# Dynamical Models in Biology [MATH 336] (Section 01), Fall 2017

## General Information

• Instructor: James Greene
• Email: j{dot}c{dot}greene{at}rutgers{dot}edu
• Office: 216 Hill Center
• Office hours: M: 11-12, Th: 12-1, or by appointment
• Class location: ARC-107 (Busch campus)
• Class times: Tuesday and Thursday, 1:40-3 pm
• Textbook: Professor Sontag's free "Lecture Notes on Mathematical Systems Biology."

## Exam Dates

• Exam 1: Tuesday, October 17th, in class

• Exam 2: Tuesday, November 21st, in class

• Exam 3 (Final): December 18th, 12-3 pm, ARC-107

## Catalog Description

Models for biological processes based on ordinary and partial differential equations. Topics selected from models of population growth, predator-prey dynamics, biological oscillators, reaction-diffusion systems, pattern formation, neuronal and blood flow physiology, neural networks, biomechanics.

## Prerequisites

(MATH 244 OR MATH 252 OR MATH 292) AND (MATH 250). In laymen’s terms, you should have a good understanding of the standard engineering calculus sequence through ordinary differential equations, as well as linear algebra. Most of the analysis of models studied in this course will rely heavily on techniques from the listed previous math courses, so it is very important to have a good understanding of the prerequisites. Of course, I will review theory as we encounter it, but it most likely won’t be sufficient as a stand-alone treatment. For a good self-check, see the material (and more importantly, problem sets) appearing in Appendix A of the textbook (“Review of ordinary differential equations.”) Also, see the review homework in the Course Calendar. If you have concerns about the prerequisites, please feel free to contact me.

Formally, grades will be determined by homework and three exams. The breakdown is as follows:

 Homework 40% Midterm I 20% Midterm II 20% Final Exam 20%
Standard grading cutoffs apply (A ≥ 90%, 80% ≤ B < 90%, etc.), but will possibly be adjusted (in the student’s favor only) for “borderline cases” and in the case I deem a curve necessary. Note that any curving will be calculated at the end of the semester, but distributions for exams and homework will be provided.

Homework Homework will be assigned weekly, and will typically be due one week after assignment. All assignments will be distributed on the webpage, and should be turned in by the end of class on the due date. The two lowest grades will be dropped. Late homework will not be graded. Assignments will consist of a combination of theoretical and computational problems. Some assignments will require the use of computer software (in particular ODE solvers/phase portrait plotters). I recommend using MATLAB, although any programming software is acceptable. You will be expected to write your own code, but I will provide samples, and am very happy to talk about MATLAB programming in general. For a basic tutorial, see the Resources section below. Based on past experience, I strongly recommend learning MATLAB immediatly, as to avoid becoming overwhlemed later in the course; in general programming expectations will increase as the course progresses. For accessing MATLAB, see Resources below. Problems requiring MATLAB will be explicitly denoted by an M; otherwise the problem is expected to be worked by hand.

MATLAB projects I may also assign a few MATLAB projects, which will involve reading a short chapter on a specific biological phenonmena, and studying a mathematical model of the biological system using MATLAB. For these assignments, template code will be provided. In general, you will have a few (2-3) weeks to complete these projects, and your grade will be included in the homework portion for the course.

Note on collaboration You are encouraged to work together on HW assignments, but problem sets should be both written up and turned in individually. Furthermore, only submit work that is your own. Plagiarism is a serious offense, and will result in a score of zero for the assignment, as well as possible punishment from the University. You must also cite any reference you use and clearly mark any quotation or close paraphrase that you include. Such citation will not lower your grade, although extensive quotation might.

Exams The Final Exam will take place during the Exam week; it appears we are scheduled for December 18th, from 12-3 pm, in our normal classroom (ARC-107). Note that it will be cumulative, but possibly more heavily weighted to the material since Midterm II. The other two exams will take place in class, and will be announced at least two weeks prior to their administration, both in class and on the webpage (Course Calendar). In general they will be closed book, and no calculators or other electronic devices will be permitted. You will be allowed one sheet of notes (back and front), where you can summarize anything you want. Material there has to be written by you; you are not permitted to paste material directly from the course notes.

## Attendance and Participation

Students are expect to attend class regularly, as well as actively participate in discussions. Although not defined as a fixed portion of your final grade, participation will influence your overall performance in the class, especially in "border cases." If a class period is missed, you are expected to read and understand the material on your own; see the Course Calendar for detailed information and readings covered that day. For information on absence reporting and missing exams, see Absences and Make-ups below.

## Tenative Schedule

This class will follow Prof. Sontag’s notes fairly carefully, although material will at times be supplemented from other sources. I will keep an updated class schedule on the webpage (Course Calendar) during the semester, which will include sections covered, homework postings with due dates, and the exam schedule. Below you will find a tentative listing of model frameworks for the course, along with the approximate number of weeks spent on the particular subject:

 Scalar difference equations 1-2 weeks Ordinary differential equations (ODEs) 8-10 weeks Partial differential equations (PDEs) 3-4 weeks Stochastic processes 0-3 weeks
Models will be taken from various life science fields, but will be primarily focused in the systems biology realm (i.e. biological components such as molecules, cells, etc.). No prior biological knowledge will be assumed, but it is recommended to read the Systems Biology Introduction link in the Resources section. Also, it is very likely that stochastic processes (last entry above) will have to be omitted due to time constraints, but in the case it is not, no prior probability theory knowledge will be assumed.

## Absences and Make-ups

Students are expected to attend all classes; if you expect to miss one or two classes, please use the University absence reporting website to indicate the date and reason for your absence. An email is automatically sent to me. Please note that there will be no make-ups for quizzes or exams. If you have a major medical or personal problem and plan to miss an exam, please contact the instructor by email, with a note from the Dean's office to authenticate an absence that is supported by appropriate documentation.

All students in the course are expected to be familiar with and abide by the academic integrity policy. Violations of this policy are taken very seriously.

## Students with Disabilities

Full disability policies and procedures are indicated here. Students with disabilites requesting accommodations must present a Letter of Accommodations to the instructor as early in the term as possible.

## Sakai

I will use Sakai for email contact, as well as to post homework solutions. All enrolled students should have automatic access to the site after logging in to Sakai. Make sure to frequently check your email associated to your Sakai account.

## Resources

• Prof. Sontag's notes, the main text for the course.
• Prof. Sontag's molecular biology introduction, a good systems biology primer.
• Phase portrait review. A quick review on computing general solutions and phase portraits for linear systems. Note that I did not write it.