Markus Dittrich’s Homepage

About me

Markus’ picture

Hello and welcome to my webpage. I am the Director of the Biomedical Applications Group at the Pittsburgh Supercomputing Center and Carnegie Mellon University. In addition, I am Adjunct Assistant Professor in the Department of Computational and Systems Biology at the University of Pittsburgh.

Contact Information:

Markus Dittrich, Ph.D
National Resource for Biomedical Supercomputing
Pittsburgh Supercomputing Center
Carnegie Mellon University
300 South Craig Street, Rm 401
Pittsburgh, PA, 15213
phone: (412) 268-1688
fax : (412) 268-8200
email: dittrich(at)psc.edu



CV of Markus Dittrich

* CV of Markus Dittrich

Education and Work History

* Director, Biomedical Applications Group, PSC, 2014 - present
* Adjunct Assistant Professor, Department of Computational and Systems Biology, Univ. of Pittsburgh, 2012 - present
* Director, National Resource for Biomedical Supercomputing, PSC, 2012 - 2014
* Group Leader, National Resource for Biomedical Supercomputing, PSC, 2011 - 2012
* Senior Scientific Specialist, National Resource for Biomedical Supercomputing, PSC, 2010 - 2011
* Postdoctoral Researcher, Center for Quantitative Biological Simulation, PSC, 2006 - 2010
* Postdoctoral Researcher, Theoretical and Computational Biophysics Group, UIUC, 2005-2006
* Ph.D. in Physics, University of Illinois at Urbana-Champaign, 2005
* Diploma in Physics, University of Regensburg, Germany, 2000

Computing

For computing related items please check out my computing page.

Teaching

Materials for Team Project "Stochastic Reaction Simulator" as part of the 2014 PGSS for the Sciences.

General Stuff

As if spending most of my day in front of several computer screens wasn’t enough, I also spend a fair amount of my (little) spare time "computing around". In the past, I used to be a developer for Gentoo Linux mostly involved with porting and maintaining scientific applications. Currently, I do a fair amount of programming, mostly in Go, Haskell, C++, C, lua, ruby, bash, and python. To keep somewhat balanced I maintain a strict running schedule of 5-6 miles several times a week and I enjoy spending time with my wife Susan.

Some Talks I’ve been giving

* Structure And Function of Synapses: Novel Insights From Spatially Realistic Cell Simulations,
Seminar, Theoretical and Computational Biophysics Group, 2012, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL.

* Insights into the mechanism of molecular motors,
Seminar, J. Stiles Laboratory, 2006, Pittsburgh Supercomputing Center, Pittsburgh, PA.

* Quantum mechanical/molecular mechanical simulations of biomolecular systems,
Seminar, 2006, Sandia National Laboratory, Albuquerque, NM.

* Quantum mechanical/molecular mechanical simulations of biomolecular systems,
Seminar, A. Sali Laboratory, 2005, UCSF, San Francisco, CA.

* Quantum mechanical/molecular mechanical simulations of biomolecular systems,
Seminar, David Baker Laboratory, 2005, Univ. of Washington, Seattle, WA.

* When light falls in LOV: A computational study of a plant photoreceptor,
Biophysics and Computational Biology Summer Symposium,
Illinois Biophysics Society, 2005, UIUC, Urbana, IL.

* Quantum mechanical/molecular mechanical simulations of biomolecular systems,
International Workshop on Classical and Quantum Dynamical Simulations
in Chemical and Biological Physics
, 2005, MPIPKS, Dresden, Germany.

* Computational study of the chemomechanical coupling and ATP hydrolysis in F1-ATPase,
BPS Annual Meeting, 2005, Long Beach, CA.

* Insights into the molecular mechanism of ATP synthase, Gordon Research Conference on
Molecular and Cellular Bioenergetics, 2004, Proctor Academy, Andover, NH

General Articles

* Protein Motors Incorporated provides a nice and non-technical description of ATP synthase
and our work on ATP hydrolysis in F1 performed on the Jonas cluster at the PSC.

Poster Presentations

* Quantitative analysis of single calcium channel openings and evoked transmitter release from active zones
Neuroscience Meeting, 2008, Washington, DC.

* Experimental and theoretical analysis of calcium channel density and opening probability in active zones,
Neuroscience Meeting, 2007, San Diego, CA.

* Computational Study of ATP Hydrolysis and Force Generation in PcrA Helicase,
Biophysical Society Annual Meeting, 2006, Salt Lake City, UT.

* QM/MM study of ATP hydrolysis in F1-ATPase,
Biophysical Society Annual Meeting, 2004, Baltimore, MD.

* ATP hydrolysis in F1-ATPase: A combined ab initio QM/MM study,
Biophysical Society Annual Meeting, 2003, San Antonio, TX.

Publications

* An excess-calcium-binding-site model predicts neurotransmitter release at the neuromuscular junction.
M. Dittrich, J. M. Pattillo, J.D. King, S. Cho, J. R. Stiles, S.D. Meriney
Biophysical Journal, 2013, 104:2751-2763

* Organization and function of transmitter release sites at the neuromuscular junction.
S.D. Meriney and M. Dittrich
The Journal of Physiology, 2013, 591:3159-3165

* Are Unreliable Release Mechanisms Conserved from NMJ to CNS?
T.B. Tarr, M. Dittrich and S.D. Meriney.
Trends in Neuroscience, 2012, 36:14-22

* Single pixel optical fluctuation analysis of calcium channel function in active zones of motor nerve terminals.
F. Luo, M. Dittrich, J.R. Stiles and S.D. Meriney.
Journal of Neuroscience, 2011, 31:11268-11281

* Domain Motion of Individual F1-ATPase β-Subunits during Unbiased Molecular Dynamics Simulations.
U. Kleinekathofer, B. Isralewitz, M. Dittrich, and K. Schulten.
J Phys Chem A, 2011, 115:7267-7274

* (R)-Roscovitine prolongs the mean open time of unitary N-type calcium channel currents.
N. R. DeStefino, A. Pilato, M. Dittrich, S. V. Cherry, S. Cho, J. R. Stiles, and S. D. Meriney.
Neuroscience, 2010, 167:838-849.

* Rapid Creation, Monte Carlo Simulation, and Visualisation of Realistic 3D Cell Models.
J. Czech, M. Dittrich, and J.R. Stiles.
Methods in Molecular Biology, Systems Biology, 2009, ed. Maly, Ivan V. Humana Press, Clifton, NJ, 237-287.

* Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces.
R. Kerr, T.M. Bartol, B. Kaminsky, M. Dittrich, J.C.J. Chang, S. Baden, T.J. Sejnowski, and J.R. Stiles.
SIAM J. Sci. Comput., 2008, 30:3126-3149.

* Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins.
Peter L. Freddolino, Markus Dittrich, and Klaus Schulten.
Biophysical Journal, 2006, 91:3630-3639.

* PcrA helicase, a prototype ATP-driven molecular motor.
Markus Dittrich and Klaus Schulten.
Structure, 2006, 14:1345-1353.

* PcrA helicase, a molecular motor studied from the electronic to the functional level.
Markus Dittrich, Jin Yu, and Klaus Schulten.
Topics in current chemistry, 2006, 268:319-347.

* Zooming in on ATP hydrolysis in F1.
Markus Dittrich and Klaus Schulten.
Journal of Bioenergetics and Biomembranes, 2005. 37:441.

* When light falls in LOV: A QM/MM study of photoexcitation in Phot-LOV1 of C. Reinhardtii.
Markus Dittrich, Peter Freddolino, and Klaus Schulten.
Journ. Phys. Chem. B, 2005, 109:13006-13013.

* ATP hydrolysis in the βTP and βDP catalytic sites of F1-ATPase.
Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten.
Biophysical Journal, 2004, 87:2954-2967.

* On the mechanism of ATP hydrolysis in F1-ATPase.
Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten.
Biophysical Journal, 2003, 85:2253-2266.

* Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations.
Rob Phillips, Markus Dittrich, and Klaus Schulten.
Annual Review of Materials Research, 2002, 32:219-233.
This page was created in 2006.
This page was last modified on July 3, 2013.
My e-mail address is dittrich(at)psc(dot)edu.


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