diagnostics , Rodney T. Tembo

Bifurcation of Limit Cycles in Smooth and Non-smooth Dynamical Systems with Normal Form Computation , Yun Tian

Understanding Recurrent Disease: A Dynamical Systems Approach , Wenjing Zhang

Theses/Dissertations from 2013 2013

Pricing and Hedging Index Options with a Dominant Constituent Stock , Helen Cheyne

On evolution dynamics and strategies in some host-parasite models , Liman Dai

Valuation of the Peterborough Prison Social Impact Bond , Majid Hasan

Sensitivity Analysis of Minimum Variance Portfolios , Xiaohu Ji

Eigenvalue Methods for Interpolation Bases , Piers W. Lawrence

Hybrid Lattice Boltzmann - Molecular Dynamics Simulations With Both Simple and Complex Fluids , Frances E. Mackay

Ecological Constraints and the Evolution of Cooperative Breeding , David McLeod

A single cell based model for cell divisions with spontaneous topology changes , Anna Mkrtchyan

Analysis of Re-advanceable Mortgages , Almas Naseem

Modeling leafhopper populations and their role in transmitting plant diseases. , Ji Ruan

Topological properties of modular networks, with a focus on networks of functional connections in the human brain , Estefania Ruiz Vargas

Computation Sequences for Series and Polynomials , Yiming Zhang

Theses/Dissertations from 2012 2012

A Real Options Valuation of Renewable Energy Projects , Natasha Burke

Approximate methods for dynamic portfolio allocation under transaction costs , Nabeel Butt

Optimal clustering techniques for metagenomic sequencing data , Erik T. Cameron

Phase Field Crystal Approach to the Solidification of Ferromagnetic Materials , Niloufar Faghihi

Molecular Dynamics Simulations of Peptide-Mineral Interactions , Susanna Hug

Molecular Dynamics Studies of Water Flow in Carbon Nanotubes , Alexander D. Marshall

Valuation of Multiple Exercise Options , T. James Marshall

Incomplete Market Models of Carbon Emissions Markets , Walid Mnif

Topics in Field Theory , Alexander Patrushev

Pricing and Trading American Put Options under Sub-Optimal Exercise Policies , William Wei Xing

Further applications of higher-order Markov chains and developments in regime-switching models , Xiaojing Xi

Theses/Dissertations from 2011 2011

Bifurcations and Stability in Models of Infectious Diseases , Bernard S. Chan

Real Options Models in Real Estate , Jin Won Choi

Models, Techniques, and Metrics for Managing Risk in Software Engineering , Andriy Miranskyy

Thermodynamics, Hydrodynamics and Critical Phenomena in Strongly Coupled Gauge Theories , Christopher Pagnutti

Molecular Dynamics Studies of Interactions of Phospholipid Membranes with Dehydroergosterol and Penetrating Peptides , Amir Mohsen Pourmousa Abkenar

Socially Responsible Investment in a Changing World , Desheng Wu

Study of Malaria Transmission Dynamics by Mathematical Models , Yanyu Xiao

Theses/Dissertations from 2010 2010

Simulation-based Valuation and Counterparty Exposure Estimation of American Options , Kin Hung Kan

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Applied Mathematics Theses

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Areas of particularly strong research activity are: numerical analysis, plasma physics, solar and magnetospheric theory, and vortex dynamics.

For more information please visit the School of Mathematics and Statistics home page.

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Recent Submissions

Applications of likelihood-free parameter inference methods on numerical models of cancer invasion , magnetohydrodynamic waves in the solar corona : a mathematical investigation of the role of resonant absorption and phase mixing in coronal heating , transition region blinkers , two-component relativistic wave equations for spin 1/2 particles , multi-dimensional modelling of physiologically and temporally structured populations .


A thesis is a more ambitious undertaking than a project. Most thesis writers within Applied Mathematics spend two semesters on their thesis work, beginning in the fall of senior year.  Students typically enroll in Applied Mathematics 91r or 99r (or Economics 985, if appropriate) during each semester of their senior year.  AM 99r is graded on a satisfactory/unsatisfactory basis.  Some concentrators will have completed their programs of study before beginning a thesis; in situations where this is necessary, students may take AM 91r for letter-graded credit, for inclusion in Breadth section (v) of the plan of study.  In the spring semester, the thesis itself may serve as the substantial paper on which the letter grade is based.  Econ 985 is also letter-graded, and may be included in the Breadth section of the plan of study in place of AM 91r.

Another, somewhat uncommon option, is that a project that meets the honors modeling requirement (either through Applied Mathematics 115 or 91r) can be extended to a thesis with about one semester of work.  Obviously the more time that is spent on the thesis, the more substantial the outcome, but students are encouraged to write a thesis in whatever time they have. It is an invaluable academic experience.

The thesis should make substantive use of mathematical, statistical or computational modeling,  though the level of sophistication will vary as appropriate to the particular problem context.  It is expected that conscientious attention will be paid to the explanatory power of mathematical modeling of the phenomena under study, going beyond data analysis to work to elucidate questions of mechanism and causation rather than mere correlation. Models should be designed to yield both understanding and testable predictions. A thesis with a suitable modeling component will automatically satisfy the English honors modeling requirement; however a thesis won't satisfy modeling Breadth section (v) unless the student also takes AM 91r or Econ 985.

Economics 985 thesis seminars are reserved for students who are writing on an economics topic. These seminars are full courses for letter-graded credit which involve additional activities beyond preparation of a thesis. They are open to Applied Mathematics concentrators with suitable background and interests.

Students wishing to enroll in AM 99r or 91r should follow the application instructions on my.harvard.

Thesis Timeline

The timeline below is for students graduating in May. For off-cycle students, a similar timeline applies, offset by one semester. The thesis due date for March 2023 graduates is Friday, November 18, 2022. The thesis deadline for May 2023 graduates is March 24, 2023 at 4:00PM.  Late theses are not accepted.

Late August or Early September:

Students often find a thesis supervisor by this time, and work with their supervisor to identify a thesis problem. Students may enroll in Econ 985 (strongly recommended when relevant), AM 91r, or AM 99r to block out space in their schedule for the thesis.

Early December:

All fourth year concentrators are contacted by the Office of Academic Programs.  Those planning to submit a senior thesis are requested to supply certain information. This is the first formal interaction with the concentration about the thesis.


A tentative thesis title approved by the thesis supervisor is required by the concentration.

Early February:

The student should provide the name and contact information for a recommended second reader, together with assurance that this individual has agreed to serve. Thesis readers are expected to be teaching faculty members of the Faculty of Arts and Sciences or SEAS. Exceptions to this requirement must be first approved by the Directors, Associate Director, or Assistant Director of Undergraduate Studies. For AM/Economics students writing a thesis on a mathematical economics topic for the March thesis deadline, the second reader will be chosen by the Economics Department. For AM/Economics students writing for the November deadline, the student should recommend the second reader.

March 24, 2023:

Thesis due at 4pm.  Late theses are not accepted.  Electronic copies in PDF format should be delivered by the student to the two readers and to [email protected] (which will forward to the Directors of Undergraduate Studies, Associate and Assistant Director of Undergraduate Studies) on or before that date and time. An electronic copy should also be submitted via the SEAS  online submission tool  on or before that date. SEAS will keep this electronic copy as a non-circulating backup and will use it to print a physical copy of the thesis to be deposited in the Harvard University Archives. During this online submission process, the student will also have the option to make the electronic copy publicly available via DASH, Harvard’s open-access repository for scholarly work.

Contemporaneously, the two readers will receive a rating sheet to be returned to the Office of Academic Programs before the beginning of the Reading Period, together with their copy of the thesis and any remarks to be transmitted to the student.

The Office of Academic Programs will send readers' comments to the student in late May, after the degree meeting to decide honors recommendations.

Thesis Readers

The thesis is evaluated by two readers, whose roles are further delineated below.  The first reader is the thesis adviser.  The second and reader is recommended by the student and adviser, who should secure the agreement of the individual concerned to serve in this capacity.  The reader must be approved by the Directors, Associate Director, or Assistant Director of Undergraduate Studies.  The second reader is normally are teaching members of the Faculty of Arts and Sciences, but other faculty members or comparable professionals will usually be approved, after being apprised of the responsibilities they are assuming.   For theses in mathematical economics, the choice of the second reader is made in cooperation with the Economics department.  The student and thesis adviser will be notified of the designated second reader by mid-March.

The roles of the thesis adviser and of the outside reader are somewhat different.  Ideally, the adviser is a collaborator and the outside reader is an informed critics.  It is customary for the adviser's report to comment not only on the document itself but also on the background and context of the entire effort, elucidating the overall accomplishments of the student.  The supervisor may choose to comment on a draft of the thesis before the final document is submitted, time permitting.  The outside reader is being asked to evaluate the thesis actually produced, as a prospective scientific contribution — both as to content and presentation.  The reader may choose to discuss their evaluation with the student, after the fact, should that prove to be mutually convenient.

The thesis should contain an informative abstract separate from the body of the thesis.  At the degree meeting, the Committee on Undergraduate Studies in Applied Mathematics will review the thesis, the reports from the two readers and the student’s academic record. The readers (and student) are told to assume that the Committee consists of technical professionals who are not necessarily conversant with the subject matter of the thesis so their reports should reflect this audience.

The length of the thesis should be as long as it needs to be to make the arguments made, but no longer!

Thesis Examples

The most recent thesis examples across all of SEAS can be found on the Harvard DASH (Digital Access to Scholarship at Harvard) repository . Search the FAS Theses and Dissertations collection for "applied mathematics" to find dozens of examples.

Note: Additional samples of old theses can be found in McKay Library. Theses awarded Hoopes' Prizes can be found in Lamont Library.

Recent thesis titles

Theses submitted in 2021, theses submitted in 2020, theses submitted in 2019, theses submitted in 2018 , senior thesis submission information for a.b. programs.

Senior A.B. theses are submitted to SEAS and made accessible via the Harvard University Archives and optionally via  DASH  (Digital Access to Scholarship at Harvard), Harvard's open-access repository for scholarly work.

In addition to submitting to the department and thesis advisors & readers, each SEAS senior thesis writer will use an online submission system to submit an electronic copy of their senior thesis to SEAS; this electronic copy will be kept at SEAS as a non-circulating backup. Please note that the thesis won't be published until close to or after the degree date. During this submission process, the student will also have the option to make the electronic copy publicly available via DASH.  Basic document information (e.g., author name, thesis title, degree date, abstract) will also be collected via the submission system; this document information will be available in  HOLLIS , the Harvard Library catalog, and DASH (though the thesis itself will be available in DASH only if the student opts to allow this). Students can also make code or data for senior thesis work available. They can do this by posting the data to the Harvard  Dataverse  or including the code as a supplementary file in the DASH repository when submitting their thesis in the SEAS online submission system.

Whether or not a student opts to make the thesis available through DASH, SEAS will provide an electronic record copy of the thesis to the Harvard University Archives. The Archives may make this record copy of the thesis accessible to researchers in the Archives reading room via a secure workstation or by providing a paper copy for use only in the reading room.  Per University policy , for a period of five years after the acceptance of a thesis, the Archives will require an author’s written permission before permitting researchers to create or request a copy of any thesis in whole or in part. Students who wish to place additional restrictions on the record copy in the Archives must contact the Archives  directly, independent of the online submission system. 

Students interested in commercializing ideas in their theses may wish to consult Dr. Fawwaz Habbal , Senior Lecturer on Applied Physics, about patent protection. See Harvard's policy for information about ownership of software written as part of academic work.

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  4. Recent Master's Theses

    Recent Master's Theses - Applied Mathematics. 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | 2018 | 2019 | 2022 | 2023

  5. Recent PhD Theses

    Recent PhD Theses - Applied Mathematics. 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | 2018 | 2019 | 2022 | 2023

  6. Applied Mathematics Theses and Dissertations

    This collection contains theses and dissertations from the Department of Applied Mathematics, collected from the [email protected] Electronic Thesis and

  7. Masters Theses

    Rochester Institute of Technology, 2014. Graduate, Masters Theses · Mathematical Biology. Browse by Fields of interest.

  8. Ph.D. Dissertations

    Name. Dissertation Title. Advising Professor(s). 2022. Yuying Liu, Neural Networks for Nonlinear Dynamical Systems, Nathan Kutz & Steven Brunton.

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    Areas of particularly strong research activity are: numerical analysis, plasma physics, solar and magnetospheric theory, and vortex dynamics.

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    A thesis is a more ambitious undertaking than a project. Most thesis writers within Applied Mathematics spend two semesters on their thesis work

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