Michael Lerner
Assistant Professor of Physics

Michael Lerner is a computational biophysicist who studies membranes, lipids, nucleic acids, proteins and dynamics, to examine problems from basic physics to drug design. He often collaborates with students on research projects.

He says of Earlham students, “in my experience, our students are all here because they are passionate about something. Even my introductory classes are entirely full of students who genuinely want to learn and explore.”

Contact Info

Campus Mail
Drawer 111

Phone
765-983-1784

E-mail
lernemi@earlham.edu

Office
221 Dennis Hall

Office Hours
Monday, Wednesday, Friday 10:00-11:00 (I generally have an open-door policy)

Website
Website Link

Programs/Departments

  • Physics and Astronomy
  • Environmental Science

Degrees

  • Ph.D., University of Michigan, Ann Arbor
  • M.S., University of Michigan, Ann Arbor
  • B.S., Haverford College

Selected Courses:

Analytical Physics I: Mechanics and Analytical Physics II: Electricity and Magnetism, Optics and Waves (Physics 125 and 235). These courses are the core introduction to our major and discipline, and I'm passionate about the material in both the classroom and the lab.

Modeling the World (Computer Science 290): We teach you the basics of Python, IPython Notebook, and NetLogo, and then develop computational models to examine the world, from social sciences to biology to physics and computer science. This class is particularly fun because of the broad range of perspectives interdisciplinary students bring.

Mathematical Physics (Physics 360). This course is cross-listed in mathematics and physics, and gives us a chance to lay down the fundamental mathematical methods needed to model the physical world. A student-chosen project is a key part of the course, and recent students have chosen to explore topics ranging from a numerical model of heat transfer for starting a fire without matches in the woods, to tensors, to the Fast Fourier Transform, to the mathematics behind AM radio.

Thermal Physics/Statistical Mechanics (Physics 375). This is one of the most fascinating fields of Physics, and one full of modern advances. We study the standard curriculum as well as computational models of non-equilibrium dynamics fresh from the literature. The course includes physical and computational labs. We also study Monte Carlo methods, and apply them to particularly important topics like predicting brackets for March Madness.

Senior Seminar: Advanced Statistical Mechanics and Molecular Simulation (Physics 480). This class combines active research topics with up-to-the-minute results from statistical mechanics.

I am a computational biophysicist (translation: I like to think like a physicist, think about problems motivated by biology, and use simulations as a "computational microscope" with which to examine the world). I study membranes, lipids, nucleic acids, proteins and dynamics, to examine problems from basic physics to drug design.

Molecular Dynamics
Diffusion of proteins and lipids within membranes
Protein structure and dynamics
Nucleic acid structure
Computational Topology Drug design

“Single molecule diffusion of membrane-bound proteins: Window into lipid contacts and bilayer dynamics”   Jefferson D. Knight, Michael G. Lerner, Joan G. Marcano-Velazquez, Richard W. Pastor and Joseph J. Falke   Biophysical Journal 99(9):2870-2887 (2010)

“Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design”  Michael G. Lerner, Kristin L. Meagher and Heather A. Carlson  Journal of Computer-aided Molecular Design 22(10):727-736 (2008)

“Protein Flexibility and Species Specificity in Structure-Based Drug Discovery: Dihydrofolate Reductase as a Test System” Anna L. Bowman, Michael G. Lerner and Heather A. Carlson  Journal of the American Chemical Society 129(12):48109-1065 (2007)

“Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery” Michael G. Lerner, Anna L. Bowman and Heather A. Carlson  Journal of Chemical Information and Modeling 47(6):2358-2365 (2007)

“Refining the Multiple Protein Structure Pharmacophore Method: Consistency across Three Independent HIV-1 Protease Models” Kristin L. Meagher, Michael G. Lerner and Heather A. Carlson  Journal of Medicinal Chemistry 49(12):3478-3484 (2006)

“Binding MOAD (mother of all databases)”  Leigi Hu, Mark L. Benson, Richard D. Smith, Michael G. Lerner and Heather A. Carlson Proteins: Structure, Function and Bioinformatics 60:333-340 (2005)

Recent poster presentations ([*] denotes research with Earlham Undergraduates):

“Molecular Dynamics Studies of Z[WC] DNA and the B to Z-DNA Transition” Michael G. Lerner, Jinhee Kim[*], Alexander K. Seewald[*]  Biophysical Society Meeting, San Francisco, 2014   

“Non-equilibrium Computation of Diffusion Constants for Water, Lipids and Proteins” Michael G. Lerner, Hoang Tran[*]  Biophysical Society Meeting, San Francisco, 2014   

“Teaching the Jarzynski equality with parallel computing” Michael G. Lerner, Laboratory Instruction Beyond the First Year of College, Philadelphia, 2012

American Association of Physics Teachers 
ALPhA (Advanced Laboratory Physics Association) 
Biophysical Society

Somewhere in the middle of my undergraduate career, I decided that I wanted to become a professor at a small, liberal arts college. I've tried several different careers (from volunteering in inner-city public schools in Chicago with City Year, to working as a computer programmer in the Bay Area during the dot-com boom), but my passion for both teaching and research kept bringing me back to academia. Earlham is the rare place that cares about all community members as people with both academic and non-academic lives, that brings the liberal arts to life in a modern setting, that values teaching excellence alongside research, and that holds Quaker ideals dear.

In my experience, Earlham students are all here because they are passionate about something. Even my introductory classes are entirely full of students who genuinely want to learn and explore, and I rarely run into a student who is just taking a class to check off a requirement. Earlham is a small, relatively intimate community, and I've found that literally every single student I've gotten to know has been an interesting, good person.

While most of the DNA structures that you see in textbooks are right-handed helices called B-DNA, it turns out that DNA can also be found in a left-handed helix, called Z-DNA. This left-handed form is important for relieving torsional strain, and is likely also involved in diverse parts of biochemistry ranging from gene regulation to Alzheimer's disease. Surprisingly, the biochemical process by which B-DNA is transformed into Z-DNA is still not well understood. Due to the size of the systems involved, direct experimental measurements range from hard to impossible. Our group works with Physics, Chemistry, Computer Science, and Biochemistry students to use computational models to understand this transition.

I help out with the Men's and Women's Ultimate Frisbee teams every spare moment that I get! I also enjoy cooking, spending time with my wife and three young children. I also enjoy power lifting, although perhaps that's not fair, as it provides some good examples for my Physics classes.

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