StatPhysBio

Pressé Group

Our Work

2017

"Hydrodynamic hunters"
Hossein Jashnsaz, Mohammad Al Jaboori, Nicholas Miller, Tyler Nguyen, Bryan McCoy, Stephanie Perkins, Ross Wallgren, Bruce Ray, Konstantinos Tsekouras, Gregory Andefson*, Steve Pressé*, Biophys. J., 112, 1282 (2017). See SI here.

See Biophysical Journal Research Highlight.
See Welt.
See Zeit.
See Bild.
See Science Direct.
See Spiegel.
See SciShow with 270k+ views.
And 40+ news articles.

"ICON: an adaptation of infinite HMMs for time traces with drift"
Ioannis Sgouralis, Steve Pressé*, Biophys. J., accepted (2017). See SI here.

Our iHMM analysis code is now available for download.

"An introduction to infinite HMMs for single molecule data analysis"
Ioannis Sgouralis, Steve Pressé*, Biophys. J., accepted (2017). See SI here.

Our iHMM analysis code is now available for download.

"Single molecule data analysis: An introduction"
Meysam Tavakoli, J, Nicholas Taylor, Chun-Biu Li, Tamiki Komatsuzaki, Steve Pressé*, Adv. Chem. Physical. , accepted (2017).

"Unraveling the thousand word picture: An Introduction to super-resolution data analysis"
Antony Lee, Konstantinos Tsekouras, Christopher Calderon, Carlos Bustamante, Steve Pressé*, Chem. Rev. , DOI: 10.1021/acs.chemrev.6b00729 (2017).

2016

"A novel method to accurately locate and count large numbers of steps by photobleaching"
Konstantinos Teskouras, Thomas C. Custer, Hossein Jashnsaz, Nils G. Walter, Steve Pressé*, Mol. Biol. Cell, 27, 3601 (2016).

Our Photobleaching analysis code is now available for download with documentation. Also available on Github .

2015

"The heat released during catalytic turnover enhances the diffusion of an enzyme"
Clément Riedel, Christian A.M. Wilson, Kambiz Hamadani, Konstantinos Tsekouras, Susan Marqusee, Steve Pressé*, Carlos J. Bustamante*, Nature,517, 227 (2015). See SI here.

See News and Views article.
See C&EN Highlight.
See Phys.org article.
See IUPUI School of Science article.

See Comment on "Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions" by R.Golestanian -- arXiv response to criticism of our work (cited therein).

"Stochastic approach to the molecular counting problem in superresolution microscopy"
Geoffrey Rollins, Jae Yen Shin, Carlos J. Bustamante, Steve Pressé*, Proc. Natl. Acad. Sc. (Direct Submission), 112, E110 (2015).

Our Python analysis code is now available for download with documentation.

See EurekaAlert!.
See PNAS Research Highlight.
See IUPUI School of Science article.

"Inferring models of bacterial dynamics toward point sources"
Hossein Jashnsaz, Tyler Nguyen, Horia Petrache, Steve Pressé*, PLoS ONE , 10, e0140428 (2015).

An APS Story is written about our work.

"A data-driven alternative to the fractional Fokker-Planck equation"
Steve Pressé*, J. Stat. Phys.: Th. and Expmt. , P07009 (2015).

"Reply to C. Tsallis' `Conceptual inadequacy of the Shore and Johnson axioms for wide classes of complex systems' "
Steve Pressé*, Kingshuk Ghosh, Julian Lee, Ken A. Dill entropy , 17, 5043 (2015).

"Inferring Diffusional Dynamics from FCS in Heterogeneous Nuclear Environments"
Konstantinos Tsekouras, Amanda Siegel, Richard N. Day, Steve Pressé*, Biophys. J. , 109, 7 (2015).

Our Mathematica analysis code is now available for download.

2014

"Nonadditive entropy maximization is inconsistent with Bayesian updating"
Steve Pressé*, Phys. Rev. E , 90, 052149 (2014).

"Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin"
Steve Pressé*, Jack Peterson, Julian Lee, Phillip Elms, Justin L. MacCallum, Susan Marqusee, Carlos J. Bustamante, Ken A. Dill, J. Phys. Chem. B , 118, 6597 (2014).

2013

"Nonadditive entropies yield probability distributions with biases not warranted by the data"
Steve Pressé*, Kingshuk Ghosh, Julian Lee, Ken A. Dill, Phys. Rev. Lett. , 111, 180604 (2013).

See Science Daily article.
See IUPUI School of Science article.
See Tsallis' rebuttal on the arXiv to our PRL. Our PRL plainly shows that Tsallis' model inference prescription imposes structure in models that are not justified from the data. The rebuttal simply asserts that our starting axioms (due to Shore & Johnson) are not applicable to out-of-equilibrium systems (where it is qualitatively argued that the Tsallis entropy applies). Actually, this is a logical error. The axioms of Shore & Johnson have no notion of equilibrium. The PRL and rebuttal stand on their own. We will probably not publish a reply unless Tsallis' rebuttal manages to get published in a refereed journal (unlikely). We add that Tsallis entropy is not a small deal. The original paper by Tsallis has been cited about 5000 times and Tsallis (who lives in Brazil) is the single most cited author in South America. We are focused on developing new, and in many ways stronger, ideas which we hope will help focus the community's attention on principled inference methods that work.

"The ClpXP protease functions as a motor with constant 'rpm' but different 'gears' "
Maya Sen, Rodrigo A. Maillard, Kristofor Nyquist, Piere Rodriguez-Aliaga, Steve Pressé, A. Martin*, C. Bustamante*, Cell , 155, 636 (2013).

See IUPUI School of Science article.

"Principles of maximum entropy and maximum caliber in statitistical physics"
Steve Pressé*, Kingshuk Ghosh, Julian Lee, Ken A. Dill, Rev. Mod. Phys. , 85, 1115 (2013).

"Extracting conformational memory from single-molecule kinetic data"
Steve Pressé*, Julian Lee, Ken A. Dill, J. Phys. Chem. B , 117, 495 (2013).

2012 and earlier

"Microcanonical origin of the maximum entropy principle for open systems"
Julian Lee*, Steve Pressé*, Phys. Rev. E , 86, 041126 (2012).

"A derivation of the master equation from path entropy maximization"
Julian Lee*, Steve Pressé*, J. Chem. Phys. , 137, 074103 (2012).

"Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology"
G. Jack Peterson*, Steve Pressé, Kristin Peterson, Ken A. Dill, PLoS ONE , 7, e39052 (2012).

"Markov Processes Follow from the Principle of Maximum Caliber"
Hao Ge*, Steve Pressé, Kingshuk Ghosh, Ken A. Dill, J. Chem. Phys. , 136, 064108 (2012) -- Selected by the Editors as a Research Highlight.

"Modeling Stochastic Dynamics in Biochemical Systems with Feedback using Maximum Caliber"
Steve Pressé*, Kingshuk Ghosh, Ken A. Dill, J. Phys. Chem. B , 115, 6202 (2011).

"Nonuniversal Power Law Scaling in the Probability Distribution of Scientific Citations"
G. Jack Peterson, Steve Pressé, Ken A. Dill*, Proc. Natl. Acad. Sc. (Contributed), 107, 16023 (2010).

See CV for earlier work.