Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory

Bowman, Gregory R.; Cox, Stephen J.; Dellago, Christoph; DuBay, Kateri H.; Eaves, Joel D.; Fletcher, Daniel A.; Frechette, Layne B.; Grünwald, Michael; Klymko, Katherine; Ku, JiYeon; Omar, Ahmad K.; Rabani, Eran; Reichman, David R.; Rogers, Julia R.; Rosnik, Andreana M.; Rotskoff, Grant M.; Schneider, Anna R.; Schwierz, Nadine; Sivak, David A.; Vaikuntanathan, Suriyanarayanan; Whitelam, Stephen; Widmer-Cooper, Asaph

doi:10.1146/annurev-physchem-101422-030127

Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory

Journal Article · Tue Jan 31 00:00:00 EST 2023 · Annual Review of Physical Chemistry

DOI:https://doi.org/10.1146/annurev-physchem-101422-030127· OSTI ID:2246865

Bowman, Gregory R. ^[1]; Cox, Stephen J. ^[2]; Dellago, Christoph ^[3]; DuBay, Kateri H. ^[4]; Eaves, Joel D. ^[5]; Fletcher, Daniel A. ^[6]; Frechette, Layne B. ^[7]; Grünwald, Michael ^[8]; Klymko, Katherine ^[9]; Ku, JiYeon ^[10]; Omar, Ahmad K. ^[11]; Rabani, Eran ^[12]; Reichman, David R. ^[13]; Rogers, Julia R. ^[13]; Rosnik, Andreana M. ^[14]; Rotskoff, Grant M. ^[15]; Schneider, Anna R. ^[16]; Schwierz, Nadine ^[17]; Sivak, David A. ^[18]; Vaikuntanathan, Suriyanarayanan ^[19] more »

Univ. of Pennsylvania, Philadelphia, PA (United States)
Univ. of Cambridge (United Kingdom)
Univ. of Vienna (Austria)
Univ. of Virginia, Charlottesville, VA (United States)
Univ. of Colorado, Boulder, CO (United States)
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Chan Zuckerberg Biohub, San Francisco, CA (United States)
Brandeis Univ., Waltham, MA (United States)
Univ. of Utah, Salt Lake City, UT (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Eloi Materials (EML) Co., Ltd., Suwon (Korea, Republic of)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Tel Aviv Univ., Tel Aviv (Israel)
Columbia Univ., New York, NY (United States)
Atomwise, San Francisco, CA (United States)
Stanford Univ., CA (United States)
Form Energy, Berkeley, CA (United States)
Univ. of Augsburg (Germany)
Simon Fraser Univ., Burnaby, BC (Canada)
Univ. of Chicago, IL (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Molecular Foundry
Univ. of Sydney, NSW (Australia)

Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Molecular Foundry

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231; SC0022917

OSTI ID:: 2246865

Journal Information:: Annual Review of Physical Chemistry, Journal Name: Annual Review of Physical Chemistry Journal Issue: 1 Vol. 74; ISSN 0066-426X

Publisher:: Annual ReviewsCopyright Statement

Country of Publication:: United States

Language:: English

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Faster strain fluctuation methods through partial volume updates Pronk, Sander; Geissler, Phillip L. The Journal of Chemical Physics, Vol. 130, Issue 19 https://doi.org/10.1063/1.3122383	journal	May 2009
Large-scale simulations of fluctuating biological membranes Pasqua, Andrea; Maibaum, Lutz; Oster, George The Journal of Chemical Physics, Vol. 132, Issue 15 https://doi.org/10.1063/1.3382349	journal	April 2010
Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA Sivak, David A.; Geissler, Phillip L. The Journal of Chemical Physics, Vol. 136, Issue 4 https://doi.org/10.1063/1.3679654	journal	January 2012
Transferable pair potentials for CdS and ZnS crystals Grünwald, Michael; Zayak, Alexey; Neaton, Jeffrey B. The Journal of Chemical Physics, Vol. 136, Issue 23 https://doi.org/10.1063/1.4729468	journal	June 2012
Preserving correlations between trajectories for efficient path sampling Gingrich, Todd R.; Geissler, Phillip L. The Journal of Chemical Physics, Vol. 142, Issue 23 https://doi.org/10.1063/1.4922343	journal	June 2015
Interfacial ion solvation: Obtaining the thermodynamic limit from molecular simulations Cox, Stephen J.; Geissler, Phillip L. The Journal of Chemical Physics, Vol. 148, Issue 22 https://doi.org/10.1063/1.5020563	journal	June 2018
Quadrupole-mediated dielectric response and the charge-asymmetric solvation of ions in water Cox, Stephen J.; Mandadapu, Kranthi K.; Geissler, Phillip L. The Journal of Chemical Physics, Vol. 154, Issue 24 https://doi.org/10.1063/5.0051399	journal	June 2021
Hydrogen bonds in liquid water are broken only fleetingly Eaves, J. D.; Loparo, J. J.; Fecko, C. J. Proceedings of the National Academy of Sciences, Vol. 102, Issue 37 https://doi.org/10.1073/pnas.0505125102	journal	August 2005
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On the fluctuations that drive small ions toward, and away from, interfaces between polar liquids and their vapors Noah-Vanhoucke, J.; Geissler, P. L. Proceedings of the National Academy of Sciences, Vol. 106, Issue 36 https://doi.org/10.1073/pnas.0905168106	journal	August 2009
Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements Zhang, Xinghua; Chen, Hu; Fu, Hongxia Proceedings of the National Academy of Sciences, Vol. 109, Issue 21 https://doi.org/10.1073/pnas.1109824109	journal	April 2012
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Elucidating the mechanism of selective ion adsorption to the liquid water surface Otten, D. E.; Shaffer, P. R.; Geissler, P. L. Proceedings of the National Academy of Sciences, Vol. 109, Issue 3 https://doi.org/10.1073/pnas.1116169109	journal	January 2012
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Native contacts determine protein folding mechanisms in atomistic simulations Best, R. B.; Hummer, G.; Eaton, W. A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 44 https://doi.org/10.1073/pnas.1311599110	journal	October 2013
Discovery of multiple hidden allosteric sites by combining Markov state models and experiments Bowman, Gregory R.; Bolin, Eric R.; Hart, Kathryn M. Proceedings of the National Academy of Sciences, Vol. 112, Issue 9 https://doi.org/10.1073/pnas.1417811112	journal	February 2015
Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation Vaikuntanathan, Suriyanarayanan; Rotskoff, Grant; Hudson, Alexander Proceedings of the National Academy of Sciences, Vol. 113, Issue 16 https://doi.org/10.1073/pnas.1513659113	journal	March 2016
Multiscale model of light harvesting by photosystem II in plants Amarnath, Kapil; Bennett, Doran I. G.; Schneider, Anna R. Proceedings of the National Academy of Sciences, Vol. 113, Issue 5 https://doi.org/10.1073/pnas.1524999113	journal	January 2016
Mechanism of ion adsorption to aqueous interfaces: Graphene/water vs. air/water McCaffrey, Debra L.; Nguyen, Son C.; Cox, Stephen J. Proceedings of the National Academy of Sciences, Vol. 114, Issue 51 https://doi.org/10.1073/pnas.1702760114	journal	August 2017
Robust nonequilibrium pathways to microcompartment assembly Rotskoff, Grant M.; Geissler, Phillip L. Proceedings of the National Academy of Sciences, Vol. 115, Issue 25 https://doi.org/10.1073/pnas.1802499115	journal	June 2018
Energy-dependent quenching adjusts the excitation diffusion length to regulate photosynthetic light harvesting Bennett, Doran I. G.; Fleming, Graham R.; Amarnath, Kapil Proceedings of the National Academy of Sciences, Vol. 115, Issue 41 https://doi.org/10.1073/pnas.1806597115	journal	September 2018
Elastic forces drive nonequilibrium pattern formation in a model of nanocrystal ion exchange Frechette, Layne B.; Dellago, Christoph; Geissler, Phillip L. Proceedings of the National Academy of Sciences, Vol. 118, Issue 52 https://doi.org/10.1073/pnas.2114551118	journal	December 2021
Transition path sampling: throwing ropes over mountains in the dark Bolhuis, Peter G.; Dellago, Christoph; Geissler, Phillip L. Journal of Physics: Condensed Matter, Vol. 12, Issue 8A https://doi.org/10.1088/0953-8984/12/8A/316	journal	February 2000
Efficiency and large deviations in time-asymmetric stochastic heat engines Gingrich, Todd R.; Rotskoff, Grant M.; Vaikuntanathan, Suriyanarayanan New Journal of Physics, Vol. 16, Issue 10 https://doi.org/10.1088/1367-2630/16/10/102003	journal	October 2014
Conditioning Boltzmann generators for rare event sampling Falkner, Sebastian; Coretti, Alessandro; Romano, Salvatore Machine Learning: Science and Technology, Vol. 4, Issue 3 https://doi.org/10.1088/2632-2153/acf55c	journal	September 2023
Two distinct overstretched DNA states Fu, Hongxia; Chen, Hu; Marko, John F. Nucleic Acids Research, Vol. 38, Issue 16 https://doi.org/10.1093/nar/gkq309	journal	April 2010
Origin of mean-field behavior in an elastic Ising model Frechette, Layne B.; Dellago, Christoph; Geissler, Phillip L. Physical Review B, Vol. 102, Issue 2 https://doi.org/10.1103/PhysRevB.102.024102	journal	July 2020
Reversible stretching of random heteropolymers Geissler, Phillip L.; Shakhnovich, Eugene I. Physical Review E, Vol. 65, Issue 5 https://doi.org/10.1103/PhysRevE.65.056110	journal	May 2002
Overstretching and force-driven strand separation of double-helix DNA Cocco, Simona; Yan, Jie; Léger, Jean-Francois Physical Review E, Vol. 70, Issue 1 https://doi.org/10.1103/PhysRevE.70.011910	journal	July 2004
Solvation versus freezing in a heteropolymer globule Geissler, Phillip L.; Shakhnovich, Eugene I.; Grosberg, Alexander Yu. Physical Review E, Vol. 70, Issue 2 https://doi.org/10.1103/PhysRevE.70.021802	journal	August 2004
Microscopic implications of S-DNA Whitelam, Stephen; Geissler, Phillip L.; Pronk, Sander Physical Review E, Vol. 82, Issue 2 https://doi.org/10.1103/PhysRevE.82.021907	journal	August 2010
Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins Mey, Antonia S. J. S.; Geissler, Phillip L.; Garrahan, Juan P. Physical Review E, Vol. 89, Issue 3 https://doi.org/10.1103/PhysRevE.89.032109	journal	March 2014
Dynamic phase transitions in simple driven kinetic networks Vaikuntanathan, Suriyanarayanan; Gingrich, Todd R.; Geissler, Phillip L. Physical Review E, Vol. 89, Issue 6 https://doi.org/10.1103/PhysRevE.89.062108	journal	June 2014
Heterogeneity-induced large deviations in activity and (in some cases) entropy production Gingrich, Todd R.; Vaikuntanathan, Suriyanarayanan; Geissler, Phillip L. Physical Review E, Vol. 90, Issue 4 https://doi.org/10.1103/PhysRevE.90.042123	journal	October 2014
Microscopic origin and macroscopic implications of lane formation in mixtures of oppositely driven particles Klymko, Katherine; Geissler, Phillip L.; Whitelam, Stephen Physical Review E, Vol. 94, Issue 2 https://doi.org/10.1103/PhysRevE.94.022608	journal	August 2016
Limits of Filopodium Stability Pronk, Sander; Geissler, Phillip L.; Fletcher, Daniel A. Physical Review Letters, Vol. 100, Issue 25 https://doi.org/10.1103/PhysRevLett.100.258102	journal	June 2008
Putting Water on a Lattice: The Importance of Long Wavelength Density Fluctuations in Theories of Hydrophobic and Interfacial Phenomena Vaikuntanathan, Suriyanarayanan; Geissler, Phillip L. Physical Review Letters, Vol. 112, Issue 2 https://doi.org/10.1103/PhysRevLett.112.020603	journal	January 2014
Consequences of Lattice Mismatch for Phase Equilibrium in Heterostructured Solids Frechette, Layne B.; Dellago, Christoph; Geissler, Phillip L. Physical Review Letters, Vol. 123, Issue 13 https://doi.org/10.1103/PhysRevLett.123.135701	journal	September 2019
Phase Diagram of Active Brownian Spheres: Crystallization and the Metastability of Motility-Induced Phase Separation Omar, Ahmad K.; Klymko, Katherine; GrandPre, Trevor Physical Review Letters, Vol. 126, Issue 18 https://doi.org/10.1103/PhysRevLett.126.188002	journal	May 2021
Direct observation of nanoparticle-surfactant assembly and jamming at the water-oil interface Chai, Yu; Hasnain, Jaffar; Bahl, Kushaan Science Advances, Vol. 6, Issue 48 https://doi.org/10.1126/sciadv.abb8675	journal	November 2020
Autoionization in Liquid Water Geissler, P. L. Science, Vol. 291, Issue 5511 https://doi.org/10.1126/science.1056991	journal	March 2001
Self-Assembly at All Scales Whitesides, George M.; Grzybowski, Bartosz Science, Vol. 295, Issue 5564, p. 2418-2421 https://doi.org/10.1126/science.1070821	journal	March 2002
Ultrafast Hydrogen-Bond Dynamics in the Infrared Spectroscopy of Water Fecko, C. J. Science, Vol. 301, Issue 5640 https://doi.org/10.1126/science.1087251	journal	September 2003
Cation Exchange Reactions in Ionic Nanocrystals Son, Dong Hee; Hughes, Steven M.; Yin, Yadong Science, Vol. 306, Issue 5698, p. 1009-1012 https://doi.org/10.1126/science.1103755	journal	November 2004
Spontaneous Superlattice Formation in Nanorods Through Partial Cation Exchange Robinson, R. D.; Sadtler, B.; Demchenko, D. O. Science, Vol. 317, Issue 5836, p. 355-358 https://doi.org/10.1126/science.1142593	journal	July 2007
How Fast-Folding Proteins Fold Lindorff-Larsen, K.; Piana, S.; Dror, R. O. Science, Vol. 334, Issue 6055 https://doi.org/10.1126/science.1208351	journal	October 2011
Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules Smith, S. B.; Cui, Y.; Bustamante, C. Science, Vol. 271, Issue 5250 https://doi.org/10.1126/science.271.5250.795	journal	February 1996
Single-particle mapping of nonequilibrium nanocrystal transformations Ye, Xingchen; Jones, Matthew R.; Frechette, Layne B. Science, Vol. 354, Issue 6314 https://doi.org/10.1126/science.aah4434	journal	November 2016
Motility-Induced Phase Separation Cates, Michael E.; Tailleur, Julien Annual Review of Condensed Matter Physics, Vol. 6, Issue 1 https://doi.org/10.1146/annurev-conmatphys-031214-014710	journal	March 2015
Water Interfaces, Solvation, and Spectroscopy Geissler, Phillip L. Annual Review of Physical Chemistry, Vol. 64, Issue 1 https://doi.org/10.1146/annurev-physchem-040412-110153	journal	April 2013
Theoretical Studies of Protein Folding Go, N. Annual Review of Biophysics and Bioengineering, Vol. 12, Issue 1 https://doi.org/10.1146/annurev.bb.12.060183.001151	journal	June 1983
Active Biological Materials Fletcher, Daniel A.; Geissler, Phillip L. Annual Review of Physical Chemistry, Vol. 60, Issue 1 https://doi.org/10.1146/annurev.physchem.040808.090304	journal	May 2009
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark Bolhuis, Peter G.; Chandler, David; Dellago, Christoph Annual Review of Physical Chemistry, Vol. 53, Issue 1 https://doi.org/10.1146/annurev.physchem.53.082301.113146	journal	October 2002
Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone DuBay, Kateri H.; Bothma, Jacques P.; Geissler, Phillip L. PLoS Computational Biology, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pcbi.1002168	journal	September 2011
Temperature Control Methods in a Laser Tweezers System Mao, Hanbin; Ricardo Arias-Gonzalez, J.; Smith, Steven B. Biophysical Journal, Vol. 89, Issue 2 https://doi.org/10.1529/biophysj.104.054536	journal	August 2005
Dynamic Pathways for Viral Capsid Assembly Hagan, Michael F.; Chandler, David Biophysical Journal, Vol. 91, Issue 1 https://doi.org/10.1529/biophysj.105.076851	journal	July 2006
Optical Measurement of Mechanical Forces Inside Short DNA Loops Shroff, Hari; Sivak, David; Siegel, Jake J. Biophysical Journal, Vol. 94, Issue 6 https://doi.org/10.1529/biophysj.107.114413	journal	March 2008
There and (Slowly) Back Again: Entropy-Driven Hysteresis in a Model of DNA Overstretching Whitelam, Stephen; Pronk, Sander; Geissler, Phillip L. Biophysical Journal, Vol. 94, Issue 7 https://doi.org/10.1529/biophysj.107.117036	journal	April 2008
A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results Sengar, A.; Ouldridge, T. E.; Henrich, O. Frontiers in Molecular Biosciences, Vol. 8 https://doi.org/10.3389/fmolb.2021.693710	journal	June 2021
Coarse-grained computer simulation of dynamics in thylakoid membranes: methods and opportunities Schneider, Anna R.; Geissler, Phillip L. Frontiers in Plant Science, Vol. 4 https://doi.org/10.3389/fpls.2013.00555	journal	January 2014
Ligand binding remodels protein side-chain conformational heterogeneity Wankowicz, Stephanie A.; de Oliveira, Saulo H.; Hogan, Daniel W. eLife, Vol. 11 https://doi.org/10.7554/eLife.74114	journal	March 2022

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