Publications

138 publications · 98 with PubMed links · view full CV · download CV (PDF)

2025

Shilei Ding, Derek Yang, Irfan Ullah, Ling Niu, Matthew Unger, Marco Díaz-Salinas, Monika Chandravanshi, Fei Zhou, Guillaume Beaudoin-Bussières, Mehdi Benlarbi, William Tolbert, Keon-Woong Yoon, Ruixue Xu, Geneviève Laroche, Fleur Gaudette, et al. “Optimization of VE607 to generate analogs with improved neutralization activities against SARS-CoV-2 variants.” Journal of Virology, vol. 99, pp. e01034-25. doi:10.1128/jvi.01034-25 · PMID:41081594

Salsabil Abou-Hatab, Cameron F. Abrams “Minimal Collective Variables for Conformational Transitions in Steered and Temperature-Accelerated MD Simulations: A T4 Lysozyme Case Study.” Journal of Physical Chemistry B, vol. 129, pp. 5176-5188. doi:10.1021/acs.jpcb.5c01129 · PMID:40375602

Bibek Parajuli, Kriti Acharya, Harry Bach, Shiyu Zhang, Cameron F. Abrams, Irwin Chaiken “Monovalent Lectin Microvirin Utilizes Hydropathic Recognition of HIV-1 Env for Inhibition of Virus Cell Infection.” Viruses, vol. 17, pp. 82. doi:10.3390/v17010082 · PMID:39742730

2024

Mehdi Benlarbi, Shilei Ding, Étienne Bélanger, Alexandra Tauzin, Raphael Poujol, Halima Medjahed, Omar El Ferri, Yuxia Bo, Catherine Bourassa, Julie Hussin, Judith Fafard, Marzena Pazgier, Inès Levade, Cameron F. Abrams, Marceline Côté, et al. “Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission.” mBio, vol. 15, pp. e0090724. doi:10.1128/mbio.0097-24 · PMID:39791898

2023

Monisha Gupta, Gabriela Canziani, Charles Ang, Mohammadjavad Mohammadi, Cameron F. Abrams, Derek Yang, Amos B. Smith, III, Irwin Chaiken “Pharmacophore Variants of the Macrocyclic Peptide Triazole Inactivator of HIV-1 Env.” Med. Chem. Res., vol. 32, pp. 1497-1509. doi:10.1007/s00044-023-03092-0 · PMID:39790932

Shilei Ding, William D. Tolbert, Huile Zhu, Daniel Lee, Tyler Higgins, Xuchen Zhao, Dung Nguyen, Rebekah Sherburn, Jonathan Richard, Gabrielle-Gendron Lepage, Halima Medjahed, Mohammadjavad Mohammadi, Cameron Abrams, Marzena Pazgier, Amos B. Smith III, et al. “Piperidine CD4-mimetic compounds expose vulnerable Env epitopes sensitizing HIV-1-infected cells to ADCC.” Viruses, vol. 15, pp. 1185. doi:10.3390/v15051185 · PMID:37243271

Christopher Fritcshi, Saumya Anang, Zhen Gong, Mohammadjavad Mohammadi, Jonathan Richard, Catherine Bourassa, Kenny T. Severino, Hannah Richter, Derek Yang, Hung-Ching Chen, Ta-Jung Chiu, Michael S. Seaman, Navid Madani, Cameron F. Abrams, Andrès Finzi, et al. “Indoline CD4-mimetic Compounds Mediate Potent and Broad HIV-1 Inhibition and Sensitization to Antibody-dependent Cellular Cytotoxicity.” Proc. Natl. Acad. Sci. USA, vol. 120, pp. e2222073120. doi:10.1073/pnas.222073120 · PMID:39435159

Giulio Alberini, S. Alexis Paz, Cameron F. Abrams, Fabio Benfenati, Luca Maragliano “Molecular Dynamics Simulations of Ion Permeation in Human NaV Channels.” J. Chem. Theory. Comput., vol. 19, pp. 2953-2972. doi:10.1021/acs.jctc.2c00990 · PMID:37116214

Ming Huang, Cameron F. Abrams “HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers.” SoftwareX, vol. 21, pp. 101303. doi:10.1016/j.softx.2022.101303

2022

Cheyenne Chaplain, Christopher Fritschi, Saumya Anang, Zhen Gong, Jonathan Richard, Shuaiyi Yang, Mohammadjavad Mohammadi, Jun Park, Andrés Finzi, Navid Madani, Joseph Sodroski, Cameron F. Abrams, Wayne Hendrickson, Amos B. Smith, III “Structural and Functional Characterization of Indane-core CD4-mimetic Compounds Substituted with Heterocyclic Amines.” ACS Med. Chem. Lett., vol. 14, pp. 51-58. doi:10.1021/acsmedchemlett.2c00376 · PMID:36655122

Natasha Gupta Vergara, Cameron F. Abrams “Entropic overcompensation of the N501Y mutation on SARS-CoV-2 S binding to ACE2.” J. Chem. Inform. Model., vol. 63, pp. 633-642. doi:10.1021/acs.jcim.2c01246 · PMID:36584335

Shilei Ding, Irfan Ullah, Shang Yu Gong, Jonathan R. Grover, Mohammadjavad Mohammadi, Yaozong Chen, Dani Vézina, Guillaume Beaudoin-Bussières, Vijay Tailor Verma, Guillaume Goyette, Fleur Gaudette, Jonathan Richard, Derek Yang, Amos B. Smith III, Marzena Pazgier, et al. “VE607 stabilizes SARS-CoV-2 Spike in the `RBD-up' conformation and inhibits viral entry.” iScience, vol. 25, pp. 104528. doi:10.1016/j.isci.2022.104528 · PMID:35233570

Ming Huang, Nicolas Alvarez, Giuseppe Palmese, Cameron Abrams “The Effect of Network Topology on Material Properties in Vinyl-ester/Styrene Thermoset Polymers using Molecular Dynamics Simulations and Time-Temperature Superposition.” Comput. Mater. Sci., vol. 27, pp. 111264. doi:10.1016/j.commatsci.2022.111264

Salman Zarrini, Cameron Abrams “Modeling sizing emulsion droplet deposition onto silica using all-atom molecular dynamics simulations.” Composites Part B: Engineering, vol. 235, pp. 109712. doi:10.1016/j.compositesb.2022.109712

2021

Christopher Fritschi, Shuaiyi Liang, Mohammadjavad Mohammadi, Saumya Anang, Francesca Moraca, Junhua Chen, Navid Madani, Joseph Sodroski, Cameron Abrams, Wayne Hendrickson, Amos Smith, III “Identification and Validation of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics.” ACS Med. Chem. Lett., vol. 12, pp. 1824-1831. doi:10.1021/acsmedchemlett.1c00437 · PMID:34795873

Ketan Khare, Cameron Abrams “Atomistic Simulation of Volumetric Properties of Epoxy Networks: Effect of Monomer Length.” Soft Matter, vol. 17, pp. 9957-9986. doi:10.1039/D1SM01128F · PMID:34698327

Sergio Ribone, Sergio Alexis Paz, Cameron Abrams, Marcos Villarreal “Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.” J. Comput. Aided Mol. Des., vol. 26, pp. 1-13. doi:10.1007/s10822-021-00432-3 · PMID:34825285

Jérémie Prévost, Jonathan Richard, Romain Gasser, Shilei Ding, Clément Fage, Sai Priya Anand, Damien Adam, Natasha Gupta Vergara, Alexandra Tauzin, Mehdi Benlarbi, Shang Yu Gong, Guillaume Goyette, Anik Privé, Sandrine Moreira, Hugues Charest, et al. “Impact of temperature on the affinity of SARS-CoV-2 Spike for ACE2.” J. Biol. Chem., vol. 297, pp. 101151. doi:10.1016/j.jbc.2021.101151 · PMID:34478710

S. Zarrini, C. F. Abrams “The Roles of Coupling Agent and Surfactant in Droplet Structure in Sizing Emulsions: A Molecular Dynamics Simulations Study.” Langmuir, vol. 37, pp. 10183-10190. doi:10.1021/acs.langmuir.1c01592 · PMID:34396774

C. G. Ang, E. Carter, A. Haftl, S. Zhang, A. A. Rashad, M. Kutzler, C. F. Abrams, I. M. Chaiken “Peptide triazole thiol irreversibly inactivates metastable HIV-1 Env by accessing conformational triggers intrinsic to virus-cell entry.” Microoganisms, vol. 9, pp. 1286. doi:10.3390/microorganisms9061286 · PMID:34204725

G. Shrivastav, C. F. Abrams “Optimizing string method's reproducibility using generalized solute tempering replica exchange.” J. Phys. Chem. B, vol. 125, pp. 6609-6616. doi:10.1021/acs.jpcb.1c02143 · PMID:34110824

A. Gaffney, A. Nangarlia, C. G. Ang, S. Gossert, A. A. Rashad Ahmed, M. A. Hossain, C. F. Abrams, A. B. Smith III, I. Chaiken “HIV-1 Env-dependent cell killing by bifunctional small-molecule/peptide conjugates.” ACS Chem. Biol., vol. 16, pp. 193-204. doi:10.1021/acschembio.0c00888 · PMID:33410670

2020

B. Parajuli, K. Acharya, A. Nangarlia, S. Zhang, B. Parajuli, A. Dick, B. Ngo, C. F. Abrams, I. Chaiken “Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate.” Biochem. J., vol. 477, pp. 4263-4280. doi:10.1042/BCJ20200495 · PMID:33057580

S. Gossert, B. Parajuli, I. Chaiken, C. F. Abrams “Roles of variable linker length in dual acting virucidal entry inhibitors on HIV-1 potency via on-the-fly free energy molecular simulations.” Protein Sci., vol. 29, pp. 2304. doi:10.1002/pro.3949 · PMID:32926485

S. P. Anand, Y. Chen, J. Prévost, R. Gasser, G. Beaudoin-Bussiéres, C. F. Abrams, M. Pazgier, A. Finzi “Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins.” Viruses, vol. 12, pp. 1104. doi:10.3390/v12101104 · PMID:33003587

Jérémie Prévost, William D. Tolbert, Halima Medjahed, Rebekah T. Sherburn, Navid Madani, Daria Zoubchenok, Gabrielle Gendron-Lepage, Althea E. Gaffney, Melissa C. Grenier, Sharon Kirk, Natasha Gupta Vergara, Changze Han, Brendan T. Mann, Agnès L. Chénine, Adel Ahmed, et al. “The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site.” mBio, vol. 11, pp. e00280-20. doi:10.1128/mBio.00280-20 · PMID:32457241

Shitao Zou, Shijian Zhang, Althea Gaffney, Haitao Ding, Maolin Lu, Jonathan Grover, Mark Farrell, Hanh Nguyen, Connie Zhao, Saumya Anang, Meiqing Zhao, Mohammadjavad Mohammadi, Scott Blanchard, Cameron Abrams, Navid Madani, et al. “Long-Acting BMS-378806 Analogues Stabilize the State-1 Conformation of the Human Immunodeficiency Virus (HIV-1) Envelope Glycoproteins.” J. Virol., vol. 94, pp. e00148-20. doi:10.1128/JVI.00148-20 · PMID:32161177

Charles Ang, Mohammed Hossain, Marg Rajpara, Harry Bach, Kriti Acharya, Alexej Dick, Adel Ahmed, Michelle Kutzler, Cameron F. Abrams, Irwin Chaiken “Metastable HIV-1 Surface Protein Env Sensitizes Cell Membranes to Transformation and Poration by Dual-Acting Virucidal Entry Inhibitors.” Biochemistry, vol. 59, pp. 818-828. doi:10.1021/acs.biochem.9b01008 · PMID:31942789

Melissa Grenier, Shilei Ding, Dani Vézina, Jean-Philippe Chapleau, William Tolbert, Rebekah Sherburn, Arne Schon, Sambasivarao Somisetti, Cameron F. Abrams, Marzena Pazgier, Andrés Finzi, Amos B. Smith, III “Optimization of Small Molecules for their Capacity to Sensitize HIV-1 Infected Cells to Antibody Dependent Cellular Cytotoxicity.” ACS Med. Chem. Lett., vol. 11, pp. 371-378. doi:10.1021/acsmedchemlett.9b00445 · PMID:32184972

2019

Jasmine Gardner, Cameron F. Abrams “Energetics of Flap Opening in HIV-1 Protease: String Method Calculations.” J. Phys. Chem. B, vol. 123, pp. 9584-9591. doi:10.1021/acs.jpcb.9b08348 · PMID:31640343

Anindya Bhaduri, Jasmine Gardner, Cameron F. Abrams, Lori Brady “Free energy calculation using space filled design and weighted reconstruction: A modified single sweep approach.” Mol. Sim., vol. 46, pp. 193-206. doi:10.1080/08927022.2019.1688325 · PMID:39780972

Shilei Ding, Melissa Grenier, William Tolbert, Dani Vézina, Rebekah Sherburn, Jonathan Richard, Jérémie Prévost, Jean-Philippe Chapleau, Gabrielle Gendron-Lepage, Halima Medjahed, Cameron F. Abrams, Joseph Sodroski, Marzena Pazgier, Amos Smith, III, Andrés Finzi “A new family of small-molecule CD4-mimetic compounds contact the highly conserved aspartic acid 368 of HIV-1 gp120 and mediates ADCC.” J. Virol., vol. 93, pp. e01325-19. doi:10.1128/JVI.01325-19 · PMID:31554684

Gourav Shrivastav, Eric Vanden-Eijnden, Cameron F. Abrams “Mapping Saddles and Minima on Free Energy Surfaces using Multiple Climbing Strings.” J. Chem. Phys., vol. 151, pp. 124112. doi:10.1063/1.5120372 · PMID:31575198

Connie Zhao, Amy Princiotto, Hanh Nguyen, Shitao Zou, Meiqing Zhao, Shijian Zhang, Alon Herschhorn, Mark Farrell, Karanbir Pahil, Bruno Melillo, Somisetti Sambasivarao, Cameron Abrams, Amos Smith III, Navid Madani, Joseph Sodroski “Strain-dependent activation and inhibition of human immunodeficiency virus (HIV-1) entry by a specific PF-68742 stereoisomer.” J. Virol., vol. 93, pp. 1-20. doi:10.1128/JVI.01197-19 · PMID:31391272

Ming Huang, Cameron F. Abrams “Effects of Reactivity Ratios on Network Topology and Thermomechanical Properties in Vinyl-Ester/Styrene Thermosets: Molecular Dynamics Simulations.” Macromol. Theory. Sim., vol. 28, pp. 1900030. doi:10.1002/mats.201900030

Arun Srikanth Sridhar, Cameron F. Abrams “Effect of molecular packing and hydrogen bonding on the properties of epoxy-amido amine systems.” Comput. Mater. Sci., vol. 169, pp. 109082. doi:10.1016/j.commatsci.2019.109082

Maolin Lu, Xiaochu Ma, Luis R. Castillo-Menendez, Jason Gorman, Nirmin Alsahafi, Utz Erme, Daniel S. Terry, Michael Chambers, Dongjun Peng, Baoshan Zhang, Tongqing Zhou, Nick Reichard, Kevin Wang, Jonathan Grover, Brennan P. Carman, et al. “Associating HIV-1 envelope glycoprotein structures with states on virus observed by smFRET.” Nature, vol. 568, pp. 415-419. doi:10.1038/s41586-019-1101-y · PMID:30971821

Arun Srikanth Sridhar, Cameron F. Abrams “Yield and Post-yield Behavior of Fatty- Acid-Functionalized Amidoamine–Epoxy Systems: A Molecular Simulation Study.” J. Dyn. Behav. Mater., vol. 5, pp. 143-149. doi:10.1007/s40870-019-00193-z · PMID:39790932

2018

Ryan Gordon, Spencer Stober, Cameron F. Abrams “Counterion Effects on Aggregate Structure of 12-Hydroxystearate Salts in Hexane: A Quantum Mechanical and Molecular Dynamics Simulation Study.” J. Phys. Chem. B, vol. 123, pp. 534-541. doi:10.1021/acs.jpcb.8b08477 · PMID:30571113

Jasmine Gardner, Cameron F. Abrams “Lipid flip-flop vs. lateral diffusion in the relaxation of hemifusion diaphragms.” BBA-Biomembranes, vol. 1860, pp. 1452-1459. doi:10.1016/j.bbamem.2018.04.007 · PMID:29684332

Steven Gossert, Bibek Parajuli, Irwin Chaiken, Cameron F. Abrams “Roles of Conserved Tryptophans in Trimerization of HIV-1 Membrane-Proximal External Regions: Implications for Virucidal Design via Alchemical Free-Energy Molecular Simulations.” Proteins, vol. 86, pp. 707-711. doi:10.1002/prot.25504 · PMID:29633345

S. Alexis Paz, Luca Maragliano, Cameron F. Abrams “The effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parameterization.” J. Chem. Theory. Comput., vol. 14, pp. 2743–2750. doi:10.1021/acs.jctc.8b00024 · PMID:29570282

Arun Sridhar, John Vergara, Emre Kinaci, Giuseppe Palmese, Cameron F. Abrams “The effect of alkyl chain length on mechanical properties of fatty-acid-functionalized amidoamine-epoxy system.” Comput. Mater. Sci., vol. 150, pp. 70-76. doi:10.1016/j.commatsci.2018.03.073

S. Alexis Paz, Cameron F. Abrams “Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers.” Computation, vol. 6, pp. 27. doi:10.3390/computation6020027

Bibek Parajuli, Kriti Acharya, Harry C. Bach, Bijay Parajuli, Shiyu Zhang, Amos B. Smith III, Cameron F. Abrams, Irwin Chaiken “Restricted HIV-1 Env Glycan Engagement by Lectin-Reengineered DAVEI Protein Chimera is Sufficient for Lytic Inactivation of the Virus.” Biochem. J., vol. 475, pp. 931-957. doi:10.1042/BCJ20170662 · PMID:29343613

Francesca Moraca, David Rinaldo, Amos B. Smith, III, Cameron F. Abrams “Specific Non-Covalent Interactions Determine Optimal Structure of a Buried Ligand Moiety: QM/MM and Pure QM Modeling of Complexes of the Small-Molecule CD4 Mimetics and HIV-1 Gp120.” ChemMedChem, vol. 13, pp. 627-633. doi:10.1002/cmdc.201700728 · PMID:29337418

2017

Jasmine Gardner, Cameron F. Abrams “Rate of hemifusion diaphragm dissipation and ability to form three-junction bound HD determined by lipid composition.” J. Chem. Phys., vol. 147, pp. 134903. doi:10.1063/1.4994320 · PMID:28987088

Ryan Gordon, Spencer Stober, Cameron F. Abrams “Effects of Optical Purity and Finite System Size on Self-Assembly of 12-Hydroxystearic Acid in Hexane: Molecular Dynamics Simulations.” J. Phys. Chem. B, vol. 121, pp. 9223-9233. doi:10.1021/acs.jpcb.7b05246 · PMID:28876930

Alon Herschhorn, Christopher Gu, Francesca Moraca, Xiaochu Ma, Mark Farrell, Amos B. Smith, III, Marie Pancera, Peter D. Kwong, Arne Schön, Ernesto Freire, Cameron Abrams, Scott C. Blanchard, Walther Mothes, Joseph G. Sodroski “The β20-β21 of gp120 is a regulatory switch for HIV-1 Env.” Nature Comm., vol. 8, pp. 1049. doi:10.1038/s41467-017-01119-w · PMID:29051495

Kriti Acharya, Adel A. Rashad, Francesca Moraca, Per Johan Klasse, John P. Moore, Cameron F. Abrams, Irwin Chaiken “Recognition of HIV-Inactivating Peptide Triazoles by a Recombinant Soluble Trimer, BG505 SOSIP.664.” Proteins, vol. 85, pp. 843-851. doi:10.1002/prot.25238 · PMID:28056499

Arun Sridhar, John Vergara, Giuseppe Palmese, Cameron F. Abrams “The Effect of Alkyl Chain Length on Material Properties of Fatty-Acid-Functionalized Amidoamine-Epoxy Systems.” Eur. Polymer J., vol. 89, pp. 1-12. doi:10.1016/j.eurpolymj.2017.01.037

Jungho Yang, Arun Srikanth, Changwoon Jang, Cameron F. Abrams “Relationships Between Molecular Structure and Thermomechanical Properties of Bio-Based Thermosetting Polymers.” J. Polym. Sci. B Pol. Phys., vol. 55, pp. 285-292. doi:10.1002/polb.24270

S. Alexis Paz, Eric Vanden-Eijnden, Cameron F. Abrams “Polymorphism at 129 Dictates Metastable Conformations of the Human Prion Protein N-terminal β-sheet.” Chem. Sci., vol. 8, pp. 1225-1232. doi:10.1039/C6SC03275C · PMID:28451263

2016

Bibek Parajuli, Kriti Acharya, Reina Yu, Adel A. Rashad, Cameron F. Abrams, Irwin M. Chaiken “Lytic Inactivation of HIV-1 by Dual Engagement of gp120 and gp41 Domains in the Virus Env Trimer.” Biochemistry, vol. 55, pp. 6100-6114. doi:10.1021/acs.biochem.6b00570 · PMID:27731975

Francesca Moraca, Kriti Acharya, Bruno Melillo, Amos B. Smith, III, Irwin M. Chaiken, Cameron F. Abrams “Computational Evaluation of HIV-1 gp120 Conformations of Soluble Trimeric gp140 Structures as Targets for de novo Docking of First- and Second-Generation Small-Molecule CD4 Mimetics.” J. Chem. Info. Model., vol. 56, pp. 2069-2079. doi:10.1021/acs.jcim.6b00393 · PMID:27602436

Tang-Qing Yu, Jianfeng Lu, Cameron F. Abrams, Eric Vanden-Eijnden “A Multiscale Implementation of Infinite-Swap Replica Exchange Molecular Dynamics.” Proc. Natl. Acad. Sci. USA, vol. 113, pp. 11744-11749. doi:10.1073/pnas.1605089113 · PMID:27698148

Changwoon Jang, Cameron F. Abrams “Thermal and Mechanical Properties of Thermosetting Polymers using Coarse-grained Simulation.” Eur. Phys. J. Spec. Top., vol. 225, pp. 1775-1783. doi:10.1140/epjst/e2016-60143-0 · PMID:27627411

Ryan Gordon, Spencer S. Stober, Cameron F. Abrams “Aggregation of 12-Hydroxystearic Acid and Its Lithium Salt in Hexane: Molecular Dynamics Simulations.” J. Phys. Chem. B., vol. 120, pp. 7164-7173. doi:10.1021/acs.jpcb.6b04193 · PMID:27387154

Jasmine Gardner, Markus Deserno, Cameron F. Abrams “Effect of Intrinsic Curvature and Edge Tension on the Stability of Binary Mixed-Membrane Three-Junctions.” J. Chem. Phys., vol. 145, pp. 74901. doi:10.1063/1.4960433 · PMID:27544120

Anthony Bucci, Tang-Qing Yu, Eric Vanden-Eijnden, Cameron F. Abrams “Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics.” J. Chem. Theory Comput., vol. 12, pp. 2964-2972. doi:10.1021/acs.jctc.6b00071 · PMID:27168219

Changwoon Jang, Majid Sharifi, Giuseppe Palmese, Cameron F. Abrams “Toughness enhancement of thermosetting polymers using a novel partially reacted substructure curing protocol: A combined molecular simulation and experimental study.” Polymer, vol. 90, pp. 249-255. doi:10.1016/j.polymer.2016.03.023 · PMID:39790414

Ramalingam Venkat Kalyana Sundaram, Huiyuan Li, Lauren Bailey, Adel A. Rashad, Rachna Aneja, Karl Weiss, James Huynh, Arangaserry Rosemary Bastian, Elisabeth Papazoglou, Cameron Abrams, Steven Wrenn, Irwin Chaiken “Impact of HIV-1 Membrane Cholesterol on Cell-Independent Lytic Inactivation and Cellular Infectivity.” Biochemistry, vol. 55, pp. 447-458. doi:10.1021/acs.biochem.5b00936 · PMID:26713837

2015

Majid Sharifi, Changwoon Jang, Cameron F. Abrams, Giuseppe Palmese “Epoxy Polymer Networks with Improved Thermal and Mechanical Properties via Controlled Dispersion of Reactive Toughening Agents.” Macromolecules, vol. 48, pp. 7495-7502. doi:10.1021/acs.macromol.5b00677

S. Alexis Paz, Cameron F. Abrams “Free Energy and Hidden Barriers of the β-Sheet Structure of Prion Protein.” J. Chem. Theory Comput., vol. 11, pp. 5024-5034. doi:10.1021/acs.jctc.5b00576 · PMID:26574287

Tang-Qing Yu, Mauro Lapelosa, Eric Vanden-Eijnden, Cameron F. Abrams “Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.” J. Amer. Chem. Soc., vol. 137, pp. 3041-3050. doi:10.1021/ja512484q · PMID:25664858

Arangassery Rosemary Bastian, Aakansha Nangarlia, Lauren D. Bailey, Andrew Holmes, R. Venkat Kalyana Sundaram, Charles Ang, Diogo R. M. Moreira, Kevin Freedman, Caitlin Duffy, Mark Contarino, Cameron Abrams, Michael Root, Irwin Chaiken “Mechanism of Multivalent Nanoparticle Encounter with HIV-1 for Potency Enhancement of Peptide Triazole Virus Inactivation.” J. Biol. Chem., vol. 290, pp. 529-543. doi:10.1074/jbc.M114.608315 · PMID:25371202

Changwoon Jang, Timothy Sirk, Jan Andzelm, Cameron F. Abrams “Comparison of Crosslinking Algorithms in Molecular Dynamics Simulations of Thermosetting Polymers.” Macromol. Theory Sim., vol. 24, pp. 260-270. doi:10.1002/mats.201400094 · PMID:39785880

2014

Michelle K. Baker, Cameron F. Abrams “Dynamics of Lipids, Cholesterol, and Transmembrane α-Helices from Microsecond Molecular Dynamics Simulations.” J. Phys. Chem. B, vol. 118, pp. 13590-13600. doi:10.1021/jp507027t · PMID:25380392

Changwoon Jang, Majid Sharifi, Giuseppe R. Palmese, Cameron F. Abrams. “Molecular Dynamics Simulation Study of Reactive Encapsulation of Solvent in Epoxy Curing.” Proceedings of 2014 ASC 29/US-Japan 16/ASTM D30 Conference.

Majid Sharifi, Chang-Woon Jang, Cameron F. Abrams, Giuseppe Palmese “Toughened epoxy polymers via rearrangement of network topology.” J. Mater. Chem. A, vol. 2, pp. 16071-16082. doi:10.1039/C4TA03051F

Chang-Woon Jang, Majid Sharifi, Giuseppe Palmese, Cameron F. Abrams “Crosslink Network Rearrangement via Reactive Encapsulation of Solvent in Epoxy Curing: A Combined Molecular Simulation and Experimental Study.” Polymer, vol. 55, pp. 3859-3868. doi:10.1016/j.polymer.2014.06.022

Ali Emileh, Caitlin Duffy, Andrew Holmes, Arangassery Rosemary Bastian, Rachna Aneja, Ferit Tuzer, Srivats Rajagopal, Huiyan Li, Cameron F. Abrams, Irwin Chaiken “Covalent conjugation of a peptide triazole to HIV-1 gp120 enables intramolecular binding site occupancy.” Biochemistry, vol. 53, pp. 3402-3414. doi:10.1021/bi500136f · PMID:24801282

Anthony Bucci, Cameron F. Abrams “Oxygen pathways and allostery in monomeric sarcosine oxidase via single-sweep free-energy reconstruction.” J. Chem. Theory Comput., vol. 10, pp. 2668-2676. doi:10.1021/ct500088z · PMID:25061440

Michelle K. Baker, Vamshi Gangupomu, Cameron F. Abrams “Characterization of the water defect at the HIV-1 gp41 membrane spanning domain in bilayers with and without cholesterol using molecular simulations.” BBA-Biomembranes, vol. 1838, pp. 1396-1405. doi:10.1016/j.bbamem.2014.01.009 · PMID:24440660

Cameron F. Abrams, Giovanni Bussi “Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration.” Entropy, vol. 16, pp. 163-199. doi:10.3390/e16010163

2013

Mark Contarino, Arangassery R. Bastian, Ramalingam Venkat Kalyana Sundaram, Karyn McFadden, Caitlin Duffy, Vamshi Gangupomu, Michelle Baker, Cameron Abrams, Irwin Chaiken “Chimeric Cyanovirin-MPER Recombinantly Engineered Proteins Cause Cell-Free Virolysis of HIV-1.” Antimicrob. Agents Ch., vol. 57, pp. 4743-4750. doi:10.1128/AAC.00309-13 · PMID:23856780

Mauro Lapelosa, Cameron F. Abrams “Transition-path theory calculations on non- uniform meshes in two and three dimensions using finite elements.” Comp. Phys. Comm., vol. 184, pp. 2310-2315. doi:10.1016/j.cpc.2013.05.017 · PMID:24014889

Harish Vashisth, Cameron F. Abrams “All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element.” Proteins, vol. 81, pp. 1017-1030. doi:10.1002/prot.24255 · PMID:23348915

Ali Emileh, Ferit Tuzer, Herman Yeh, Muddegowda Umashankara, Diogo Moreira, Judith LaLonde, Carole Bewley, Cameron F. Abrams, Irwin Chaiken “A Model of the Peptide Triazole Entry Inhibitor Binding to HIV-1 gp120 and Mechanism of Bridging Sheet Disruption.” Biochemistry, vol. 52, pp. 2245-2261. doi:10.1021/bi400166b · PMID:23470147

Mauro Lapelosa, Cameron F. Abrams “A computational study of water and CO migration sites and channels inside myoglobin.” J. Chem. Theory Comput., vol. 9, pp. 1265-1271. doi:10.1021/ct300862j · PMID:23505344

2012

Cameron F. Abrams, Eric Vanden-Eijnden “On-the-fly free energy parameterization via temperature-accelerated molecular dynamics.” Chem. Phys. Lett., vol. 547, pp. 114-119. doi:10.1016/j.cplett.2012.07.064 · PMID:23226688

Spencer Stober, Cameron F. Abrams “Energetics and mechanism of the normal-to-amyloidogenic isomerization of b2-microglobulin: On-the-fly string method calculations.” J. Phys. Chem. B, vol. 116, pp. 9371-9375. doi:10.1021/jp304805v · PMID:22793795

Harish Vashisth, Luca Maragliano, Cameron F. Abrams “DFG-flip in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop.” Biophys. J., vol. 102, pp. 1979-1987. doi:10.1016/j.bpj.2012.03.031 · PMID:22768955

Miao Zhang, Cameron F. Abrams, Liping Wang, Anthony Gizzi, Liping He, Ruihe Lin, Yuan Chen, Patrick J. Loll, John M. Pascal, Ji-Fang Zhang “Structural Basis for Calmodulin as a Dynamic Calcium Sensor.” Structure, vol. 20, pp. 1-13. doi:10.1016/j.str.2012.03.019 · PMID:22579256

Spencer Stober, Cameron F. Abrams “Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors.” Protein Sci., vol. 21, pp. 307-317. doi:10.1002/pro.2016 · PMID:22170867

2011

Ali Emileh, Cameron F. Abrams “A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered HIV-1 gp120.” Proteins, vol. 79, pp. 537-546. doi:10.1002/prot.22901 · PMID:21117239

2010

Vamshi Gangupomu, Cameron F. Abrams “All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics.” Biophys. J., vol. 99, pp. 3438-3444. doi:10.1016/j.bpj.2010.09.054 · PMID:21081093

Harish Vashisth, Cameron F. Abrams “All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor.” J. Mol. Biol., vol. 400, pp. 645-658. doi:10.1016/j.jmb.2010.05.025 · PMID:20488191

Debashish Mukherji, Cameron F. Abrams “Slip-stick fracture and toughness enhancement in thermoset/thermoplastic polymer alloys under shear.” Europhys. Lett., vol. 90, pp. 26003. doi:10.1209/0295-5075/90/26003

Nikos Ch. Karayiannis, Katerina Foteinopoulou, Cameron F. Abrams, Manuel Laso “Modeling of crystal nucleation and growth in athermal polymers: Self-assembly of layered nano-morphologies.” Soft Matter, vol. 6, pp. 2160-2173. doi:10.1039/B923369E

Cameron F. Abrams, Eric Vanden-Eijnden “Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.” Proc. Natl. Acad. Sci. USA, vol. 107, pp. 4961-4966. doi:10.1073/pnas.0914540107 · PMID:20194785

Heather L. Nyce, Spencer Stober, Cameron F. Abrams, Michael M. White “Mapping spatial relationships between residues in the ligand-binding domain of the 5-HT3 receptor using a molecular ruler.” Biophys. J., vol. 98, pp. 1847-1855. doi:10.1016/j.bpj.2010.01.034 · PMID:20441748

Harish Vashisth, Cameron F. Abrams “Docking of insulin to a structurally equilibrated insulin receptor ectodomain.” Proteins, vol. 78, pp. 1531-1543. doi:10.1002/prot.22670 · PMID:20112420

2009

Debashish Mukherji, Cameron F. Abrams “Mechanical behavior of highly cross-linked polymer networks and its direct links to microscopic structure.” Phys. Rev. E, vol. 79, pp. 61802. doi:10.1103/PhysRevE.79.061802 · PMID:19658517

Debashish Mukherji, Cameron F. Abrams “Anomalous ductility in thermoset/thermoplastic polymer alloys.” Phys. Chem. Chem. Phys., vol. 11, pp. 2113-2115. doi:10.1039/B818039C · PMID:19280022

Debashish Mukherji, Cameron F. Abrams “Anomalous ductility in thermoset/thermoplastic polymer alloys: An explanation based on overlap concentration and cavity growth.” Europhys. Lett., vol. 88, pp. 56001. doi:10.1209/0295-5075/88/56001

2008

Debashish Mukherji, Cameron F. Abrams “Microvoid formation and strain hardening in highly cross-linked polymer networks.” Phys. Rev. E, vol. 78, pp. 50801. doi:10.1103/PhysRevE.78.050801 · PMID:19113085

Harish Vashisth, Cameron F. Abrams “Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex.” Biophys. J., vol. 95, pp. 4193-4204. doi:10.1529/biophysj.108.139675 · PMID:18676643

2007

Yelena Sliozberg, Cameron F. Abrams “Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations.” Biophys. J., vol. 93, pp. 1906-1916. doi:10.1529/biophysj.107.108043 · PMID:17513353

Ehsan Jabbarzadeh, Cameron F. Abrams “Strategies to enhance capillary formation inside biomaterials: A computational study.” Tissue Eng., vol. 13, pp. 2073-2086. doi:10.1089/ten.2006.0057 · PMID:17590150

David Richardson, Cameron F. Abrams “The effects of nanotube fillers on craze formation in simulated glassy polymers under tensile load.” Mol. Sim., vol. 33, pp. 421-427. doi:10.1080/08927020601154637

Ehsan Jabbarzadeh, Cameron F. Abrams “Simulations of chemotaxis and random motility in 2D random porous domains.” Bull. Math. Biol., vol. 69, pp. 747-764. doi:10.1007/s11538-006-9153-1 · PMID:17216402

2006

Cameron F. Abrams, Nam-Kyung Lee, Albert Johner “Diffusion/reaction in confined polymer chains.” Macromolecules, vol. 39, pp. 3655-3663. doi:10.1021/ma060044d · PMID:39744149

David Richardson, Cameron F. Abrams “Polymer chain winding in the melt.” Macromolecules, vol. 39, pp. 2330-2339. doi:10.1021/ma051985d · PMID:39744149

Cameron F. Abrams “Molecule-Based Coarse-Graining for Polymer Simulation.” Handbook of Theoretical and Computational Nanotechnology, vol. 4, pp. 463-517.

2005

Nam-Kyung Lee, Cameron F. Abrams, Albert Johner “Optimal confinement for internal polymer binding.” Europhys. Lett., vol. 72, pp. 922-928. doi:10.1209/epl/i2005-10328-3 · PMID:38755852

Cameron F. Abrams “Concurrent dual-resolution Monte Carlo simulation of liquid methane.” J. Chem. Phys., vol. 123, pp. 234101. doi:10.1063/1.2136884 · PMID:16392908

Yelena Sliozberg, Cameron F. Abrams “The effects of confinement on the thermodynamics of a collapsing heteropolymer: An off-lattice Wang-Landau Monte Carlo simulation study.” Macromolecules, vol. 38, pp. 5321-5329. doi:10.1021/ma050443t

Ehsan Jabbarzadeh, Cameron F. Abrams “Fundamental limits on the efficacy of intercellular communication by diffusion.” J. Phys. Soc. Japan, vol. 74, pp. 1139-1141.

Ehsan Jabbarzadeh, Cameron F. Abrams “Chemotaxis and random motility in unsteady chemoattractant fields: A computational study.” J. Theor. Biol., vol. 235, pp. 221-232. doi:10.1016/j.jtbi.2005.01.005 · PMID:15862591

Yelena Sliozberg, Cameron F. Abrams “Structural correlations in comb heteropolymers in good and backbone-selective solvents.” J. Polym. Sci. B. Polym. Phys., vol. 43, pp. 983-993. doi:10.1002/polb.20388

Ehsan Jabbarzadeh, Cameron F. Abrams “Simulations of Chemotaxis and Random Motility in Finite Domains.” Nanoscale Materials Science in Biology and Medicine, vol. 845, pp. 37-48. doi:10.1557/PROC-845-AA1.9

2004

Nam-Kyung Lee, Cameron F. Abrams “Kinetics of a polysoap collapse.” J. Chem. Phys., vol. 121, pp. 7484-7493. doi:10.1063/1.1793151 · PMID:15473823

Yelena Sliozberg, Cameron F. Abrams “Polysoaps in backbone-selective solvents: Effects of side-chain length on collapse dynamics.” Soft Materials, vol. 2, pp. 11-25. doi:10.1081/SMTS-120030472

Nam-Kyung Lee, Cameron F. Abrams, Albert Johner, Sergei Obukhov “Swelling dynamics of collapsed polymers.” Macromolecules, vol. 37, pp. 651-661. doi:10.1021/ma034808q · PMID:39744149

Cameron F. Abrams “Inhomogeneous Coarse-Graining of Polymers and Polymer/Metal Interfaces.” Computational Soft Matter: From Synthetic Polymers to Proteins, vol. 23, pp. 275-288.

Cameron F. Abrams “Dual Resolution Molecular Simulation of Bisphenol-A Polycarbonate Adsorption onto Nickel (111): Chain Length Effects.” Multiscale Modeling and Simulation, vol. 39, pp. 131-142.

2003

Nam-Kyung Lee, Cameron F. Abrams, Albert Johner, Sergei Obukhov “Arrested swelling of highly entangled polymer globules.” Phys. Rev. Lett., vol. 90, pp. 225504. doi:10.1103/PhysRevLett.90.225504 · PMID:12857321

Luigi Delle Site, Ali Alavi, Cameron F. Abrams “Adsorption energies and geometries of phenol on the (111) surface of nickel: An ab initio study.” Phys. Rev. B, vol. 67, pp. 193406. doi:10.1103/PhysRevB.67.193406

Cameron F. Abrams, Luigi Delle Site, Kurt Kremer “Dual-resolution coarse-grained/atomistic simulation of the bisphenol-A-polycarbonate/nickel interface.” Phys. Rev. E, vol. 67, pp. 21807. doi:10.1103/PhysRevE.67.021807 · PMID:12636708

Cameron F. Abrams, Kurt Kremer “Combined coarse-grained and atomistic simulation of liquid bisphenol-A-polycarbonate: Liquid packing and intramolecular structure.” Macromolecules, vol. 36, pp. 260-267. doi:10.1021/ma0213495 · PMID:39744149

2002

Luigi Delle Site, Cameron F. Abrams, Ali Alavi, Kurt Kremer “Polymers near metal surfaces: Selective adsorption and global conformations.” Phys. Rev. Lett., vol. 89, pp. 156103. doi:10.1103/PhysRevLett.89.156103 · PMID:12366003

Cameron F. Abrams, Namkyung Lee, Sergei Obukhov “Collapse dynamics of a homopolymer: Theory and simulation.” Europhys. Lett., vol. 59, pp. 391-397. doi:10.1209/epl/i2002-00207-5

Cameron F. Abrams, Kurt Kremer “Effects of excluded volume and bond length on the dynamics of dense bead-spring polymer melts.” J. Chem. Phys., vol. 116, pp. 3162-3165. doi:10.1063/1.1445107

Cameron F. Abrams, Luigi "Delle Site", Kurt Kremer “Multiscale Computer Simulations for Polymeric Materials in Bulk and near Surfaces.” Bridging Time Scales: Molecular Simulations for the Next Decade, vol. 605, pp. 143.

2001

Cameron F. Abrams, Kurt Kremer “The effect of bond length on the structure of dense bead-spring polymer melts.” J. Chem. Phys., vol. 115, pp. 2776-2785. doi:10.1063/1.1385791 · PMID:39425435

Cameron F. Abrams, David B. Graves “Atomistic simulation of fluorocarbon deposition on Si by continuous bombardment with energetic CF+ and CF2+.” J. Vac. Sci. Technol. A, vol. 19, pp. 175-181. doi:10.1116/1.1322652

2000

Cameron F. Abrams, David B. Graves. “Atomistic simulation of Si etching by energetic CF3+: Product distributions and energies.” Thin Solid Films, vol. 374, pp. 150-156.

Cameron F. Abrams, David B. Graves. “Molecular dynamics simulations of Si etching with energetic F+: Sensitivity of results to the interatomic potential.” J. Appl. Phys., vol. 88, pp. 3734-3738. doi:10.1063/1.1288701 · PMID:39425435

Junichi Tanaka, Cameron F. Abrams, David B. Graves. “New C-F interatomic potential for molecular dynamic simulation of fluorocarbon film formation.” J. Vac. Sci. Technol. A, vol. 18, pp. 938-945. doi:10.1116/1.582279

Cameron F. Abrams, David B. Graves “On the active surface layer in CF3+ etching of Si: Atomistic simulation and a simple mass balance model.” J. Vac. Sci. Technol. A, vol. 18, pp. 411-416. doi:10.1116/1.582202

1999

Cameron F. Abrams, David B. Graves “Molecular dynamics simulations of Si etching by energetic CF3+ ions.” J. Appl. Phys., vol. 86, pp. 5938-5948. doi:10.1063/1.371637

Cameron F. Abrams, David B. Graves “Three-dimensional spatiokinetic distributions of sputtered and scattered products of Ar+ and Cu+ impacts onto the Cu surface: Molecular dynamics simulations.” IEEE Trans. Plas. Sci., vol. 27, pp. 1426-1432. doi:10.1109/27.799821

Michael A. Vyvoda, Cameron F. Abrams, David B. Graves “Feature evolution simulation of copper seed layer deposition: Using atomic level particle scattering information.” IEEE Trans. Plas. Sci., vol. 27, pp. 1433-1440. doi:10.1109/27.799822

Cameron F. Abrams, David B. Graves “Cu sputtering and deposition by off-normal, near-threshold Cu+ bombardment: Molecular dynamics simulations.” J. Appl. Phys., vol. 86, pp. 2263-2267. doi:10.1063/1.371040

1998

Cameron F. Abrams, David B. Graves “Energetic ion bombardment of SiO2 surfaces: Molecular dynamics simulations.” J. Vac. Sci. Technol. A, vol. 16, pp. 3006-3019. doi:10.1116/1.581452

1997

W. S. Ahn, Yaping Zhong, Cameron F. Abrams, P. K. Lim, P. A. Brown “Biphasic autoxidation of tetralin catalyzed by surface-active transition metal complexes.” J. Phys. Chem. B, vol. 101, pp. 596-602. doi:10.1021/jp9627234

1995

Yaping Zhong, Cameron F. Abrams, P. K. Lim. “Biphasic synthesis of poly(2,6-dimethyl-1,4-phenylene oxide) using a surface-active coupling catalyst. 2. Process improvements, additional kinetic results, and proposed reaction mechanism.” Ind. Eng. Chem. Res., vol. 34, pp. 1529-1535. doi:10.1021/ie00044a003 · PMID:39744149