

MATHEMATICAL BIOLOGY Department of Applied Mathematics University of Washington
Overview Mathematical biology is a large and wellestablished branch of applied mathematics. The size of the field reflects both the importance of the biological and biomedical sciences and an appreciation for the mathematical subtleties and challenges that arise in modelling complex biological systems. Our interest, as a group, lies in understanding the spatial and temporal patterns that arise in dynamic biological systems and in understanding how these patterns affect biological function. Our mathematical activities range from nonlinear and chaotic dynamics, to reactiondiffusion equations, to optimization. We employ a variety of tools and models to study problems that arise in biomechanics, cell biology, development, ecology, epidemiology, neuroscience, and resource management. We maintain collaborations with a large number and variety of biologists and with biological and biomedical departments both here and elsewhere. Courses We teach a number of courses in mathematical biology including: Undergraduate/Graduate:
Graduate:
AMATH 422/522 Computational Modeling of Biological Systems Fundamental models that arise in biology and their analysis through modern scientific computing. Discrete and continuoustime dynamics, in deterministic and stochastic settings, with applications from molecular biology to neuroscience to population dynamics. Statistical analysis of experimental data. MATLAB or R programming taught from scratch. Prerequisites: Either a course in differential equations or permission of the instructor Course Web Page (Winter 2013)AMATH 423/523 Mathematical Analysis in Biology and Medicine This course focuses on developing and analyzing mechanistic, dynamic models of biological systems and processes, to better understand their behavior and function. Applications are drawn from many branches of biology and medicine. Students will gain experience in applying differential equations, difference equations, and dynamical systems theory to biological problems. Prerequisites: Either courses in differential equations and probability and statistics, or permission of the instructor Course Web Page (Spring 2013)AMATH 504 Mathematical Epidemiology Focuses on the construction and analysis of mathematical models for infectious disease transmission and control. Emphasizes evaluation and comparison of vaccination programs. Applications are presented for a variety of diseases such as measles, rubella, smallpox, rabies, etc. Prerequisites: AMATH 351 or equivalentAMATH 531 Mathematical Theory of Cellular Dynamics Biological cells are biochemical systems that obey the laws of physics. This course develops a coherent mathematical theory for processes inside living cells. It focuses on analyzing dynamics leading to functions of cellular components (gene regulation, signaling biochemistry, metabolic networks, cytoskeletal biomechanics, epigenetic inheritance) using deterministic and stochastic models. Prerequisites: Either courses in dynamical systems, partial differential equations, and probability, or permission of the instructor Course Web Page (Autumn 2012)AMATH 532 Mathematics of Genome Analysis and Molecular Modeling Genome analysis, i.e., bioinformatics, and molecular modeling in terms of molecular dynamics (MD) and Brownian dynamics are now fast growing areas of applied mathematics in molecular biology. This course introduces the fundamentals of these approaches in terms of discrete probability, classical mechanics, theory of diffusion, and Monte Carlo simulations. Prerequisites: Either Amath 506 or permission of the instructorAMATH 533 Neural Control of Movement This class provides a comprehensive view of how the brain controls movement. It brings together elements of biomechanics and muscle physiology, neuroanatomy and neurophysiology of the motor system, sensorimotor psychophysics and kinesiology, and movement disorders. Empirical data are interpreted in the context of controltheoretic models whenever possible. Prerequisites: Vector calculus, linear algebra, MATLAB, or permission of the instructorAMATH 534 Dynamics of Neurons and Networks Mathematical analysis and computational modeling on three interconnected scales \(em neurons, networks, and populations \(em including (1) oscillations and synchrony, (2) role of network structure and symmetry, (3) statistical mechanics tools for largescale models, (4) bifurcation and reduction methods for biophysical models. Emphasizes links between system dynamics and signal processing. Prerequisites: Eithr CSE/NBB 528 or permission of the instructorAMATH 535 Mathematical Ecology This course considers models, methods, and issues in population ecology. Topics include the effects of density dependence, delays, demographic stochasticity, and age structure on population growth; population interactions (predation, competition, and mutualism); and applications of optimal control theory to the management of renewable resources. Prerequisites: Either a course in differential equations or permission of the instructor Course Web Page (Spring 2011)AMATH 536 Spatial Models in Ecology and Epidemiology This course considers models for the growth and dispersal of biological populations. Topics include population persistence, climateinduced range shifts, and rates of spread of invading organisms. We will consider reactiondiffusion equations, integrodifference equations, branching random walks, and other relevant classes of models. Prerequisites: Either a course in partial differential equations or permission of the instructor Course Web Page (Spring 2014)Flier Here is a course flier to help you remember our courses.Schedule Schedule of Mathematical Biology Courses: Academic Year: 20102011
20112012
20122013
20132014
Journals Some of the better known journals of mathematical biology include:
All journals are not created equal.
Journal Clubs Mathematical Ecology Theoretical Neuroscience Biology The Mathematical Biology Journal Club (MBJC) is a group of students and faculty in mathematics, biological and physical sciences, medicine, as well as engineering who are interested in the interface of biology, medical science, and mathematics. MBJC meets once a week and encourages participants to explore topics of common interest. During autumn, 2013, MBJC will meet Friday, from 11:0012:00, in Lewis 208Ecology The Mathematical Ecology Journal Club (MEJC) is a group of students and faculty in applied mathematics, biology, and quantitative ecology and resource management who are interested in the mathematical aspects of ecology and resource management. MEJC meets once a week and encourages participants to explore topics of common interest. During autumn, 2013, MEJC will meet Tuesday, from 3:304:20 pm, in Lewis 208 (Please follow the link for registration information.)This fall, the journal club will read through the new book Post, E. 2013. Ecology of Climate Change: The Importance of Biotic Interactions. Princeton University Press. The schedule for the quarter is:
Neuroscience The Theoretical Neuroscience Journal Club (TNJC) is a group of students and faculty in applied mathemaics, biology, and neurobiology who are interested in theoretical neurobiology. TNJC meets once a week, on
and encourages participants to explore topics of common interest. Faculty Adjunct Faculty Temporary Faculty Visiting Faculty Core Faculty Hong Qian Eric SheaBrown Emanuel TodorovAdjunct Faculty Elizabeth HalloranTemporary Faculty Braden Brinkman Joel Zylberberg
Visiting Faculty
Postdocs
