Publications



2016


• Xingchen Ye, Matthew R. Jones, Layne B. Frechette, Qian Chen, Alexander S. Powers, Peter Ercius, Gabriel Dunn, Grant M. Rotskoff, Son C. Nguyen, Vivekananda P. Adiga, Alex Zettl, Eran Rabani, Phillip L. Geissler, and A. Paul Alivisatos. "Single-particle mapping of nonequilibrium nanocrystal transformations", Science 2016, 354, 874–877. PDF

• J. Weichsel and P.L. Geissler. "The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation", PLoS Comp. Bio. 2016. PDF

• E. M. Schmid, M. H. Bakalar, K. Choudhuri, J. Weichsel, H. S. Ann, P. L. Geissler, M. L. Dustin, and D. A. Fletcher. "Size-dependent protein segregation at membrane interfaces", Nature Physics 2016. PDF

• K. Klymko, P.L. Geissler, and S. Whitelam. "On the microscopic origin and macroscopic implications of lane formation in mixtures of oppositely-driven particles", ArXiv:1602.01878 2016

• T. R. Gingrich, G.M. Rotskoff, G.E. Crooks, and P.L. Geissler. "Near-optimal protocols in complex nonequilibrium transformations", Proc. Natl. Acad. Sci. 2016, 113 10263–10268.PDF

• A. Widmer-Cooper and P.L. Geissler. "Ligand-Mediated Interactions between Nanoscale Surfaces Depend Sensitively and Nonlinearly on Temperature, Facet Dimensions, and Ligand Coverage", ACS Nano 2016. PDF


2015


• R. Noriega, D. T. Finley, J. Haberstroh, P. L. Geissler, M. B. Francis, and N. S. Ginsberg. "Extensive Conformational Heterogeneity within Protein Cores", J. Phys. Chem. B 2014, 119, 6963–6973. PDF

• K.H. Dubay, G.R. Bowman, and P.L. Geissler. "Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation", Acc. Chem. Res. 2015, 48, , 1098–1105. PDF

• N. Schwierz, C. V. Frost, P.L. Geissler, M. Zacharias. "Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step", J. Am. Chem. Soc. 2015. PDF

• M. Gruenwald, S. Tricard, G.M. Whitesides, and P.L. Geissler. "Exploiting non-equilibrium phase separation for self-assembly", Soft Matt. 2015. PDF

• T. R. Gingrich and P.L. Geissler. "Preserving correlations between trajectories for efficient path sampling", J. Chem. Phys. 2015, 142, 234104. PDF

• S. Vaikuntanathan, G.M. Rotskoff, A. Hudson, P.L. Geissler. "Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation", Proc. Natl. Acad. Sci. 2015, 113. PDF


2014


• G.R. Bowman and P.L. Geissler. "Extensive Conformational Heterogeneity within Protein Cores", J. Phys. Chem. B 2014, 118, 6417–6423. PDF

• E. Hohlfeld and P.L. Geissler. "Dominance of extreme statistics in a prototype many-body Brownian ratchet", J. Chem. Phys. 2014, 141, 161101. PDF

• T.R. Gingrich, G.M. Rotskoff, S. Vaikuntanathan, and P.L. Geissler. "Efficieny and large deviations in time-asymmetric stochastic heat engines", New J. Phys. 2014, 16, 102003. PDF

• T.R. Gingrich, S. Vaikuntanathan, and P.L. Geissler. "Heterogeneity-induced large deviations in activity and (in some cases) entropy production", Phys. Rev. E 2014, 90, 042123. PDF

• B. Onoa, A.R. Schneider, M.D. Brooks, P. Grob, E. Nogales, P.L. Geissler, K.K. Niyogi, C. Bustamante. "Atomic Force Microscopy of Photosystem II and Its Unit Cell Clustering Quantitatively Delineate the Meoscale Variability in Arabidopsis Thylakoids", PLoS ONE 2014, 9, 1–12. PDF

• S. Vaikuntanathan, T.R. Gingrich and P.L. Geissler. "Dynamic phase transitions in simple driven kinetic networks", Phys. Rev. E 2014, 89, 062108. PDF

• A.R. Schneider and P.L. Geissler. "Coarse-grained computer simulation in thylakoid membranes: methods and opportunities", Front. Plant Sci. 2014, PDF

• M. Grünwald and P.L. Geissler. "Patterns without Patches: Hierarchical Self-Assembly of Complex Structures from Simple Building Blocks", ACS Nano 2014. PDF

• A.S. Mey, J.P. Garrahan, and P.L. Geissler. "Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins", Phys. Rev. E 2014, 89, 032109. PDF

• S. Vaikuntanathan and P.L. Geissler. "Putting water on a lattice: The importance of long wavelength density fluctuations in theories of hydrophobic and interfacial phenomena", Phys. Rev. Lett. 2014, 112, 020603 1–5. PDF


2013


• A. Widmer-Cooper and P.L. Geissler. "Orientational Ordering of Passivating Ligands on CdS Nanorods in Solution Generates Strong Rod–Rod Interactions", Nano Lett. 2013. PDF

• P.L. Geissler. "Water Interfaces, Solvation, and Spectroscopy", Annu. Rev. Phys. Chem. 2013, 64, 317–337. PDF

• A.R. Schneider and P.L. Geissler. "Coexistence of fluid and crystalline phases of proteins in photosynthetic membranes", Biophys. J. 2013, 103, 1161–1170. PDF

• S. Vaikuntanathan, P.R. Shaffer and P.L. Geissler. "Adsorption of solutes at liquid-vapor interfaces: Insights from lattice gas models", Faraday Discuss. 2013, 160, 63–74. PDF

• M. Grünwald, K. Lutker, P. Alivisatos, E. Rabani and P.L. Geissler. "Metastability in Pressure-Induced Structural Transformations of CdSe/ZnS Core/Shell Nanocrystals", Nano Lett. 2013, 13, 1367–1372. PDF


2012


• D. Chandler, C. Dellago, and P.L. Geissler. "Ion dynamics: Wired-up water", Nature Chemistry 2012, 4, 245–247. PDF

• J. Park, H. Zheng, W. C. Lee, P.L. Geissler, E. Rabani, A.P. Alivisatos. "Direct Observation of Nanoparticle Superlattice Formation by Using Liquid Cell Transmission Electron Microscopy", ACS Nano 2012, 6, 2078–2085. PDF

• A. Crow, K.D. Webster, E. Hohlfeld, W.P. Ng, P.L. Geissler, and D.A. Fletcher. "Contractile equilibrium of single cells to step changes in extracellular stiffness", Biophys. J. 2012, 102, 443-451. PDF

• J.C. Stachowiak, E.M. Schmid, C.J. Ryan, H.S. Ann, D.Y. Sasaki, M.B. Sherman, P.L. Geissler, D.A. Fletcher, and C.C. Hayden. "Membrane bending by protein-protein crowding", Nat. Cell. Bio. 2012, 14, 944-949. PDF

• M. Grünwald, A. Zayak, J.B. Neaton, P.L. Geissler and E. Rabani. "Transferable pair potentials for CdS and ZnS crystals", J. Chem. Phys. 2012, 136, 234111. PDF

• G.R. Bowman and P.L. Geissler. "Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites", Proc. Natl. Acad. Sci. 2012, 109, 11681–11686. PDF

• V.I. Risca, E.B. Wang, O. Chaudhuri, J.J. Chia, P.L. Geissler, and D.A. Fletcher. "Actin filament curvature biases branching direction", Proc. Natl. Acad. Sci. 2012, 109, 2913–2918. PDF

• J. Henzie, M. Grünwald, A. Widmer-Cooper, and P.L. Geissler. "Self-assembly of uniform polyhedral silver nanocrystals into densest packings and exotic superlattices", Nature Materials 2012, 11, 131–137. PDF

• D.E. Otten, P.R. Shaffer, P.L. Geissler, and R.J. Saykally. "Elucidating the mechanism of selective ion adsorption to the liquid water surface", Proc. Natl. Acad. Sci. 2012, 109, 701–705. PDF

• D.A. Sivak and P.L. Geissler. "Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA", J. Chem. Phys. 2012, 136, 045102. PDF


2011


• J. Ku, D.M. Aruguete, A.P. Alivisatos, and P.L. Geissler. "Self-assembly of magnetic nanoparticles in evaporating solution", J. Am. Chem. Soc. 2011, 133, 838–848. PDF

• S.J. Byrnes, P.L. Geissler, and Y.R. Shen. "Ambiguities in surface nonlinear spectroscopy calculations", Chem. Phys. Lett. Frontiers 2011, 516, 115–124. PDF

• K.H. DuBay, J.P. Bothma, and P.L. Geissler. "Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone", PLoS Comp. Bio. 2011, 7, 1–11. PDF


2010


• R.A. Miller, N. Stephanopoulos, J.M. McFarland, A.S. Rosko, P.L. Geissler, and M.M. Francis. "Impact of assembly state on the defect tolerance of TMV-based light harvesting arrays", J. Am. Chem. Soc. 2010, 132, 6068–6074. PDF

• J.L. Baker, A. Widmer-Cooper, M.F. Toney, P.L. Geissler, and A.P. Alivisatos. "Device-scale perpendicular alignment of colloidal nanorods", Nano Lett. 2010, 10, 195–201. PDF

• S. Whitelam, P.L. Geissler, and S. Pronk. "Microscopic implications of S-DNA", Phys. Rev. E 2010, 82, 021907. PDF

• W. Browne and P.L. Geissler. "The susceptibility of α-helical secondary structure to steric strain: coarse-grained simulation of dendronized polypeptides", J. Chem. Phys. 2010, 133, 145102. PDF

• A. Pasqua, L. Maibaum, G. Oster, D.A. Fletcher, and P.L. Geissler. "Large-scale simulations of fluctuating biological membranes", J. Chem. Phys. 2010, 132, 154107. PDF


2009


• B.C. Gin, J.P. Garrahan, and P.L. Geissler. "The limited role of nonnative contacts in the folding pathways of a lattice protein", J. Mol. Bio. 2009, 392, 1303–1314. PDF

• J. Noah-Vanhoucke, J.D. Smith, and P.L. Geissler. "Statistical mechanics of sum frequency generation spectroscopy for the liquid–vapor interface of dilute aqueous salt solutions", Chem. Phys. Lett. 2009, 470, 21–27. PDF

• S. Whitelam, E.H. Feng, M.F. Hagan, and P.L. Geissler. "The role of collective motion in examples of coarsening and self-assembly", Soft Matt. 2009, 5, 1251–1262. PDF

• S. Whitelam, C. Rogers, A. Pasqua, C. Paavola, J. Trent, and P.L. Geissler. "The impact of conformational fluctuations on self-assembly: cooperative aggregation of archaeal chaperonin proteins", Nano Lett. 2009, 9 292–297. PDF

• J. Noah-Vanhoucke, J.D. Smith, and P.L. Geissler. "Toward a simple molecular understanding of sum frequency generation at air–water interfaces", J. Phys. Chem. B 2009, 113, 4065–4074. PDF

• A.J. Mastroianni, D.A. Sivak, P.L. Geissler, and A.P. Alivisatos. "Probing the conformational distributions of subpersistence length DNA", Biophys. J. 2009, 97, 1408–1417. PDF

• D.A. Fletcher and P.L. Geissler. "Active biological materials", Ann. Rev. Phys. Chem. 2009, 60, 469–486. PDF

• K.H. DuBay and P.L. Geissler. "Calculation of proteins' total side-chain torsional entropy and its influence on protein–ligand interactions", J. Mol. Bio. 2009, 391, 484–497. PDF

• J. Noah-Vanhoucke and P.L. Geissler. "On the fluctuations that drive small ions toward, and away from, interfaces between polar liquids and their vapors", Proc. Natl. Acad. Sci. 2009, 36, 15125–15130. PDF

• S. Pronk and P.L. Geissler. "Faster strain fluctuation methods through partal volume updates", J. Chem. Phys. 2009, 130, 194706. PDF


2008


• M.J. Park, A.J. Nedoma, P.L. Geissler, and N.P. Balsara. "Humidity-induced phase transitions in ion-containing block copolymer membranes", Macromolecules 2008, 41, 2271–2277. PDF

• S. Whitelam, S. Pronk, and P.L. Geissler. "There and (slowly) back again: entropy-driven hysteresis in a model of DNA overstretching", Biophys. J. 2008, 94, 2452–2469. PDF

• H. Shroff, D. Sivak, J.J. Siegel, A.L. McEvoy, M. Siu, A. Spakowitz, P.L. Geissler, and J. Liphardt. "Optical measurement of mechanical forces inside short DNA loops", Biophys. J. 2008, 94, 2179–2186. PDF

• S. Pronk, P.L. Geissler, and D.A. Fletcher. "Limits of filopodium stability", Phys. Rev. Lett. 2008, 100, 258102. PDF

• A.P. Liu, D.L. Richmond, L. Maibaum, S. Pronk, P.L. Geissler, and D.A. Fletcher. "Membrane-induced bundling of actin filaments", Nature Physics 2008, 4, 789–793. PDF

• S. Whitelam, S. Pronk, and P.L. Geissler. "Stretching chimeric DNA: a test for the putative S-form", J. Chem. Phys. 2008, 129, 205101. PDF

• M. Grünwald, C. Dellago, and P.L. Geissler. "Precision shooting: sampling long transition pathways", J. Chem. Phys. 2008, 129, 194101. PDF


2007


• M. Grünwald, C. Dellago, and P.L. Geissler. "An efficient transition path sampling algorithm for nanoparticles under pressure", J. Chem. Phys. 2007, 127, 154718. PDF

• R.L. York, W.K. Browne, P.L. Geissler, and G.A. Somorjai. "Peptides adsorbed on hydrophobic surfaces—a sum frequency generation vibrational spectroscopy and modeling study", Israel J. Chem. 2007, 47, 51–58. PDF

• S. Whitelam and P.L. Geissler. "Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles", J. Chem. Phys. 2007, 127, 154101. PDF

• E.H. Trepagnier, A. Radenovic, D. Sivak, P. Geissler, and J. Liphardt. "Controlling DNA capture and propagation through artificial nanopores", Nano Lett. 2007, 7, 2824–2830. PDF

• J.D. Smith, R.J. Saykally, and P.L. Geissler. "The effects of dissolved halide anions on hydrogen bonding in liquid water", J. Am. Chem, Soc. 2007, 129, 13847–13856. PDF


2006


• S. Whitelam and P.L. Geissler. "Two-stage coarsening mechanism in a kinetically constrained model of an attractive colloid", Phys. Rev. E 2006, 73, 016115. PDF

• W. Lechner, H. Oberhofer, C. Dellago, and P.L. Geissler. "Equilibrium free energies from fast-switching trajectories with large time steps", J. Chem. Phys. 2006, 124, 044113. PDF


2005


• P.L. Geissler. "Temperature dependence of inhomogeneous broadening: on the meaning of isosbestic points", J. Am. Chem. Soc. 2005, 127, 14930–14935. PDF

• D.R. Reichman, E. Rabani, and P.L. Geissler. "Comparison of dynamical heterogeneity in hard-sphere and attractive glass formers", J. Chem. Phys. B 2005, 109, 14654–14658. PDF

• H. Oberhofer, C. Dellago, and P.L. Geissler. "Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?", J. Chem. Phys. B 2005, 109, 6902–6915. PDF

• J.D. Eaves, J.J. Loparo, C.J. Fecko, S.T. Roberts, A. Tokmakoff, and P.L. Geissler. "Hydrogen bonds in liquid water are broken only fleetingly", Proc. Natl. Acad. Sci. 2005, 102, 13019–13022. PDF

• J.D. Eaves, A. Tokmakoff, and P.L. Geissler. "Electric field fluctuations drive vibrational dephasing in water", J. Phys. Chem. A 2005, 109, 9424–9436. PDF

• J.D. Smith, C.D. Cappa, K.R. Wilson, R.C. Cohen, P.L. Geissler, and R.J. Saykally. "Unified description of temperature-dependent hydrogen-bond rearrangements in liquid water", Proc. Natl. Acad. Sci. 2005, 102, 14171–14174. PDF


2004


• P.L. Geissler, E.I. Shakhnovich, and A.Y. Grosberg. "Solvation versus freezing in a heteropolymer globule", Phys. Rev. E 2004, 70, 021802. PDF

• P.L. Geissler and C. Dellago. "Equilibrium time correlation functions from irreversible transformations in trajectory space", J. Phys. Chem. B 2004, 108, 6667–6672. PDF

• P.L. Geissler and D.R. Reichman. "Nature of slow dynamics in a minimal model of frustration-limited domains", Phys. Rev. E 2004, 69, 021501. PDF

• P.L. Geissler and D.R. Reichman. "Short-ranged attractions in jammed liquids: how cooling can melt a glass", Phys. Rev. E 2004, 71, 031206. PDF


2003


• C.J. Fecko, J.D. Eaves, J.J. Loparo, A. Tokmakoff, and P.L. Geissler. "Ultrafast hydrogen-bond dynamics in the infrared spectroscopy of water", Science 2003, 301, 1698–1702. PDF

• P.L. Geissler and D.R. Reichman. "Reply to 'Comment on the nature of slow dynamics in a minimal model of frustration-limited domains'", arXiv:cond-mat 2003, 0307176. PDF

• C. Dellago and P.L. Geissler. "Monte Carlo sampling in path space: calculating time correlation functions by transforming ensembles of trajectories", Proceedings of the Monte Carlo method in the Physical Sciences: Celebrating 50th anniversary of the Metropolis algorithnm, AIP Conference proceedings, AIP: Melville, NY 2003, 690, 192–199. PDF

• E. Rabani, D.R. Reichman, P.L. Geissler, and L.E. Brus. "Drying-mediated self-assembly of nanoparticles", Nature 2003, 426, 271–274. PDF


2002


• P.L. Geissler and E.I. Shakhnovich. "Reversible stretching of random heteropolymers", Phys. Rev. E 2002, 65, 056110. PDF

• P.L. Geissler and E.I. Shakhnovich. "Mechanical response of random heteropolymers", Macromolecules 2002, 35, 4429–4436. PDF

• P.G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler. "Transition path sampling: throwing ropes over rough mountain passes, in the dark", Ann. Rev. Phys. Chem. 2002, 53, 291–318. PDF

• C. Dellago, P.G. Bolhuis, and P.L. Geissler. "Transition path sampling", Adv. in Chem. Phys. 2002, 123, 1–84. PDF

• C. Dellago, P.L. Geissler, D. Chandler, J. Hutter, and M. Parrinello. "Comment on 'Dissociation of water under pressure'", Phys. Rev. Lett. 2002, 89, 199601-1. PDF


2001


• D.M. Huang, P.L. Geissler, and D. Chandler. "Scaling of hydrophobic solvation free energies", J. Phys. Chem. B 2001, 105, 6704–6709. PDF

• P.L. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello. "Autoionization in liquid water", Science 2001, 291, 2121–2124. PDF


2000


• P.G. Bolhuis, C. Dellago, P.L. Geissler, and D. Chandler. "Transition path sampling: throwing ropes over mountains in the dark", J. Phys.: Condens. Matter 2000, 12, A147–A152. PDF

• P.L. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello. "Ab initio analysis of proton transfer dynamics in (H2O)3H+", Chem. Phys. Lett. 2000, 321, 225–230. PDF

• P.L. Geissler and D. Chandler. "Importance sampling and theory of nonequilibrium solvation dynamics in water", J. Chem. Phys. 2000, 113, 9759–9765. PDF

• P.L. Geissler, T. Van Voorhis, and C. Dellago. "Potential energy landscape for proton transfer in (H2O)3H+: comparison of density functional theory and wavefunction-based methods", Chem. Phys. Lett. 2000, 324, 149–155. PDF


1999


• P.L. Geissler, C. Dellago, and D. Chandler. "Kinetic pathways of ion pair dissociation in water", J. Phys. Chem. B 1999, 103, 3706–3710. PDF

• P.L. Geissler, C. Dellago, and D. Chandler. "Chemical dynamics of the protonated water trimer analyzed by transition path sampling", Phys. Chem. Chem, Phys. 1999, 1, 1317–1322. PDF


1996


• A.P. Chatterjee, P.L. Geissler, and R.F. Loring. "Stress relaxation in unentangled and entangled polymer liquids", J. Chem. Phys. 1996, 104, 5284–5293. PDF







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