# Dr. Gary G. Sackett Awards

After a B.S. and M.S. in Mathematics at MSU in the early 1960s, Dr. Sackett completed
a Ph.D. in Applied Mathematics at the University of Southern California. He held
positions at the University of New Mexico and Idaho State University mathematics departments
and the Idaho National Laboratory before turning to the law. He is now a semi-retired
lawyer in Salt Lake City, with a continuing interest in supporting applied mathematics
students at his alma mater.

Thanks to the generosity of Dr. Sackett, the Department of Mathematical Sciences is
able to provide support for students pursuing a PhD degree with a research program
in Applied Mathematics. The **Gary G. Sackett Scholarships for Academic Excellence in Applied Mathematics** were established in 2014, and they are awarded to graduate students pursuing a PhD
in mathematics with the research component in the area of Applied Mathematics. The
**Gary G. Sackett Travel Awards in Applied Mathematics** support graduate students in Applied Mathematics by providing travel funds for those
who aim to disseminate the results of their dissertation research to their academic
peers at national conferences. The travel awards may also support graduate student
travel to special summer workshops and institutes that help provide short-term intensive
training in the foundational concepts of their research topic from leading experts
in their respective fields. Information about the various scholarship recipients
is given below.

2014-2015 Scholarship Recipients

2014-2015 Travel Award Recipients

# 2016 Scholarship Recipients

### Dan Kanewske

In his research, Dan has developed a novel visco-elastic fluid flow model which captures the flow of a viscous fluid flowing over a visco-elastic fluid. The purpose of the model is to describe the resulting elastic stress in the visco-elastic fluid. The motivation is to better understand and analyze the common growth of bacterial colonies inside of industrial pipes, catheters etc. He is working under the direction of Dr. Tianyu Zhang.

### Nate McClanahan

Nate's research examines mathematical models of biofilm growth and movement mechanisms. Biofilms are attached microbial communities made up of many different components, and they are found throughout nature as well as in industrial and medical settings. Understanding how these biofilms spread is important in helping the prevention and treatment of diseases and to prevent contamination. Under the direction of Dr. Tianyu Zhang, he studies a model that is designed to model the mixing and separating that occurs within a biofilm. The starting point was the Flory- Huggins free energy density and the Cahn-Hilliard Equation. The model balances the energy terms describing the mixing of molecules, the interaction between molecules, and an energy due to sharp changes in composition. Nate's work also introduces a new term into the energy model that allows the components of the biofilm to move around within the biofilm. This term addresses the movement energy and gives preference to certain locations within the domain for where the biofilm should be in order to minimize the energy. In some cases it acts as an attachment term giving preference to the entire biofilm being at the bottom of the domain - simulating a biofilm attached to a wall or bottom of a stream. Numerical implementations in one and two space dimensions using a finite difference method in C++ are used to explore various aspects of the model.

# 2016 Travel Award Recipients

### Chris Barbour

Chris will use the money provided through Gary Sackett to attend the University of Washington Summer Institute in Statistics for Big Data. The Institute consists of 5 two-and-a-half-day short courses (modules) covering various aspects of the collection, preprocessing, analysis, and interpretation of biomedical big data. This is a subject area that combines many aspects of statistical learning, computer science, and applied mathematics. Each of the five modules are taught by 2 instructors who are leading experts in their respective fields, both at UW and from around the country. Attending will benefit his research involving high-dimensional data analysis with his advisor Dr. Mark Greenwood as well as their long term collaboration with researchers at the National Institutes of Health working involving the analysis of CSF proteins in Multiple Sclerosis patients.

### Eric Berry

Eric used the money provided to attend the Second Chicago Summer School in Geometry and Topology at the University of Chicago. The emphasis of this year's summer school was on algebraic topology, a current area of research and interest for Eric. The summer school consisted of 4 lectures a day, followed by problem sessions in the evenings to enhance comprehension. Eric currently has research projects in topological data analysis and topological methods in the study of dynamical systems.

### Nathan McClanahan

### Diana Schepens

Diana attended the Séminaire de Mathématiques Supérieures in Biological Dynamics, June 2016 at the University of Alberta in Edmonton. This summer intensive included lectures and group work on methods for modeling reaction kinetics, molecular networks, pattern formation, epidemics, and populations. Diana is currently studying population dynamics of microbial consortia and the conditions under which cooperative behavior and specialization emerge.

# 2014-2015 Scholarship Recipients

### Tamra Heberling

Tamra's research focuses on constructing stochastic models describing transcription
of DNA by RNA polymerases while incorporating new breakthroughs found in single-molecule
experiments. One of the results of these experiments is that the torsional forces
applied to a DNA strand by an RNA polymerase during transcription can be measured
and connected with transcriptional velocity. In a paper published in *Science* in 2013, experimentalists were able to measure the torque and its relationship to
both transcriptional pausing and velocity. Using these results to incorporate torque
into a basic stochastic model, her numerical simulation results agree well with transcription
times observed experimentally and reported within the literature. After finishing her PhD in May of 2016, Tamra joined Los Alamos National Laboratory
as a postdoctoral fellow.

### Ben Jackson

Ben's research is highly interdisciplinary, and his dissertation work involved two projects developing and parameterizing two flow channel models in collaboration with experimenters in the department of Land Resources and Environmental Sciences as well as MSU’s Center for Biofilm Engineering (CBE). The first model, which used data Ben and others collected at Mushroom Spring in Yellowstone National Park, estimated erosion and adhesion rates of cells settling in the flow of one of the spring's effluent channels. The second model, a work in collaboration with the CBE, used a Markov Chain Monte Carlo (MCMC) method to estimate parameters in a biomineralization application.

### Dan Kanewkske

Dan's research area is applied mathematics with an emphasis in computational fluid dynamics and a specific application to the viscoelastic flow of a biofilm. Working under the direction of Dr. Tianyu Zhang, he is using a novel model to capture viscoelastic biofilm behavior for the purpose of predicting mechanical stresses on the inside of a biofilm. Should such stresses exceed a biofilm dependent attachment threshold, detachment can be predicted. Subsequently, scouring information could be generated to facilitate biofilm volume reductions along the inside of a contaminated pipe.

### Ryan Waters

Ryan plans to enter the medical field combining his interests in mathematical biology and immunology. His research includes several projects studying diverse biological systems with a variety of mathematical and statistics tools. In particular, these projects include exploring the role of cytokines in immune response regulation, looking at hepatocyte lineages and regeneration from stem cells, understanding the kinetics of co-encapsulated enzymes, and analyzing the CRISPR adaptive immune system in bacteria. As a part of these projects, Ryan has participated in a variety of collaborations with biochemist, biologist, and immunologist, even starting a collaboration with a friend and colleague studying biochemistry at the University of Indiana. This collaboration has lead to a publication exploring the function of enzymes when they are confined in viral cages both individually and in tandem (forming a molecular pathway).

# 2014-2015 Travel Award Recipients

### Danielle Ciesielski

Danielle attended the Atlantic Association for Research in the Mathematical Sciences and Pacific Institute for the Mathematical Sciences Summer School in Differential Equations and Numerical Analysis at Dalhousie University in Halifax, Nova Scotia, Canada. Of the four courses offered, she took courses on waves and patterns in nonlinear systems and numerical analysis of singularly perturbed problems with a group of 40 other students.

### Tamra Heberling

Tamra presented her research on Torque on Transcription at the XIII International Conference on Systems Biology in Zurich, Switzerland. Her presentation was titled “You Spin Me Round: A Mathematical Discussion of Torque on Transcription.” She was also invited to be the session chair for the conference. Tamra’s research focuses on modeling stochastically the transcription of DNA by RNA polymerases while incorporating new breakthroughs found in single-molecule experiments.

### Diana Schepens

Diana attended the Joint 2015 CAMBAM-MBI-NIMBioS Summer School at Mcgill University in Montreal, Canada, and had the opportunity to work with a small group using XXPAUT to investigate and present the bifurcation diagram of the Hodgkin-Huxley equations.

Diana’s current research is with Dr. Tomas Gedeon and a group from the Chemical and Biological Engineering department to model microbiome communities. In her research, the metabolic pathways of E. Coli bacteria are modeled using a deterministic model and reaction kinetics. They are then looked at in the context of bacterial communities where the modeled bacteria adapt to being able to work together to maximize the growth of the community. Many of the computational and mathematical tools discussed during the summer school have been helpful in the development and analysis of this model.

### Michael Broome

Michael attended Dalhousie University in Halifax, Nova Scotia to take a course in Reaction-Diffusion Systems to help better understand his research on improving mathematical models of biofilm growth, as well as the numerical simulations of these models.