Publications

See the full list of publications at Google Scholar.

2020 – present

Hemanta Bhattarai, Kathie E. Newman, and J. Daniel Gezelter, “The Role of Polarizability in the Interfacial Thermal Conductance at the Gold-Water Interface,”  J. Chem. Phys. 153, 204703 (2020).
DOI: 10.1063/5.0027847

Suzanne M. Neidhart and J. Daniel Gezelter, “Thermal Conductivity of Gold-Phenylethanethiol (Au₁₄₄PET₆₀) Nanoarrays: A Molecular Dynamics Study,”  J. Phys. Chem. C 124(5), pp. 3389-3395 (2020).
DOI: 10.1021/acs.jpcc.9b10895

2010 – 2019

Hemanta Bhattarai, Kathie E. Newman, and J. Daniel Gezelter, “Polarizable Potentials For Metals: The Density Readjusting Embedded Atom Method (DR-EAM),” Phys. Rev. B 99, 094106 (2019).
DOI: 10.1103/PhysRevB.99.094106, arXiv:1904.00263

Patrick B. Louden and J. Daniel Gezelter, “Why is Ice Slippery? Simulations of Shear Viscosity of the Quasi-Liquid Layer on Ice,”  J. Phys. Chem. Lett. 9, pp. 2686-3691 (2018).
DOI: 10.1021/acs.jpclett.8b01339

Suzanne M. Neidhart and J. Daniel Gezelter, “Thermal Transport is Influenced by Nanoparticle Morphology: A Molecular Dynamics Study,” J. Phys. Chem. C,  122(2), pp. 1430-1436, (2018).
DOI: 10.1021/acs.jpcc.7b12362

Patrick B. Louden and J. Daniel Gezelter, “Friction at Ice-I_h / Water Interfaces Is Governed by Solid / Liquid Hydrogen-Bonding,” J. Phys. Chem. C 121 (48), pp 26764–26776 (2017).
DOI: 10.1021/acs.jpcc.7b07169

Joseph R. Michalka, Andrew P. Latham, and J. Daniel Gezelter, “CO-induced restructuring on stepped Pt surfaces: A molecular dynamics study” J. Phys. Chem. C 120 (32), pp. 18180-18190, (2016).
DOI: 10.1021/acs.jpcc.6b06619, arXiv: 1608.05833

Madan Lamichhane, Thomas Parsons, Kathie E. Newman, and J. Daniel Gezelter, “Real Space Electrostatics for multipoles. III. Dielectric properties,” J. Chem. Phys. 145, 074108 (2016).
DOI: 10.1063/1.4960957, arXiv: 1608.04970

Kelsey M. Stocker, Suzanne M. Neidhart and J. Daniel Gezelter, “Interfacial Thermal Conductance of Thiolate-Protected Gold Nanospheres,”  J. Appl. Phys. 119 (2), 025106, (2016).
DOI: 10.1063/1.4939956, arXiv:1601.03315

Joseph R. Michalka, and J. Daniel Gezelter, “Island Formation on Pt/Pd(557) Surface Alloys in the Presence of Adsorbed CO: A Molecular Dynamics Study,” J. Phys. Chem. C, 119 (25), pp 14239–14247 (2015).
DOI: 10.1021/acs.jpcc.5b03586

Daniel C. Hannah, J. Daniel Gezelter, Richard D. Schaller, and George C. Schatz, “Reverse Non-Equilibrium Molecular Dynamics Demonstrates that Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces,”ACS Nano 9 (6), pp 6278–6287 (2015).
DOI: 10.1021/acsnano.5b01724

J. Daniel Gezelter, “Open Source and Open Data Should be Standard Practices,” J. Phys. Chem. Lett. 6 (7), pp. 1168-1169 (2015).
DOI: 10.1021/acs.jpclett.5b00285

Madan Lamichhane, J. Daniel Gezelter, and Kathie E. Newman, “Real Space Electrostatics for Multipoles. I. Development of Methods,” J. Chem. Phys. 141 (13), 134109 (2014).
DOI: 10.1063/1.4896627

Madan Lamichhane, Kathie Newman, and J. Daniel Gezelter, “Real Space Electrostatics for multipoles. II. Comparison with the Ewald Sum,” J. Chem. Phys. 141 (13), 134110 (2014).
DOI: 10.1063/1.4896628

James M. Marr and J. Daniel Gezelter, “Nitrile vibrations as reporters of field-induced phase transitions in 4-cyano-4′-pentylbiphenyl (5CB),” J. Phys. Chem. B 118 (28) pp. 8441-8448 (2014)
DOI: 10.1021/jp503235s

Kelsey M. Stocker and J. Daniel Gezelter, “A method for creating thermal and angular momentum fluxes in non-periodic simulations,” J. Chem. Theory Comput. 10 (5), pp. 1878-1886 (2014)
DOI: 10.1021/ct500221u

Patrick B. Louden and J. Daniel Gezelter, “Simulations of solid-liquid friction at ice-I_h / water interfaces,” J. Chem. Phys. 139, 194710 (2013)
DOI: 10.1063/1.4832378

Joseph R. Michalka, Patrick W. McIntyre , and J. Daniel Gezelter, “Molecular Dynamics Simulations of the Surface Reconstructions of Pt(557) and Au(557) under Exposure to CO,” J. Phys. Chem. C 117, pp 14579–14587 (2013)
DOI: 10.1021/jp402798n

Kelsey M. Stocker and J. Daniel Gezelter, “Simulations of Heat Conduction at Thiolate-Capped Gold Surfaces: The Role of Chain Length and Solvent Penetration,” J. Phys. Chem. C 117(15) pp. 7605-7612 (2013)
DOI: 10.1021/jp312734f

Shenyu Kuang and J. Daniel Gezelter, “Velocity Shearing and Scaling RNEMD: a minimally perturbing method for simulating temperature and momentum gradients,” Mol. Phys. 110, pp. 691-701 (2012)
DOI: 10.1080/00268976.2012.680512

Shenyu Kuang and J. Daniel Gezelter, “Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents,” J. Phys. Chem. C, 115(45), pp. 22475-22483, (2011)
DOI: 10.1021/jp2073478

Charles F. Vardeman II, Kelsey M. Stocker and J. Daniel Gezelter, “The Langevin Hull: Constant pressure and temperature dynamics for non-periodic systems,” J. Chem. Theory Comput. 7(4), 834-842 (2011)
DOI: 10.1021/ct100670m

Shenyu Kuang and J. Daniel Gezelter, “A gentler approach to RNEMD: Non-isotropic Velocity Scaling for computing thermal conductivity and shear viscosity,” J. Chem. Phys. 133, 164101 (2010)
DOI: 10.1063/1.3499947

Victoria Stodden, David Donoho, Sergey Fomel, Michael P. Friedlander, Mark Gerstein, Randy LeVeque, Ian Mitchel^†, Lisa Larrimore Ouellette, Chris Wiggins, Nicholas W. Bramble, Patrick O. Brown, Vincent J. Carey, Laura DeNardis, Robert Gentleman, J. Daniel Gezelter, Alyssa Goodman, Matthew G. Knepley, Joy E. Moore, Frank A. Pasquale, Joshua Rolnick, Michael Seringhaus, and Ramesh Subramanian, “Reproducible Research: Addressing the Need for Data and Code Sharing in Computational Science,” Computing in Science and Engineering 12(5) pp. 8-13 (2010)
DOI:10.1109/MCSE.2010.113

2000 – 2009

Xiuquan Sun and J. Daniel Gezelter, “Langevin Dynamics for Rigid Bodies of Arbitrary Shape,” J. Chem. Phys. 128, 24107 (2008)
DOI: 10.1063/1.2936991

Charles F. Vardeman II and J. Daniel Gezelter, “Simulations of laser-induced glass formation in Ag-Cu nanoparticles,” J. Phys. Chem. C. 112, 3283-3293 (2008)
DOI: 10.1021/jp710063g

Xiuquan Sun and J. Daniel Gezelter, “Dipolar ordering in the ripple phases of molecular-scale models of lipid membranes,” J. Phys. Chem. B. 112, pp. 1968- 1975 (2008)
DOI: 10.1021/jp0762020

Xiuquan Sun and J. Daniel Gezelter, “Spontaneous Corrugation of Dipolar Membranes,” Phys. Rev. E 75, 031602 (2007)
DOI: 10.1103/PhysRevE.75.031602

Christopher J. Fennell and J. Daniel Gezelter, “Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics,” J. Chem. Phys., 124, 234104 (2006)
DOI: 10.1063/1.2206581

Christopher J. Fennell and J. Daniel Gezelter, “Computational free energy studies of a new ice polymorph which exhibits greater stability than Ice Ih,” J. Chem. Theory Comput. 1, pp. 662-667 (2005)
DOI: 10.1021/ct050005s

Matthew A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher J. Fennell and J. Daniel Gezelter, “OOPSE: An Object-Oriented Parallel Simulation Engine for Molecular Dynamics,” J. Comput. Chem. 26, pp. 252-271 (2005)
DOI: 10.1002/jcc.20161

Charles F. Vardeman II, Patrick F. Conforti, Megan M. Sprague, and J. Daniel Gezelter, “Breathing Mode Dynamics and Elastic Properties of Gold Nanoparticles,” J. Phys. Chem. B 109 (35), pp 16695–16699 (2005).
DOI: 10.1021/jp051575r

Christopher J. Fennell and J. Daniel Gezelter, “On the structural and transport properties of the Soft Sticky Dipole (SSD) and related single-point water models,” J. Chem. Phys. 120, 9175-9184 (2004)
DOI: 10.1063/1.1697381

Tomohiro Shibata, Bruce A. Bunker, Zhenyuan Zhang, Dan Meisel, Charles F. Vardeman II, and J. Daniel Gezelter, “Size Dependent Spontaneous Alloying of Au-Ag Nanoparticles,” J. Am. Chem. Soc. 124, 11898-11996 (2002)
DOI: 10.1021/ja026764r

Matthew A. Meineke and J. Daniel Gezelter, “A Random Sequential Adsorption model for the differential coverage of Gold (111) surfaces by two related Silicon phthalocyanines, J. Phys. Chem. B. 105, 6515-6519 (2001)
DOI: 10.1021/jp010985m

Charles F. Vardeman II and J. Daniel Gezelter, “Comparing models for diffusion in supercooled liquids: The eutectic composition of the Ag-Cu alloy, J. Phys. Chem. A, 105, 2568-2574 (2001)
DOI: 10.1021/jp0035784

Eran Rabani, J. Daniel Gezelter, and B.J. Berne, “Response to ‘Comment on “Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function”’,” Phys. Rev. Lett. 85, 467 (2000)
DOI: 10.1103/PhysRevLett.85.467

1990 – 1999

Eran Rabani, J. Daniel Gezelter, and B.J. Berne, “Direct Observation of Stretched- Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function” Phys. Rev. Lett. 82, 3649 (1999)
DOI: 10.1103/PhysRevLett.82.3649

J. Daniel Gezelter, Eran Rabani, and B.J. Berne, “Calculating the hopping rate for diffusion in molecular liquids: CS₂,” J. Chem. Phys. 110, 3444 (1999)
DOI: 10.1063/1.478211

J. Daniel Gezelter, Eran Rabani, and B.J. Berne, “Response to ‘Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion’,” J. Chem. Phys. 109, 4695 (1998)
DOI: 10.1063/1.477081

Eran Rabani, J. Daniel Gezelter, and B.J. Berne, “Calculating the hopping rate for self-diffusion on rough potential energy surfaces: cage correlations,” J. Chem. Phys. 107, 6867 (1997)
DOI: 10.1063/1.474927

J. Daniel Gezelter, Eran Rabani, and B.J. Berne, “Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?” J. Chem. Phys. 107, 4618 (1997)
DOI: 10.1063/1.474822

J. Daniel Gezelter and William H. Miller, “Dynamics of the Photodissociation of Triplet Ketene,” J. Chem. Phys. 104, 3546 (1996)
DOI: 10.1063/1.471059

J. Daniel Gezelter and William H. Miller, “Resonant features in the energy dependence of the rate of ketene isomerization,” J. Chem. Phys. 103, 7868 (1995)
DOI: 10.1063/1.470204

Simon W. North, David A. Blank, J. Daniel Gezelter, Cheryl A. Longfellow, and Yuan T. Lee, “Evidence for Stepwise Dissociation Dynamics of Acetone at 248 nm and 193 nm,” J. Chem. Phys. 102, 4447 (1995)
DOI: 10.1063/1.469493

Thomas D. Sewell, Donald L. Thompson, J. Daniel Gezelter, and William H. Miller, “Some problems of correcting the zero-point energy problem in classical trajectories,” Chem. Phys. Lett. 193, 512 (1992)
DOI: 10.1016/0009-2614(92)85841-W

J. Daniel Gezelter and Ray Freeman, “Use of Neural Networks to Design Shaped Radio-Frequency Pulses,” J. Magn. Reson. 90, 397 (1990)
DOI: 10.1016/0022-2364(90)90149-4