Eric Dufresne

Professor

Publications

  • Etienne Jambon-Puillet, Andrea Testa, Charlotta M Lorenz, Robert W Style, Aleksander Rebane, Eric Robert Dufresne, “Phase-Separated Droplets Swim to Their Dissolution” bioRxiv (2023)
  • Carla Fernández-Rico, Sanjay Schreiber, Hamza Oudich, Charlotta Lorenz, Alba Sicher, Tianqi Sai, Stefanie Heyden, Pietro Carrara, Laura De Lorenzis, Robert W. Style, Eric R. Dufresne “Elastic Microphase Separation Produces Robust Bicontinuous Materials” arXiv (2023) https://arxiv.org/abs/2304.11419
  • Maria Feofilova, Silvan Schüepp, Roman Schmid, Florian Hacker, Hendrik T. Spanke, Nicolas Bain, Katharine E. Jensen, Eric R. Dufresne “Geometrical frustration of phase-separated domains in Coscinodiscus diatom frustules” Proc. Nat. Acad. Sci. (2022) https://doi.org/10.1073/pnas.2201014119
  • Thomas J. Böddeker, Kathryn A. Rosowski, Doris Berchtold, Leonidas Emmanouilidis, Yaning Han, Frédéric H. T. Allain, Robert W. Style, Lucas Pelkmans, Eric R. Dufresne ” Non-specific adhesive forces between filaments and membraneless organelles” Nature Physics (2022) https://doi.org/10.1038/s41567-022-01537-8
  • C. Fernandez-Rico, T. Sai, A. Sicher, R. W. Style, and E. R. Dufresne “Putting the Squeeze on Phase Separation”  JACS Au (2021) https://doi.org/10.1021/jacsau.1c00443
  • N. Bain, A. Jagota, K. Smith-Mannschott, S. Heyden, R. Style, E.R. Dufresne ”Surface tension and the strain-dependent topography of soft solids”Physical Review Letters (2021)
  • A. Testa*, M. Dindo*, A. Rebane, B. Nasouri, R.W. Style, R. Golestanian, E.R. Dufresne, P. Laurino “Sustained Enzymatic Activity and Flow in Crowded Protein Droplets” Nature Communications (2021) https://www.nature.com/articles/s41467-021-26532-0
  • V. Saranathan, S. Narayanan, A., E.R. Dufresne, R. O. Prum, “Single Gyroid and Inverse b.c.c. Photonic Crystals in Bird Feathers” Proc. Nat. Acad. Sci. (2021) https://doi.org/10.1073/pnas.2101357118  
  • H.T. Spanke, R. W. Style, C. François-Martin, M. Feofilova, M. Eisentraut, H. Kress, J. Agudo-Canalejo, E. R. Dufresne, “Wrapping of Microparticles by Floppy Lipid Vesicles” Phys. Rev. Lett. (2020) https://doi.org/10.1103/PhysRevLett.125.198102
  • K.A. Rosowski*, T. Sai*, R.W. Style, E.R. Dufresne “Elastic ripening and inhibition of liquid-liquid phase separationNature Physics (2020) https://www.nature.com/articles/s41567-019-0767-2.pdf?draft=collection

Stephen Levy

Adjunct Professor

Publications

L. Dai, J. Jones, A. Klotz, S. Levy, P. Doyle. "Nanoconfinement greatly speeds up the nucleation and the annealing in single-DNA collapse." Soft Matter, 2017, Advance Article.

A. Klepinger, M. Greenier, and S. Levy. "Stretching DNA Molecules in Strongly Confining Nanoslits." Macromolecules, 2015, 48 (24), 9007–9014.

L. Wu and S. Levy. "Fluctuations of DNA mobility in nanofluidic entropic traps." Biomicrofluidics 2014, 8, 044103.

S. Levy, H. G. Craighead. "DNA Manipulation, Sorting, and Mapping in Nanofluidic Systems. " Chemical Society Reviews 2010, 39 (3), 1133–1152.

Michelle Wang

James Gilbert White Distinguished Professor of the Physical Sciences, Howard Hughes Medical Institute Investigator

Publications

T.T. Le, X. Gao, S. Park, J. Lee, J. T. Inman, J.H. Lee, J.L. Killian, R.P. Badman, J.M. Berger, and M.D. Wang. “Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity.” Cell 179: 619–631 (2019).

T.T. Le, Y. Yang, C. Tan, M.M. Suhanovsky, R.M. Fulbright, Jr., J.T. Inman, M. Li, J. Lee, S. Perelman, J.W. Roberts, A.M. Deaconescu, and M.D. Wang. “Mfd dynamically regulates transcription via a release and catch-up mechanism.” Cell 172, 344-357 e315 (2018).

M. Soltani, J. Lin, R.A. Forties, J.T. Inman, S.N. Saraf, R.M. Fulbright, M. Lipson, and M.D. Wang. “Nanophotonic trapping for precise manipulation of biomolecular Arrays.” Nature Nanotechnology 9:448-52 (2014).

J. Ma, L. Bai, and M.D. Wang. “Transcription under torsion.” Science 340:1580-3 (2013).

B. Sun, D.S. Johnson, G. Patel, B.Y. Smith, M. Pandey, S.S. Patel, and M.D. Wang. “ATP-induced helicase slippage reveals highly coordinated subunits.” Nature 478:132 -5 (2011).

D.S. Johnson, L. Bai, B.Y. Smith, S.S. Patel, and M.D. Wang. “Single molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.” Cell 129:1299-309 (2007).

C. Deufel, S. Forth, C.R. Simmons, S. Dejgosha, and M.D. Wang. “Nanofabricated quartz cylinders for angular optical trapping: torque detection during DNA supercoiling.” Nature Methods 4:223-5 (2007).

Jane Wang

Professor

Publications

Z. J. Wang, J. Melfi Jr., A. Leonardo, Recovery mechanisms in the dragonfly righting reflex, Science (2022).

H. Li, T. Goodwill, Z. J. Wang, and L. Ristroph, Center of mass location, flight modes, stability and dynamic modeling of gliders, Journal of Fluid Mechanics (2022)

 Z. J. Wang, R. Chang, L. Ristroph, Dragonfly righting reflex, APS-DFD Gallery of Fluids (2021)

A. El-Yacoubi, S. Xu, Z. J. Wang, A New method for computing particle collisions in Navier-Stokes flows , Journal of Computational Physics (2019)

R.M. Noest, Z. J. Wang, Optimal wing hinge location for fast ascent in a model fly , Journal of Fluid Mechanics (2018)

Z. Jane Wang, Insect Flight: From Newton's Law to Neurons , Annual Review of Condensed Matter Physics (2016)

S. Chang, Z. J. Wang, Predicting fruit fly's sensing rate with insect flight simulations, Proceedings of the National Academy of Sciences of the United States of America 1314738111 (2014)

A. J. Bergou, L. Ristroph, J. Guckenheimer, I. Cohen, Z. J. Wang, Fruit Flies Modulate Passive Wing Pitching to Generate In-Flight Turns, Physical Review Letters 104,148101 (2010)

U. Pesavento, Z. Jane Wang, Flapping Wing Flight Can Save Aerodynamic Power Compared to Steady Flight, Physical Review Letters 103,118102 (2009)

G. Berman, and Z. J. Wang, Energy-minimizing kinematics in hovering insect flight, Journal of Fluid Mechanics 582, 153-168 (2007)

Sheng Xu and Z. Jane Wang, An Immersed Interface Method for Simulating the Interaction of a Fluid with Moving Boundaries, Journal of Computational Physics 201, 454-493 (2006)

A. Andersen, U. Pesavento, and Z. Jane Wang, Unsteady aerodynamics of fluttering and tumbling plates, Journal of Fluid Mechanics 541, 65-90 (2005)

Z. Jane Wang, Dissecting Insect Flight, Annu. Rev. Fluid Mech. 2005.37, 183-210 (2005)

Z. Jane Wang, Two Dimensional Mechanism for Insect Hovering, Physical Review Letters 85.10, 2216-2219 (2000)

Robert Thorne

Professor, Stephen H. Weiss Presidential Fellow

Publications

Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection.  J. A. Clinger, D. W. Moreau, M. J. McLeod, T. Holyoak, and R. E. Thorne. IUCrJ 8, 784-792 (2021). DOI: 10.1107/S2052252521007053

High-resolution single-particle cryo-EM of samples vitrified in boiling nitrogen.  T. Engstrom, J. A. Clinger, K. A. Spoth, O. B. Clarke, R. Jayne, B. A. Apker and R. E. Thorne.  IUCrJ 8, 867-877 (2021). DOI: 10.1107/S2052252521008095

Integrated sample handling and mounting system for fixed-target serial synchrotron crystallography.  G. Illava, R. Jayne, A. D. Finke, D. Closs, W. Zeng, S. K. Milano, Q. Huang, I. Kriksunov, P. Sidorenko, F. W. Wise, W. R. Zipfel, B. A. Apker and R. E. Thorne.  Acta Cryst. D 77, 628-644 (2021). DOI: 10.1107/S2059798321001868.

Hypothesis for a mechanism of beam-induced motion in cryo-electron microcopy.  R. E. Thorne. IUCrJ 7, 416-421 (2020). DOI: 10.1107/S2052252520002560.

Resolution and dose dependence of radiation damage in biomolecular systems. H. Atakisi, L. Conger, D. W. Moreau, and R. E. Thorne. IUCrJ 6, 1040-1053 (2019).  DOI: 10.1107/S2052252519008777

Solvent flows, conformation changes and lattice reordering in a cold protein crystal. D. W. Moreau, H. Atakisi and R. E. Thorne.  Acta Cryst. D 75, 980-994 (2019). DOI: 10.1107/S2059798319013822

Ice formation and solvent nanoconfinement in protein crystals. D. W. Moreau, H. Atakisi, and R. E. Thorne.  IUCrJ 6, 346-356 (2019).  DOI: 10.1107/S2052252519001878

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams.  M. A. Warkentin, H. Atakisi, J. B. Hopkins, D. Walko, and R. E. Thorne, IUCrJ 4, 785-794 (2017).  DOI: 10.1107/S2052252517013495

Mapping the Conformational Landscape of a Dynamic Enzyme by XFEL and Multitemperature Crystallography. D. A. Keedy, L. R. Kenner, M. Warkentin, J. B. Hopkins, R. A. Woldeyes, M. C. Thompson, A. S. Brewster, A. H. Van Benschoten, E. L. Baxter, M. Uervirojnangkoorn, J. M. Holton, W. I. Weis, A. T. Brunger, S. M. Soltis, H. Lemke, A. Gonzalez, N. K. Sauter, A. E. Cohen, H. van den Bedem, R. E. Thorne and J. S. Fraser. Elife 4, e07574 (2015). DOI: 10.7554/eLife/07574

Breaking the radiation damage limit with cryo-SAXS. S. P. Meisburger, M. Warkentin, H. Chen, J. B. Hopkins, R. E. Gillilan, L. Pollack and R. E. Thorne. Biophys. J. 104, 227-236 (2013). DOI: 10.1016/j.bpj.2012.11.3817

Application of X-ray fluorescence imaging to ceramics from the American Southwest. E. C. Geil, S. A. LeBlanc, D. S. Dale and R. E. Thorne. J. Arch. Sci. 40, 4780-4784 (2013). DOI: 10.1016/j.jas.2013.05.014

Critical droplet theory explains the glass formability of aqueous solutions. M. Warkentin, J. P. Sethna and R. E. Thorne. Phys. Rev. Lett. 110, 015703 (2013). DOI: 10.1103/PhysRevLett.110.015703

X-ray fluorescence recovers writing from ancient inscriptions.  J. Powers, N. Dimitrova, R. Huang, D. M. Smilgies, D. H. Bilderback, K. Clinton, and R. E. Thorne. Zeitschrift fur Papyrologie und Epigraphik 152, 221 (2005).

Growth and disorder of macromolecular crystals: insights from atomic force microscopy and X-ray diffraction studies. A. J. Malkin and R. E. Thorne. Methods 34, 273 (2004). DOI: 10.1016/j.ymeth.2004.03.020

Charge-density-wave conductors. R. E. Thorne. Physics Today. May 1996, p. 42. DOI: 10.1063/1.881498

Eric Siggia

Adjunct Professor

Publications

A 3D model of a human epiblast revelas BMP4-driven symmetry breaking. Simunovic, M.;Metzger, JJ.; Etoc, F.; Yoney, A.; Ruzo, A.; Martyn, I.; Croft, G.; You, DS.; Brivanlou, AH.; Siggia, ED. Nat. Cell. Biol. 2019, July:21(7):900-910.

Self-organization of stem cells into embryos: A window on early mammalian development. Shahbazi, MN; Siggia, ED; Zernicka-Goetz, M. Science. 2019, June 7: 364(6444): 948-951.

Gene-free methodology for cell fate dynamics during development. Corson, F; Siggia, ED. Elife. 2017, Dec 13:6.

“A Balance between secreted inhibitor and edge-sensing controls gastruloid self-organization”, F.Etoc, J Metzger, A. Ruzo, C. Kirst, A. Yoney, Z. Ozair, A. Brivanlou, E. Siggia, Dev Cell 2016 (to appear).

“Encoding of Temporal Signals by the TGF-β Pathway and Implications for Embryonic Patterning.”, Sorre B1, Warmflash A1, Brivanlou AH2, Siggia ED3, Dev Cell. 2014 Jul 23. pii: S1534-5807(14)00342-6. doi: 10.1016/j.devcel.2014.05.022. Epub 2014 Jul 24, PMCID: PMC4165855.

“A method to recapitulate early embryonic spatial patterning in human embryonic stem cells”, Warmflash A, Sorre B, Etoc F, Siggia ED, Brivanlou AH, Nat Methods. 2014 Jun 29. doi: 10.1038/nmeth.3016. Epub 2014 Jun 29, PMCID:PMC4341966.

“Predicting embryonic patterning using mutual entropy fitness and in silico evolution”, François P, Siggia ED, Development, 2010 Jul;137(14):2385-95.

“Stretching DNA”, by Marko JF and Siggia ED, Macromolecules, 28, 8759 (1995).

“Fluctuations and supercoiling of DNA”, Marko JF, Siggia ED, Science, Jul 22;265(5171):506-8 (1994).

James Sethna

James Gilbert White Professor of Physical Sciences

Publications

Visualizing probabilistic models with Intensive Principal Component Analysis, Katherine N. Quinn, Colin B. Clement, Francesco De Bernardis, Michael D. Niemack, and James P. Sethna, Proceedings of the National Academy of Sciences 116, 13762-13767 (2019). See also Data visualization could reveal nature of the universe (Cornell Chronicle article by Melanie Lefkowitz), and Algorithm to map universe, solve mysteries: Study(Times of India, June 26, 2019).

Chebyshev approximation and the global geometry of sloppy models , Katherine N. Quinn, Heather Wilber, Alex Townsend, and James P. Sethna Phys. Rev. Lett 122, 158302 (2019)

Cluster representations and the Wolff algorithm in arbitrary external fields, Jaron Kent-Dobias and James P Sethna, Phys. Rev. E 98, 063306 (2018).

Normal form for renormalization groups, Archishman Raju, Colin B. Clement, Lorien X. Hayden, Jaron P. Kent-Dobias, Danilo B. Liarte, D. Zeb Rocklin and James P. Sethna, Phys. Rev. X 9, 021014 (2019).

Deformation of crystals: Connections with statistical physics, James P. Sethna, Matthew K. Bierbaum, Karin A. Dahmen, Carl P. Goodrich, Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, Edward D. Lee, Danilo B. Liarte, Xiaoyue Ni, Katherine N. Quinn, Arichishman Raju, D. Zeb Rocklin, Ashivni Shekhawat, Stefano Zapperi, Annual Review of Materials Research 47 217-246 (2017).

Canonical sectors and evolution of firms in the US Stock markets, Lorien X. Hayden, Ricky Chachra, Alexander A. Alemi, Paul H. Ginsparg, and James P. Sethna, Quantitative Finance, 1-16 (2018). See also our stock analysis website.

Weirdest martensite: Smectic liquid crystal microstructure and Weyl-Poincaré invariance, Danilo B. Liarte, Matthew Bierbaum, Ricardo A. Mosna, Randall D. Kamien, and James P. Sethna, Phys. Rev. Lett. 116, 147802 (2016), pdf. (Cover story and Editor's Choice for PRL, Cornell chronicle story, and "Two different crystals can be described by the same mathematical rules", by Lisa Zyga at Phys.org.)

You Can Run, You Can Hide: The Epidemiology and Statistical Mechanics of Zombies, Alexander A. Alemi, Matthew Bierbaum, Christopher R. Myers, and James P. Sethna Phys. Rev. E 92, 022146 (2015). Much national media coverage (over 75 articles in the first week, starting with Popular Science, New Scientist, and the Washington Post; over half a million hits on both the Zombie simulator and the photo views.)

Sloppiness and Emergent Theories in Physics, Biology, and Beyond, Mark K. Transtrum, Benjamin B. Machta, Kevin S. Brown, Bryan C. Daniels, Christopher R. Myers, and James P. Sethna, J. Chem. Phys. 143, 010901 (2015).

Parameter Space Compression Underlies Emergent Theories and Predictive Models, Benjamin B. Machta, Ricky Chachra, Mark K. Transtrum, James P. Sethna, Science 342, 604-607 (2013); pdffull text. See also Physicists unify the structure of scientific theories in the Cornell Chronicle (Anne Ju) and Kathryn McGill's vblog Soft Matters with Jim Sethna from The Physics Factor.

Collective motion of humans in mosh and circle pits at heavy metal concerts, Jesse L. Silverberg, Matthew Bierbaum, James P. Sethna, and Itai Cohen, Phys. Rev. Lett. 110, 228701 (2013). See Jesse Silverberg's TED talk.  Extensive press coverage (AtlanticPhysics WorldPopular ScienceNew ScientistNBCNational Geographic ...); full listing at Silverberg's Mosh-pit page

Christopher Myers

Adjunct Professor

Publications

P. Graystock, W.H. Ng, K. Parks, A.D. Tripodi, P.A. Muniz, A.A. Fersch, C.R. Myers, Q.S. McFrederick & S.H. McArt, "Dominant bee species and floral abundance drive parasite temporal dynamics in plant-pollinator communities", Nature Ecology & Evolution, https://doi.org/10.1038/s41559-020-1247-x (2020). 

L.L. Figueroa, H. Grab, W.H. Ng, C.R. Myers, P. Graystock, Q.S. McFrederick, S.H. McArt, "Landscape simplification shapes pathogen prevalence in plant-pollinator networks", Ecology Letters, https://doi.org/10.1111/ele.13521 (2020). 

S. P. Ellner, W. H. Ng, C.R. Myers, "Individual specialization and multi-host epidemics: Disease spread in plant-pollinator networks", The American Naturalist 195, no. 5 (May 2020): E118-E131.

S. Mehringer, C.R. Myers, J. Houchins, L. Rivera, "Mining online training data", Proceedings of PEARC '19: Practice and Experience in Advanced Research Computing, article 84 (2019).  

C.R. Myers, "Zen and the art of parameter estimation in systems biology", invited chapter in Systems Immunology: An Introduction to Modeling Methods for Scientists, J. Das and C. Jayaprakash (eds.), CRC Press (2018). 

O. Kogan, K. O'Keeffe, C.R. Myers, "Fragility of reaction-diffusion models with respect to competing advective processes",  Phys. Rev. E 96, 022220 (2017). 

E. Bogart and C.R. Myers, “Multiscale metabolic modeling of C4 plants: connecting nonlinear genome-scale models to leaf-scale metabolism in developing maize leaves”, PLoS ONE 11(3): e0151722 (2016).

A.A. Alemi, M. Bierbaum, C.R. Myers, and J.P. Sethna, “You can run, you can hide: The epidemiology and statistical mechanics of zombies”, Phys. Rev. E 92, 052081 (2015).

J. Hindes and C.R. Myers, “Driven synchronization in random networks of oscillators”, Chaos 25, 073119 (2015).

M.K. Transtrum, B. Machta, K. Brown, B.C. Daniels, C.R. Myers, and J. P. Sethna, “Sloppiness and emergent theories in physics, biology, and beyond”, J. Chem. Phys. 143, 010901 (2015).

O. Kogan, M. Khasin, B. Meerson, D. Schneider, and C.R. Myers, “Two-strain competition in quasineutral stochastic disease dynamics”, Phys. Rev. E 90, 042149 (2014).

S. Singh and C.R. Myers, “Outbreak size statistics and scaling laws for externally driven epidemics”, Phys. Rev. E 89, 042108 (2014).

S. Singh, D.J. Schneider, and C.R. Myers, “Using multitype branching processes to quantify statistics of disease outbreaks in zoonotic epidemics”, Phys. Rev. E 89, 032702 (2014).

J. Hindes, S. Singh, C.R. Myers, and D.J. Schneider, “Epidemic fronts in complex networks with metapopulation structure", Phys. Rev. E 88, 012809 (2013).

Sol Gruner

John L. Wetherill Emeritus Professor of Physics

Publications

Publications may be found at http://bigbro.biophys.cornell.edu/publications/.

Carl Franck

Associate Professor

Publications

Please see http://franckgroup.lassp.cornell.edu.

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