Publications



2014


• 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

• T.R. Gingrich, S. Vaikuntanathan, and P.L. Geissler. "Heterogeneity-induced large deviations in activity and (in some cases) entropy production", arXiv:1406.3311 2014. 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


• E. Hohfeld and P.L. Geissler. "Dominance of extreme statistics in a prototype many-body Brownian ratchet", arXiv 2012. 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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