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Pressé Lab Publications/Code

In Review

2019

        Our Confocal analysis code assuming a single diffusive species and Multi-diffusive species confocal analysis code are now available for download.

       See   Springer Nature

       See  Phys.org

       See  Science Daily

       See  Nanowerk      

       See   7th Space Family Portal

       See   Photonics.com   

            Our analysis code is now available for download.

            Our Single particle confocal tracking analysis code is now available for download.

           Our  SI available for download.

          Our FRET analysis code is now available for download.

2018 

           Our XL-ICON analysis code is now available for download.

2017

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

           Our ICON analysis code is now available for download.

           Our iHMM analysis code is now available for download.

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.

"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.

"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 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).

"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).

"Dynamical Fluctuations in biochemical reactions and cycles"
Steve Pressé*, Kingshuk Ghosh, R. Phillips, Ken A. Dill, Phys. Rev. E , 82, 031905 (2010).

"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).

"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).

 "Memory effects on the convergence properties of the Jarzynsky equality"
 Steve Pressé, R.J.Silbey*, Phys. Rev. E., 74, 061105 (2006).

See CV for even earlier Ph.D. and postdoc work...