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This is the wiki page associated with PHYS/BIOL 4803/4804 Physical Principles of Living Systems.

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PHYS/BIOL 4803/4804 is an undergraduate level course taught by Professor Daniel I. Goldman in the School of Physics at the Georgia Institute of Technology. The TA is Megan Matthews.

This course is built around modules on topics from protein folding to cell motility to neuromechanics to dynamical systems in ecology and evolution; each module is taught by Dr. Goldman using materials from PoLS colleagues. In each module:

1st week: Lecture based around materials from colleagues, textbooks, and literature, on a different topic every other week; curriculum mirroring BIOL 1510. On Thursday of week one in each module, students “meet the expert”; a colleague visits and provides input in his/her area of expertise.

2nd week: Hands on-lab, “Micro-labs” (one week experiences, every other week) use low cost sensors (e.g. in smartphones) and open source computational packages to provide hands-on introduction to a particular area. Students work in teams of 2 (4-5 groups). The goal is to get a scientific result comparing experiment and theory/model by the end of the week. Micro-lab pedagogy is built off Dr. Goldman’s experience teaching in the International Hands-On Schools and see GT-FIRE experience.

There is no textbook for this class; source material is pulled from open source texts (e.g. http://openstaxcollege.org/), papers, and expertise from guest lecturers.

Learning Outcomes[edit]

Through work on modules, students will be introduced to PoLS topics and gain confidence and experience with relevant multi-scale biophysical experimental, computational, and theoretical techniques, as well as be introduced to a common language of nonlinear dynamics. After completing this class, students will be able to: (1) Construct low-cost laboratory equipment to investigate fundamental biophysical processes, (2) Integrate measurement, mechanism, and modeling in the study of these systems, and (3) Analyze biophysical systems with computational and theoretical tools (i.e. nonlinear dynamics, molecular dynamics simulations, and statistical mechanics).

Image Gallery[edit]

All photos and videos are taken with the smartphone microscope (magnification ~100X) using a 0.7mm diameter glass bead.

Course Details[edit]

To view each semester separately, use the links below:

Module 1: Measurement, Mechanism, and Modeling[edit]

Description: Introduction to the intersection of physics and biology including information on the tools (3D printing, microscopy, electronics, MATLAB, etc.) and methods used in studying the physics of living systems.

Protocols[edit]

Assignments & Results[edit]

Fall 2015
Spring 2016 


Resources:

Module 2: Evolution[edit]

Description: This module explores the history of life on Earth and various mechanisms of evolution through mathematical modeling and simulation as well as hands-on laboratory experiments. Key concepts include Earth geohistory, emergence, and the evolution of multicellularity.

Protocols[edit]

Assignments & Results[edit]

Fall 2015
Spring 2016 

Resources:

Module 3: Biomolecules[edit]

Description: By employing techniques from statistical mechanics and nonlinear dynamics, we are able to study the underlying mechanisms of how biomolecules move and interact to perform cellular processes. Processes such as transcription, diffusion, and other molecular interactions are explored by studying energy landscapes of given molecules as well as running molecular dynamics (MD) simulations of biomolecules in specific landscapes.

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Protocols[edit]

Assignments & Results[edit]

Fall 2015

Spring 2016

Resources:

Module 4: Ecology[edit]

Description: Studying the population dynamics of groups of organisms provides an example of how physics (nonlinear dynamics, ODEs, limit cycles, chaos, etc.) can be used to gain further insight into fundamental biological processes.

Rotifer-algae culture imaged with 10X microscope objective lens.

Protocols[edit]

Assignments & Results[edit]

Fall 2015 Spring 2016

Resources:

Module 5: Cells, Tissues, & Organs[edit]

Description: Cells accumulate to form groups of moving parts whose dynamics are distinct from single cell behavior and, depending on the level of organization, different methods must be used. This process, known as emergence, can be seen in the ability of individual cells, such as cardiac cells, to work collectively as tissues. Cellular processes like phagocytosis also provide an example of how individual cells can work together towards a common goal.

Macrophage (possibly) undergoing frustrated phagocytosis, captured on smartphone with phonescope (~100X)

Protocols[edit]

Assignments & Results[edit]

Fall 2015 Spring 2016

Resources:

Module 6: Neuro- & Biomechanics[edit]

Description: Organisms use feedback and control systems to dynamically interact with their environment and by investigating these biological systems we can learn more about animal physiology, locomotion, and neuromechanics.

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Protocols[edit]

Assignments & Results[edit]

Fall 2015 Spring 2016

Resources:

Module 7: Create-your-own (DIY) Microlab[edit]

DIY Microlab Topics[edit]

Fall 2015:

a. Homemade PCR and build a gel electrophoresis chamber to run a gel

b. Behavior of fire ant rafts composed of uniform v. mixed colonies

c. Cockroach muscle activity during running (flat, incline, & rough terrain) and (vertical) climbing

Spring 2016:

a. Quantification of Electric Potential in Zebrafish Hearts

b. Phonescope Redesign

c. Study of Balance During Weight-Shifting for Standard Indoor Rowing

Future modules:

a. Giant axon nerve recording in earthworm

b. Evolution of beak shapes in finches (Brenner)

c. Zoo Atlanta project (animal locomotion)

d. Build a robot to test template control (servo + Arduino)

e. Sarcomere laser diffraction, lobster claw (red laser pointer)

f. Calcium optical mapping of a zebrafish heart

g. Development of phase contrast microscopy for smartphone microscope

h. Development of an oscilloscope app for Android/iPhone

i. Muscle work-loop in cockroach leg

About[edit]

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