Publications of the Hocky Research Group
Ph.D. Theses
- Gaurav Mitra (July 2024): Coarse-Grained Simulation Studies of Self-Organization in Soft Matter Systems Interacting via Dynamic Bonds
- Yuvraj Singh (May 2024): Unravelling the Mechanobiology Landscape of Force Sensing Paradigms through Molecular Simulations and Enhanced Sampling Methodologies
Forthcoming
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A Tribello, Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Blake I Armstrong, Andrea Arsiccio, Simone Aureli, Federico Ballabio, Mattia Bernetti, Luigi Bonati, Samuel GH Brookes, Z Faidon Brotzakis, Riccardo Capelli, Michele Ceriotti, Kam-Tung Chan, Pilar Cossio, Siva Dasetty, Davide Donadio, Bernd Ensing, Andrew L Ferguson, Guillaume Fraux, Julian D Gale, Francesco Luigi Gervasio, Toni Giorgino, Nicholas SM Herringer, Glen M Hocky, Samuel E Hoff, Michele Invernizzi, Olivier Languin-Cattöen, Vanessa Leone, Vittorio Limongelli, Olga Lopez-Acevedo, Fabrizio Marinelli, Pedro Febrer Martinez, Matteo Masetti, Shams Mehdi, Angelos Michaelides, Mhd Hussein Murtada, Michele Parrinello, Pablo M Piaggi, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Claire Pritchard, Paolo Raiteri, Stefano Raniolo, Daniele Rapetti, Valerio Rizzi, Jakub Rydzewski, Matteo Salvalaglio, Christoph Schran, Aniruddha Seal, Armin Shayesteh Zadeh, Tomás FD Silva, Vojtech Spiwok, Guillaume Stirnemann, Daniel Sucerquia, Pratyush Tiwary, Omar Valsson, Michele Vendruscolo, Gregory A Voth, Andrew D White, and Jiangbo Wu
Submitted, arXiv:2412.03595 (2024)
A direct computational assessment of vinculin-actin unbinding kinetics reveals catch bonding behavior
Willmor J. Pena Ccoa, Fatemah Mukadum, Aubin Ramon, Guillaume Stirnemann*, and Glen M. Hocky*
biorxiv:2024.10.10.617580 (2024)
Beta-barrel proteins dictate the effect of core oligosaccharide composition on outer membrane mechanics
Dylan Fitzmaurice, Anthony Amador, Tahj Starr, Glen M Hocky, and Enrique R. Rojas
biorxiv:2024.09.02.610904 (2024)
Self-assembly of colloidal diamond: roles of particle shape and entropy
Jonathan P. Gales, Min Jae Kim, Glen M. Hocky, and David J. Pine
In review (2024)
Direct observation and control of non-classical crystallization pathways in binary colloidal systems
Shihao Zang, Sanjib Paul+, Cheuk W Leung+, Michael S. Chen, Theodore Hueckel, Glen M. Hocky*, and Stefano Sacanna*
Submitted, doi:10.26434/chemrxiv-2024-rmhsr (2024)
Published
An interdisciplinary effort to integrate coding into science courses
Christina L. Vizcarra, Ryan Trainor, Ashley Ringer McDonald, Chris Richardson, Davit Potoyan, Jessica A. Nash, Britt Lundgren, Tyler Luchko, Glen M. Hocky, Jonathan J. Foley IV, Timothy J. Atherton, and Grace Y. Stokes
Nat Comput Sci (online) (2024)
Polysome collapse and RNA condensation fluidize the cytoplasm
Ying Xie, Tong Shu, Tiewei Liu, Marie-Christin Spindler, Julia Mahamid, Glen M. Hocky, David Gresham, and Liam J. Holt
Mol. Cell, 84 (14), 2698-2716e9 (2024)
Research Highlight: Eytan Zlotorynski, Far from the cytoplasmic crowd, Nat. Rev. Mol. Cell Biol. (2024)
Mesoscale molecular assembly is favored by the active, crowded cytoplasm
Tong Shu, Gaurav Mitra, Jonathan Alberts, Matheus Viana, Emmanuel Levy, Glen M. Hocky*, and Liam J. Holt*
PRX Life, 2, 033001 (2024)
Good rates from bad coordinates: the exponential average time-dependent rate approach
Nicodemo Mazzaferro, Subarna Sasmal, Pilar Cossio*, and Glen M. Hocky*
J. Chem. Theory Comput. 20 (14), 5901-5912 (2024)
Enabling three-dimensional real space analysis of ionic colloidal crystallization
Shihao Zang, Adam W. Hauser, Sanjib Paul, Glen M. Hocky*, and Stefano Sacanna*
Nat. Mater., 23, 1131-1137 (2024)
Research Highlight: Theodore Hueckel and Robert J. Macfarlane, Illuminating defects in crystal clear colloidal assemblies, Nat. Mater. 23, 1023-1024 (2024)
NYU press release: Scientists Develop X-Ray Vision Technique to See Inside Crystals
Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM
Subarna Sasmal, Triasha Pal, Glen M. Hocky*, and Martin McCullagh*
J. Chem. Theory Comput., 20 (9), 3492–3502 (2024)
Arp23 complex- and formin-mediated actin cytoskeleton networks facilitate actin binding protein sorting in fission yeast
Kaitlin E. Homa, Glen M. Hocky, Cristian Suarez, and David R. Kovar
Eur. J. Cell Biol., 103 (2), 151404 (2024)
Connecting molecular properties with plain language
Glen M. Hocky*
Nat. Mach. Intell., 6, 249-250 (2024)
Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton
Fatemah Mukadum, Willmor J. Pena Ccoa, and Glen M. Hocky*
Cytoskeleton, 81 (8), 318-327 (2024)
Computing equilibrium free energies through a nonequilibrium quench
Kangxin Liu, Grant M. Rotskoff, Eric Vanden-Eijnden*, and Glen M. Hocky*
J. Chem. Phys., 160, 034109 (2024)
Improved prediction of molecular response to pulling by combining force tempering with replica exchange methods
Yuvraj Singh and Glen M. Hocky*
J. Phys. Chem. B, 128, 706-715 (2024)
Neural potentials of proteins extrapolate beyond training data
Geemi P. Wellawatte, Glen M. Hocky, and Andrew D. White
J. Chem. Phys., 159, 085103 (2023)
Molecular dynamics simulations support a multi-step Arp23 complex activation pathway
Yuvraj Singh, Glen M. Hocky*, and Brad J. Nolen*
J. Biol. Chem., 299 (9), 105169 (2023)
Reaction Coordinates for Conformational Transitions using Linear Discriminant Analysis on Positions
Subarna Sasmal, Martin McCullagh*, and Glen M. Hocky*
J. Chem. Theory Comput., 19 (14), 4427-4435 (2023)
A Coarse-Grained Simulation Model for Colloidal Self-Assembly via Explicit Mobile Binders
Gaurav Mitra, Chuan Chang, Angus McMullen, Daniela Puchall, Jasna Brujic, and Glen M. Hocky*
Soft Matter, 19, 4223-4236 (2023)
Assessment of chemistry knowledge in large language models that generate code
Andrew D. White*, Glen M. Hocky*, Heta A. Gandhi, Mehrad Ansari, Sam Cox, Geemi P. Wellawatte, Subarna Sasmal, Ziyue Yang, Kangxin Liu, Yuvraj Singh, and Willmor J. Pena Ccoa
Digit. Discov., 2, 368-376 (2023)
Catching actin proteins in action
Pilar Cossio and Glen M. Hocky*
Nature, 611, 241-243 (2022)
Structure of Arp23 complex at a branched actin filament junction resolved by single-particle cryo-EM
Bojian Ding, Heidy Y. Narvaez-Ortiz, Yuvraj Singh, Glen M. Hocky, Saikat Chowdhury, and Brad J. Nolen
Proc. Natl. Acad. Sci., 19 (22), e2202723119 (2022)
Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories
Heidi Klem, Glen M. Hocky, and Martin McCullagh
J. Chem. Theory Comput., 18 (5), 3218-3230 (2022)
Assessing models of force-dependent unbinding rates via infrequent metadynamics
Willmor J. Pena Ccoa and Glen M. Hocky*
J. Chem. Phys. 156, 125102 (2022)
Natural Language Processing Models That Automate Programming Will Transform Chemistry Research and Teaching
Glen M. Hocky* and Andrew D. White*
Digit. Discov., 1, 79-83 (2022)
Molecular paradigms for biological mechanosensing
David Gomez, Willmor J. Pena Ccoa, Yuvraj Singh, Enrique Rojas, and Glen M. Hocky*
J. Phys. Chem. B, 125 (44), 12115-12124 (2021)
Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture
Yashar Bashirzadeh, Steven A. Redford, Chatipat Lorpaiboon, Alessandro Groaz, Thomas Litschel, Petra Schwille, Glen M. Hocky, Aaron R. Dinner, and Allen P. Liu
Comms. Biol., 4, 1136 (2021)
A strong non-equilibrium bound for sorting of crosslinkers on growing biopolymers
Yuqing Qiu, Michael Nguyen, Glen M. Hocky, Aaron R. Dinner, and Suriyanarayanan Vaikuntanathan
Proc. Natl. Acad. Sci. U.S.A., 118 (38) e2102881118 (2021)
Total synthesis of colloidal matter
Theodore Hueckel, Glen M. Hocky, and Stefano Sacanna
Nat. Rev. Mater., 6, 1053-1069 (2021)
Structural basis of fast- and slow-severing actin-cofilactin boundaries
Glen M. Hocky*, Charles V. Sindelar, Wenxiang Cao, Gregory A. Voth, and Enrique M. De La Cruz*
J. Biol. Chem., 296, 100337 (2021)
A Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water
Paul Calio, Glen M. Hocky, and Gregory A. Voth
J. Chem. Theory Comput., 16 (9), 5675–5684 (2020)
Infinite Switch Simulated Tempering in Force (FISST)
Michael J. Hartmann, Yuvraj Singh, Eric Vanden-Eijnden, and Glen M. Hocky*
J. Chem. Phys., 152, 244120 (2020)
Simulation replicability information: 
Ionic Solids from Common Colloids
Theodore Hueckel, Glen M. Hocky, Jeremie Palacci, and Stefano Sacanna
Nature, 580, 487-490 (2020)
Research Highlight: G. Graziano, A controlled attraction, Nat. Rev. Chem. (2020)
NYU Press Release: Researchers Use Electrostatic Charge to Assemble Particles into Materials Mimicking Gemstones and Salt Crystals
Residue-Level Allostery Propagates Through the Effective Coarse-Grained Hessian
Peter T. Lake, Russell B. Davidson, Heidi Klem, Glen M. Hocky, and Martin McCullagh
J. Chem. Theory Comput., 16 (5), 3385-3395 (2020)
A burst of genetic innovation in Drosophila actin-related proteins for testis-specific function
Courtney M. Schroeder, John R. Valenzuela, Isabel M. Natividad, Glen M. Hocky, and Harmit S. Malik
Mol. Biol. Evol., 37 (3), 757-772 (2020)
Mechanical and kinetic factors drive sorting of F-actin crosslinkers on bundles
Simon L. Freedman, Cristian Suarez, Jonathan D. Winkelman, David R. Kovar, Gregory A. Voth, Aaron R. Dinner*, and Glen M. Hocky*
Proc. Natl. Acad. Sci. U.S.A., 116 (33), 16192--16197 (2019)
Plastic deformation and fragmentation of strained actin filaments
Anthony C. Schramm, Glen M. Hocky, Gregory A. Voth, Jean-Louis Martiel, and Enrique M. De La Cruz
Biophys. J, 117, 453--463 (2019)
Promoting transparency and reproducibility in enhanced molecular simulations
Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth A. Tribello, Pavel Banas, Alessandro Barducci, Mattia Bernetti, Peter G. Bolhuis, Sandro Bottaro, Davide Branduardi, Riccardo Capelli, Paolo Carloni, Michele Ceriotti, Andrea Cesari, Haochuan Chen, Wei Chen, Francesco Colizzi, Sandip De, Marco De La Pierre, Davide Donadio, Viktor Drobot, Bernd Ensing, Andrew L. Ferguson, Marta Filizola, James S. Fraser, Haohao Fu, Piero Gasparotto, Francesco Luigi Gervasio, Federico Giberti, Alejandro Gil-Ley, Toni Giorgino, Gabriella T Heller, Glen M. Hocky, Marcella Iannuzzi, Michele Invernizzi, Kim E. Jelfs, Alexander Jussupow, Evgeny Kirilin, Alessandro Laio, Vittorio Limongelli, Kresten Lindorff-Larsen, Thomas Lohr, Fabrizio Marinelli, Layla Martin-Samos, Matteo Masetti, Ralf Meyer, Angelos Michaelides, Carla Molteni, Tetsuya Morishita, Marco Nava, Cristina Paissoni, Elena Papaleo, Michele Parrinello, Jim Pfaendtner, Pablo Piaggi, Giovanni Maria Piccini, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Davide Provasi, David Quigley, Paolo Raiteri, Stefano Raniolo, Jakub Rydzewski, Matteo Salvalaglio, Gabriele Cesare Sosso, Vojtech Spiwok, Jiri Sponer, David W. H. Swenson, Pratyush Tiwary, Omar Valsson, Michele Vendruscolo, Gregory A. Voth, and Andrew White
Nat. Methods 16, 670--673 (2019)
Insights into the cooperative nature of ATP hydrolysis in actin filaments
Harshwardhan H. Katkar, Aram Davtyan, Aleksander E. P. Durumeric, Glen M. Hocky, Anthony C. Schramm, Enrique M. De La Cruz, and Gregory A. Voth
Biophys. J, (115) 8, 1589-1602 (2018)
Nonequilibrium phase diagrams for actomyosin networks
Simon L. Freedman, Glen M. Hocky, Shiladitya Banerjee, and Aaron R. Dinner
Soft Matter, 14, 7740-7747 (2018)
Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments
W. Austin Elam+, Wenxiang Cao+, Hyeran Kang, Andrew Huehn, Glen M. Hocky, Ewa Prochniewicz, Anthony C. Schramm, Karina Nieves-Torres, Jean Garcia, Teresa Bonello, Thomas Fath, Peter W. Gunning, David D. Thomas, Gregory A. Voth, Charles V. Sindelar, and Enrique M. De La Cruz
J. Biol. Chem. 292 (48) 19565-19579 (2017)
Mechanosensitive inhibition of formin facilitates contractile ring assembly in fission yeast
Dennis Zimmermann, Kaitlin E. Homa+, Glen M. Hocky+, Luther W. Pollard, Enrique M. De La Cruz, Gregory A. Voth, Matthew J. Lord, Kathleen M. Trybus, and David R. Kovar
Nature Comm., (8), 703 (2017)
Feature article: D. Vavylonis and B. Horan, Capturing Formin’s Mechano-Inhibition, Curr. Biol. (27) 19, R1078-R1080 (2017)
Coarse-Grained Directed Simulation
Glen M. Hocky, Thomas Dannenhoffer-Lafage, and Gregory A. Voth
J. Chem. Theory Comput., 13 (9), 4593-4603 (2017)
Simulation replicability information: 
A versatile method for simulating the dynamic mechanical structure of cytoskeletal networks
Simon Freedman, Shiladitya Banerjee, Glen M. Hocky, and Aaron R. Dinner
Biophys. J, 113 (2), 448-460 (2017)
Actin filament strain promotes severing and cofilin dissociation
Anthony C. Schramm, Glen M. Hocky, Gregory A. Voth, Laurent Blanchoin, Jean-Louis Martiel, and Enrique M. De La Cruz
Biophys. J., 112 (12), 2624-2633 (2017)
Competition between Tropomyosin, Fimbrin, and ADF/Cofilin drives their sorting to distinct actin filament networks
Jenna R. Christensen, Glen M. Hocky, Kaitlin E. Homa, Alisha N. Morganthaler, Sarah E. Hitchcock-DeGregori, Gregory A. Voth, and David R. Kovar
eLife 2017;10.7554/eLife.23152 (2017)
Communication: Improved ab initio molecular dynamics by minimal biasing with experimental data
Andrew D. White, Christopher Knight, Glen M. Hocky, and Gregory A. Voth
J. Chem. Phys., 146, 041102 (2017)
Fascin- and alpha-Actinin-Bundled Networks Contain Intrinsic Structural Features that Drive Protein Sorting
Jonathan D. Winkelman+, Cristian Suarez+, Glen M. Hocky, Alyssa J. Harker, Alisha N. Morganthaler, Jenna R. Christensen, Gregory A. Voth, James R. Bartles, and David R. Kovar
Curr. Biol., 26 (20), 2697 (2016)
Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits
Glen M. Hocky+, Joseph L. Baker+, Michael J. Bradley, Anton V. Sinitskiy, Enrique M. De La Cruz, and Gregory A. Voth
J. Phys. Chem. B., 120 (20), 4558-4567 (2016)
The F-actin bundler alpha-actinin Ain1 is tailored for ring assembly and constriction during cytokinesis in fission yeast
Yujie Li, Jenna R. Christensen+, Kaitlin E. Homa+, Glen M. Hocky, Alice Fok, Jennifer A. Sees, Gregory A. Voth, and David R. Kovar
Mol. Biol. Cell., 27 (11), 1821-1833 (2016)
Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction
James F. Dama, Glen M. Hocky, Rui Sun, and Gregory A. Voth
J. Chem. Theory Comput., 11 (12), 5638-5650 (2015)
Equilibrium ultrastable glasses produced by random pinning
Glen M. Hocky, Ludovic Berthier, and David R. Reichman
J. Chem. Phys., 141, 224503 (2014)
Correlation of Local Order with Particle Mobility in Supercooled Liquids Is Highly System Dependent
Glen M. Hocky, Daniele Coslovich, Atsushi Ikeda, and David R. Reichman
Phys. Rev. Lett., 113, 157801 (2014)
Crossovers in the dynamics of supercooled liquids probed by an amorphous wall
Glen M. Hocky, Ludovic Berthier, Walter Kob, and David R. Reichman
Phys. Rev. E, 89, 052311 (2014)
A small subset of normal modes mimics the properties of dynamical heterogeneity in a model supercooled liquid
Glen M. Hocky and David R. Reichman
J. Chem. Phys., 138, 12A537 (2013)
Growing point-to-set length scale correlates with growing relaxation times in model supercooled liquids
Glen M. Hocky, Thomas E. Markland, and David R. Reichman
Phys. Rev. Lett., 108, 22506 (2012)
Protein structure prediction enhanced with evolutionary diversity: SPEED
Joe DeBartolo, Glen Hocky, Michael Wilde, Jinbo Xu, Karl F. Freed, and Tobin R. Sosnick
Prot. Sci., 19 (3), 520-534 (2010)
Towards petascale ab initio protein folding through parallel scripting
Glen Hocky, Michael Wilde, Joe DeBartolo, Mihael Hategan, Ian Foster, Tobin R. Sosnick, and Karl F. Freed
Argonne technical report, MCS-P1645-0609 (2009)
Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model
Haipeng Gong, Glen Hocky, and Karl F. Freed
Proc. Natl. Acad. Sci. U.S.A., 105 (32), 11146-11151 (2008)