Biophysics and Physiological Modeling

There is a growing movement within biology to transform the undergraduate curriculum. Major goals are to develop active-learning teaching materials based on educational research, and to engage students in discovery-based activities so that they perceive biology as an evidence-based science with testable hypotheses that are supported by experimental data. As part of a National Science Foundation (NSF) grant, I'm developing a series of modules that engage students in inquiry-based activities to introduce them to the process of scientific modeling and validation. The modules are a self-contained series of self-study guides for undergraduates (both with and without calculus). The modules are designed so that students can complete them without additional assistance, making them suitable for use as stand-alone homework exercises or biophysics computer labs, or for a complete discovery-based active-learning course.

BIO 2010 - Transforming Undergraduate Education for Future Research Biologists (National Academies Press 2003) motivated me to write the NSF CCLI proposal for this project. The modules also address many of the core competencies identified in the report of the AAMC-HHMI Committee: Scientific Foundations for Future Physicians published by the Association of American Medical Colleges (AAMC) 2009 and they address many of the issues discussed by the "Overarching and unifying key concepts and competencies - Group B - Quantitative Competency" working group at the AAAS conference: Transforming Undergraduate Biology Education: Mobilizing the Community for Change (July 15-19, 2009) sponsored by the NSF. My presentation at this conference was about this Biophysics and Physiological Modeling project.

The modules are aimed at biology, pre-med and physical science majors interested in learning about physiological systems and processes. In the modules, we’ll develop simple models that can be implemented in an Excel spreadsheet. Using the spreadsheet, we’ll discover what the practical implications of the model are, and then we’ll compare the model predictions with experimental data (if available). For example, in the early modules, we’ll develop a simple (pharmacokinetic) model of how penicillin is eliminated from the body. While this model (and the other models we’ll develop) are particularly simple (and are therefore easy to understand :-) ), the molecular modeling approach is actually a cutting-edge research technique!

Once we’ve developed the drug elimination model, we’ll compare the model predictions with published data for healthy volunteers and intensive care patients on heart-lung machines to interpret the experimental data... There are numerous other topics that we can investigate with a similar approach including:

distribution of oxygen, carbon dioxide and glucose osmosis and homeostasis of erythrocytes fluid dynamics and blood flow kinetics of motors, carriers, and RNA

membrane transport and drug delivery diffusion of neurotransmitters ion channel permeation and gating ion channels and the action potential

I’m currently working on developing new topics and approaches. If there is a topic that you’re interested in, that you think might be fun to do, please let me know.

Beta testing and evaluation

A preliminary set of modules are now available (password required). If you’re interested in trying out these modules and evaluating them, please email me and I'll send you the password and details of the evaluation plan.

Self-study guides

The modules are self-contained workbooks. Hence, you (or your teaching assistant (TA)) can use them as supplemental Homework assignments or Biophysics computer labs, or for a discovery-based active-learning course.

Prerequisites and level

The modules assume a minimum of one year of college-level chemistry, and one year of (algebra-based) college-level physics. No calculus required! However, optional sections are included for those students with a year of university-level calculus. Hence, the modules can be done by advanced high school students with AP chemistry and physics. They are also suitable as an introduction to scientific modeling and validation for students who don’t take a formal course in biophysics or physiology e.g. graduate or medical students in interdisciplinary Biophysics or Molecular Biology PhD programs or MD/PhD programs.

Notwithstanding that the materials are accessible to well-prepared intermediate undergraduates; they also contain materials that have traditionally been taught at the graduate level. As an example, the kMC simulation technique (or the chemical master equation) is not in the traditional undergraduate curriculum even for chemistry or physics majors. The primary focus of the modules is quantitative scientific modeling with physiology applications.

Summer research opportunities

Students interested in working with me over the summer on this project should check out the Natural Science Summer Student Research Program.

Student researchers/testers

I would like to thank my students at BU in Biol/Chem/Phys 323 - "Biophysics" and Biol 310 - "Biophysics and Physiological Modeling", for their patience, support, encouragement and enthusiasm. I couldn’t have done it without you!

I would also like to thank the following students for their assistance: Nathan Kucera, Jonathan Rink, Ashley Rink, Stephanie Denny, David Faber, Matthew Harrison, James Norris, Muzamil Arshad, Amar Khatri, Luke Cox, Rama Wahood, Tricia Avanzado, Joy Holowicki, Madhish Patel, and Jacob Polaski.

Funding and awards

NSF Grant DUE-0836833
AAAS Conference: Transforming Undergraduate Biology Abstracts
AAMC MedEdPORTAL for Undergraduate Science (uScience)
HHMI Grant 52002669
Title III Grant - Benedictine University
NIH Post-Doctoral Fellowship in Quantitative Biology GM20584

Searching, resourses and portals

NSDL, ben (BiosciEdNet), CSERD, the Gateway, www.the-aps.org, www.apsarchive.org, Disseminating CCLI Educational Innovations, SALG, URSSA, Mobilizing STEM Education for a Sustainable Future, ESTEEM, DiscoverEd, Open Courseware, HHMI's BioInteractive, Biophysical Mechanisms (Biophysics Textbook Online - Biophysical Society), HHMI Membrane Awakening, BPM Hotlist

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This material is based upon work supported by the National Science Foundation under Grant No. 0836833.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

This page was last updated on September 2, 2010 by pHn.
© Peter Hugo Nelson 2009-10
All Rights Reserved

If you use these materials, you must attribute the work in the following manner. Cite the project as a whole as:
        Nelson, P. H. (2010) Biophysics and Physiological Modeling; Available from: http://circle4.com/biophysics/
Cite an individual module (e.g. Module 1) as:
        Nelson, P. H. (2010) Biophysics and Physiological Modeling - Module 1: Introduction - marble game (v.1.5); Available from: http://circle4.com/biophysics/