Biomedical Computer Simulation Methods BME 210 Syllabus - 2011 Spring Semester

1. Basic Information Course: Place and time: Faculty: Office: Telephone Email: Office Hours: TAs Prerequisite: Co-requisites: Class web page: Biomedical Computer Simulation Methods, BME 210, 3 units THH 212, MW: 2:00 pm-3:15 pm David Z. DArgenio, Ph.D. Professor, BME Denny Research Center, Suite 140, Room 154 740-0341 dargenio@usc.edu M 3:30 to 5:00 pm Niharika Gajawelli, DRB 140, gajawell@usc.edu, T. 1:00pm-3:00pm Devyani Nanduri, DRB 140, nanduri@usc.edu, T. 11:00am-1:00pm Madison Zitting, DRB 140, zitting@usc.edu, Th. 10:am-noon. EE 150 MATH 245 https://blackboard.usc.edu/ (follow links to BME 210)

2. Motivation for BME 210 While the computer has been an essential scientific and engineering problem-solving tool since the 1960s, much of its early use involved data reduction problems. With the dramatic advances in the computational power of more recent machines, however, the computer has become more of a tool for simulation, exploration and discovery of underlying principles describing the natural world. For example, we can now realistically tackle some of the nonlinear partial differential equations for general geometries that describe a great portion of the phenomena of nature (von Neumanns goal). The mathematician James Glimm has written, computers will affect science and technology as profoundly as did the invention of calculus. This is a very bold prediction when one considers that calculus has been central to the discovery of electromagnetism, gas and fluid dynamics, statistical mechanics and general relativity. Other scientific computing enthusiasts speak of a paradigm shift a new mode of doing science and engineering. They use terms such as experimental theory and numerical experiments, and point to such sub-fields as numerical relativity, computational fluid dynamics, and computational biology, as well as radically new approaches in mathematics like Efrons bootstrap method for statistical inference. Regardless of ones level of enthusiasm, it would seem irrefutable that the computer will occupy an even more central role in solving future problems in science and engineering. Consequently, it is imperative that as undergraduates you are exposed to scientific computing as a central and essential tool for scientific exploration and engineering problem solving. There is a relatively small number of basic concepts and principles that are the foundation for a large portion of modern-day science and engineering (e.g., principles of mass, momentum, energy and information transfer). Extensive treatment of many of these concepts traditionally does not take place until upper division courses in specific departments, after an adequate

background is achieved in mathematics, physics, chemistry and biology. Some of these important cross-disciplinary concepts, however, can be introduced in a preliminary yet rigorous manner early in the undergraduate curriculum using the computer to implement simulations of these fundamental processes. 3. Course Goals, Learning Objectives, and relationship to Program Outcomes 3.1. Goals: The overall goal of BME 210 is to introduce you to the computer as a tool for studying biomedical phenomena and for solving biomedical engineering problems. You will learn a number of important computational techniques and you will use them to explore different biological principles and solve a variety of biomedical problems. In the course, you will learn about: measuring cardiac output; receptor kinetics; medical imaging; therapeutic drug kinetics; spread of infectious diseases; intraocular drug delivery. numerical quadrature; spline approximation; solution of ordinary differential equations; solution of systems of linear equations; function minimization; simulation of random processes; solving partial differential equations. 3.2 Learning objectives and relationship to program outcomes: After successfully completing this course, you should be able to: describe the principle of indicator dilution and its application to measuring cardiac output (outcomes a, e, l, m); explain the basic idea for receptor-ligand interactions and mathematical models used to describe this process (outcomes a, e, l, m); explain the processes governing the transport of molecules (e.g., therapeutics drugs) in the body and the compartment modeling framework used to characterize the time course of transport (outcomes a, e, l, m); describe the principle of x-ray computed tomography for medical imaging and how to formulate the image reconstruction problem (outcomes a, e, l, m); explain the steps involved in the spread of disease in a population, and how to model the process using random events (outcomes a, e, l, m); describe computational methods for numerical quadrature, and to design software that applies the different methods to indicator dilution data for calculating cardiac output (outcomes 1 and 3); describe methods for numerically solving differential equations, and to implement these methods in software to solve receptor-ligand and drug kinetic models (outcomes 1 and 3); explain methods for solving the systems of linear equations that arise in medical image reconstruction, and to use MATLAB to solve the image reconstruction problem (outcomes a, e, k, l, m); use MATLAB to simulate and analysis the results from a stochastic simulation of the spread of disease (outcomes a, e, k, l, m); describe methods for numerically solving partial differential equations, and to implement these methods in software to solve intraocular drug delivery model (outcomes a, e, k, l, m);

 prepare written reports that document solutions to homework projects and present
simulations results and analyses (outcome g); supplement through independent study of reference readings the biological and computational concepts presented in class (outcomes i)

Relationship to BME program outcomes: This course contributes strongly to Program Outcomes a, e, l, m and moderately to Program Outcomes g, i, k. 4. Schedule of Classes Date Jan 10 Jan 12 Jan 17 Jan 19 Jan 24 Jan 26 Jan 31 Feb 2 Feb 7 Feb 9 Feb 14 Feb 16 Feb 21 Feb 23 Feb 28 March 2 March 7 March 9 March 14-18 March 21 March 23 March 28 March 30 April 4 April 6 April 11 April 13 April 18 April 20 April 25 April 27 Day M W M W M W M W M W M W M W M W M W M W M W M W M W M W M W Topic Introduction MATLAB Review MLK Holiday Measuring Cardiac Output Measuring Cardiac Output Measuring Cardiac Output Measuring Cardiac Output Receptor Kinetics Receptor Kinetics Receptor Kinetics Receptor Kinetics Receptor Kinetics Presidents Day Holiday Examination 1 Medical Imaging Medical Imaging Medical Imaging Therapeutic Drug Development Spring Recess Therapeutic Drug Development Therapeutic Drug Development Therapeutic Drug Development Spread of Disease Examination 2 Spread of Disease Spread of Disease Spread of Disease Ocular Drug Delivery Ocular Drug Delivery Ocular Drug Delivery Ocular Drug Delivery Home Work

HW1 Assigned

HW1 Due/ HW2 Assigned

HW2 Due Noon Feb. 22 HW 3 Assigned

HW3 Due/HW4 Assigned

HW4 Due/ HW5 Assigned

HW 5 Due, HW6 Assigned HW6 Due (April 29)

May 9

Final Examination (2:00-4:00pm)

5. Source Materials 1. MATLAB. The Math Works. A Campus wide license is available (PC and Mac). Download the software via http://software.usc.edu. (A valid USC login is required.) 2. BME 210 Notebook. For purchase at BME office. 6. Work Load, Grading, Academic Integrity Your grade will be based on your performance on class tests and homework assignments as follows: Percent of final grade Examination 1 25 Examination 2 25 Final Exam 25 Homework assignments 25 100 The homework will consist of both written assignments and computer work. The computer work will involve solving problems using the MATLAB software system. While you may consult with classmates regarding the homework assignments, you are expected to write your own computer code and homework reports. Direct plagiarism of another's work (including computer program code) is a very serious offense and all suspected cases will be dealt with according to University regulations (see SCampus). All homework assignments are to be turned in at the beginning of class on the day they are due, or as indicated on the home assignement. For every day (or portion of a day) an assignment is late, 25% will be subtracted from its maximum point total. 7. Web Page This course uses Blackboard and can be accessed via https://blackboard.usc.edu. Be sure to CHANGE YOUR EMAIL to the one you use most frequently as we will send out email messages during the semester using your email address that is associated with Blackboard. 8. Special Accommodations Students requesting academic accommodations based on a disability are required to register with Disability Services and Programs (DSP) each semester. A letter of verification for approved accommodations can be obtained from DSP when adequate documentation is filed. Please be sure the letter is delivered to me within the first few weeks of the semester. DSP is open Monday-Friday, 8:30-5:00. The office is in Student Union 301 and the phone number is (213) 740-0776.

USC BIOMEDICAL ENGINEERING PROGRAM OUTCOMES

Graduates of the program are able to: (a) an ability to apply knowledge of mathematics, science, and engineering (b) an ability to design and conduct experiments, as well as to analyze and interpret data (c) an ability to design a system, component, or process to meet desired needs within realistic constraints such as economic, environmental, social, political, ethical, health and safety, manufacturability, and sustainability (d) an ability to function on multidisciplinary teams (e) an ability to identify, formulate, and solve engineering problems (f) an understanding of professional and ethical responsibility (g) an ability to communicate effectively (h) the broad education necessary to understand the impact of engineering solutions in a global, economic, environmental, and societal context (i) a recognition of the need for, and an ability to engage in life-long learning (j) a knowledge of contemporary issues (k) an ability to use the techniques, skills, and modern engineering tools necessary for engineering practice. (l) an understanding of biology and physiology (m) the capability to apply advanced mathematics (including differential equations and statistics), science, and engineering to solve problems at the interface of engineering and biology** (n) an ability to make measurements on and interpret data from living systems (o) an ability to address problems associated with the interaction between living and non-living materials and systems