Publications

@article{nokey,

title = {Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission},

author = {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 Abrams; Marceline Côté; Andrés Finzi},

year  = {2024},

date = {2024-05-28},

urldate = {2024-05-28},

journal = {mBio},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Ang2023,

title = {Pharmacophore Variants of the Macrocyclic Peptide Triazole Inactivator of HIV-1 Env},

author = {Monisha Gupta and Gabriela Canziani and Charles G. Ang and Mohammadjavad Mohammadi and Cameron F. Abrams and Derek Yang and Amos B. Smith, III and Irwin Chaiken},

url = {https://doi.org/10.1007/s00044-023-03092-0},

doi = {10.1007/s00044-023-03092-0},

year  = {2023},

date = {2023-06-27},

urldate = {2023-05-23},

journal = {Medicinal Chemistry Research},

volume = {32},

pages = {1497-1509},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ding2023,

title = {Piperidine CD4-mimetic compounds expose vulnerable Env epitopes sensitizing HIV-1-infected cells to ADCC},

author = {Shilei Ding and William D. Tolbert and Huile Zhu and Daniel Lee and Tyler Higgins and Xuchen Zhao and Dung Nguyen and Rebekah Sherburn and Jonathan Richard and Gabrielle-Gendron Lepage and Halima Medjahed and Mohammadjavad Mohammadi and Cameron Abrams and Marzena Pazgier and Amos B. Smith III and Andrés Finzi},

url = {https://www.mdpi.com/1999-4915/15/5/1185},

doi = {10.3390/v15051185},

year  = {2023},

date = {2023-05-17},

urldate = {2023-05-17},

journal = {Viruses},

volume = {15},

number = {5},

pages = {1185},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Alberini2023,

title = {Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels},

author = {Giulio Alberini and Sergio Alexis Paz and Beatrice Corradi and Cameron Abrams and Fabio Benfenati and Luca Maragliano},

url = {https://doi.org/10.1021/acs.jctc.2c00990},

doi = {10.1021/acs.jctc.2c00990},

year  = {2023},

date = {2023-04-28},

urldate = {2023-01-01},

journal = {Journal of Chemical Theory and Computation},

volume = {19},

issue = {10},

pages = {2953–2972},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fritschi2023,

title = {Indoline CD4-mimetic Compounds Mediate Potent and Broad HIV-1 Inhibition and Sensitization to Antibody-dependent Cellular Cytotoxicity},

author = {Christopher Fritcshi and Saumya Anang and Zhen Gong and Mohammadjavad Mohammadi and Jonathan Richard and Catherine Bourassa and Kenny T. Severino and Hannah Richter and Derek Yang and Hung-Ching Chen and Ta-Jung Chiu and Michael S. Seaman and Navid Madani and Cameron F. Abrams and Andrès Finzi and Wayne A. Hendrickson and Joseph Sodroski and Amos B. Smith III},

url = {https://doi.org/10.1073/pnas.2222073120},

doi = {10.1073/pnas.2222073120},

year  = {2023},

date = {2023-03-24},

urldate = {2023-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {120},

pages = {e2222073120},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huang2023,

title = {HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers},

author = {Ming Huang and Cameron F. Abrams},

url = {https://doi.org/10.1016/j.softx.2022.101303},

doi = {10.1016/j.softx.2022.101303},

year  = {2023},

date = {2023-01-09},

urldate = {2023-01-01},

journal = {SoftwareX},

volume = {21},

pages = {101303},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GuptaVergara2022,

title = {Entropic overcompensation of the N501Y mutation on SARS-CoV-2 S binding to ACE2},

author = {Natasha Gupta Vergara and Megan Gatchel and Cameron F. Abrams},

url = {https://doi.org/10.1021/acs.jcim.2c01246},

doi = {10.1021/acs.jcim.2c01246},

year  = {2022},

date = {2022-12-30},

urldate = {2022-01-01},

journal = {Journal of Chemical Information and Modeling},

volume = {63},

pages = {633-642},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chaplain2022,

title = {Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines},

author = {Cheyenne Chaplain and Christopher J. Fritschi and Saumya Anang and Zhen Gong and Jonathan Richard and Catherine Bourassa and Shuaiyi Liang and Mohammadjavad Mohammadi and Jun Park and Andrés Finzi and Navid Madani and Joseph G. Sodroski and Cameron F. Abrams and Wayne A. Hendrickson and Amos B. Smith III},

url = {https://doi.org/10.1021/acsmedchemlett.2c00376},

doi = {10.1021/acsmedchemlett.2c00376},

year  = {2022},

date = {2022-12-06},

urldate = {2023-01-01},

journal = {ACS Medicinal Chemistry Letters},

volume = {14},

pages = {51-58},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ding2022,

title = {VE607 Stabilizes SARS-CoV-2 Spike In the RBD-up Conformation and Inhibits Viral Entry},

author = {Shilei Ding and Irfan Ullah and Shang Yu Gong and Jonathan Grover and Mohammadjavad Mohammadi and Yaozong Chen and Dani Vézina and Guillaume Beaudoin-Bussi`eres and Vijay Tailor Verma and Guillaume Goyette and Fleur Gaudette and Jonathan Richard and Derek Yang and A. Smith III and Marzena Pazgier and Marceline C^oté and Cameron Abrams and Priti Kumar and Walther Mothes and Pradeep Uchil and Andrés Finzi and Christian Baron},

url = {https://doi.org/10.1016/j.isci.2022.104528},

doi = {10.1016/j.isci.2022.104528},

issn = {2589-0042},

year  = {2022},

date = {2022-06-01},

journal = {iScience},

volume = {25},

pages = {104528},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huang2022,

title = {The Effect of Network Topology on Material Properties in Vinyl-ester/Styrene Thermoset Polymers using Molecular Dynamics Simulations and Time-Temperature Superposition},

author = {Ming Huang and Nicolas Alvarez and Giuseppe Palmese and Cameron F. Abrams},

url = {https://doi.org/10.1016/j.commatsci.2022.111264},

doi = {10.1016/j.commatsci.2022.111264},

year  = {2022},

date = {2022-01-01},

journal = {Computational Materials Science},

volume = {27},

pages = {111264},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zarrini2022,

title = {Modeling Sizing Emulsion Droplet Deposition onto Silica Using All-Atom Molecular Dynamics Simulations},

author = {Salman Zarrini and Cameron F. Abrams},

url = {https://doi.org/10.1016/j.compositesb.2022.109712},

doi = {10.1016/j.compositesb.2022.109712},

year  = {2022},

date = {2022-01-01},

journal = {Composites Part B: Engineering},

volume = {235},

pages = {109712},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ribone2021,

title = {Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking},

author = {Sergio Ribone and Sergio Alexis Paz and Cameron Abrams and Marcos Villarreal},

url = {https://doi.org/10.1007/s10822-021-00432-3},

doi = {10.1007/s10822-021-00432-3},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Journal of Computer Aided Molecular Design},

volume = {26},

pages = {1-13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fritschi2021,

title = {Identification and Validation of gp120 Residue His105 as a Novel Target for HIV-1 

Neutralization by Small-Molecule CD4-Mimics},

author = {Christopher Fritschi and Shuaiyi Liang and Mohammadjavad Mohammadi and Saumya Anang and Francesca Moraca and Junhua Chen and Navid Madani and Joseph Sodroski and Cameron Abrams and Wayne Hendrickson and Amos B. Smith III},

url = {https://doi.org/10.1021/acsmedchemlett.1c00437},

doi = {10.1021/acsmedchemlett.1c00437},

year  = {2021},

date = {2021-01-01},

journal = {ACS Medicinal Chemistry Letters},

volume = {12},

pages = {1824-1831},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Khare2021,

title = {Atomistic Simulation of Volumetric Properties of Epoxy Networks: Effect of Monomer Length},

author = {Ketan Khare and Cameron F. Abrams},

url = {https://doi.org/10.1039/D1SM01128F},

doi = {10.1039/D1SM01128F},

year  = {2021},

date = {2021-01-01},

journal = {Soft Matter},

volume = {17},

pages = {9957-9986},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Prevost2021,

title = {Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2},

author = {Jérémie Prévost and Jonathan Richard and Romain Gasser and Shilei Ding and Clément Fage and Sai Priya Anand and Damien Adam and Natasha Gupta Vergara and Alexandra Tauzin and Mehdi Benlarbi and Shang Yu Gong and Guillaume Goyette and Anik Privé and Sandrine Moreira and Hugues Charest and Michel Roger and Walther Mothes and Marzena Pazgier and Emmanuelle Brochiero and Guy Boivin and Cameron F Abrams and Arne Schön and Andrés Finzi},

url = {https://doi.org/10.1016/j.jbc.2021.101151},

doi = {10.1016/j.jbc.2021.101151},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Biological Chemistry},

volume = {297},

number = {4},

pages = {11051},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zarrini2021a,

title = {The Roles of Coupling Agent and Surfactant in Droplet Structure in Sizing Emulsions: A Molecular Dynamics Simulations Study},

author = {Salman Zarrini and Cameron F. Abrams},

url = {https://doi.org/10.1021/acs.langmuir.1c01592},

doi = {10.1021/acs.langmuir.1c01592},

year  = {2021},

date = {2021-01-01},

journal = {Langmuir},

volume = {37},

number = {33},

pages = {10183-10190},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ang2021,

title = {Peptide Triazole Thiol Irreversibly Inactivates Metastable HIV-1 Env by Accessing Conformational Triggers Intrinsic to Virus–Cell Entry},

author = {Charles Gotuaco Ang and Erik Carter and Ann Haftl and Shiyu Zhang and Adel A. Rashad and Michele Kutzler and Cameron F. Abrams and Irwin M. Chaiken},

url = {https://www.mdpi.com/2076-2607/9/6/1286},

doi = {10.3390/microorganisms9061286},

issn = {2076-2607},

year  = {2021},

date = {2021-01-01},

journal = {Microorganisms},

volume = {9},

number = {6},

abstract = {KR13, a peptide triazole thiol previously established to inhibit HIV-1 infection and cause virus lysis, was evaluated by flow cytometry against JRFL Env-presenting cells to characterize induced Env and membrane transformations leading to irreversible inactivation. Transiently transfected HEK293T cells were preloaded with calcein dye, treated with KR13 or its thiol-blocked analogue KR13b, fixed, and stained for gp120 (35O22), MPER (10E8), 6-helix-bundle (NC-1), immunodominant loop (50-69), and fusion peptide (VRC34.01). KR13 induced dose-dependent transformations of Env and membrane characterized by transient poration, MPER exposure, and 6-helix-bundle formation (analogous to native fusion events), but also reduced immunodominant loop and fusion peptide exposure. Using a fusion peptide mutant (V504E), we found that KR13 transformation does not require functional fusion peptide for poration. In contrast, simultaneous treatment with fusion inhibitor T20 alongside KR13 prevented membrane poration and MPER exposure, showing that these events require 6-helix-bundle formation. Based on these results, we formulated a model for PTT-induced Env transformation portraying how, in the absence of CD4/co-receptor signaling, PTT may provide alternate means of perturbing the metastable Env-membrane complex, and inducing fusion-like transformation. In turn, the results show that such transformations are intrinsic to Env and can be diverted for irreversible inactivation of the protein complex.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shrivastav2021,

title = {Optimizing String Method’s Reproducibility Using Generalized Solute Tempering Replica Exchange},

author = {Gourav Shrivastav and Cameron F. Abrams},

url = {https://doi.org/10.1021/acs.jpcb.1c02143},

doi = {10.1021/acs.jpcb.1c02143},

year  = {2021},

date = {2021-01-01},

journal = {The Journal of Physical Chemistry B},

volume = {125},

number = {24},

pages = {6609-6616},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gaffney2021,

title = {HIV-1 Env-Dependent Cell Killing by Bifunctional Small-Molecule/Peptide Conjugates},

author = {Althea Gaffney and Aakansha Nangarlia and Charles G. Ang and Steven Gossert and Adel Ahmed Rashad Ahmed and Md Alamgir Hossain and Cameron F. Abrams and Amos B. Smith III and Irwin Chaiken},

url = {https://doi.org/10.1021/acschembio.0c00888},

doi = {10.1021/acschembio.0c00888},

year  = {2021},

date = {2021-01-01},

journal = {ACS Chemical Biology},

volume = {16},

number = {1},

pages = {193-204},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Parajuli2020,

title = {Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate},

author = {Bibek Parajuli and Kriti Acharya and Aakansha Nangarlia and Shiyu Zhang and Bijay Parajuli and Alexej Dick and Brendon Ngo and Cameron F. Abrams and Irwin Chaiken},

url = {https://portlandpress.com/biochemj/article/477/21/4263/226680/Identification-of-a-glycan-cluster-in-gp120},

doi = {10.1042/BCJ20200495},

issn = {0264-6021},

year  = {2020},

date = {2020-11-01},

journal = {Biochemical Journal},

volume = {477},

number = {21},

pages = {4263--4280},

abstract = {We previously discovered a class of recombinant lectin conjugates, denoted lectin DLIs (‘dual-acting lytic inhibitors') that bind to the HIV-1 envelope (Env) protein trimer and cause both lytic inactivation of HIV-1 virions and cytotoxicity of Env-expressing cells. To facilitate mechanistic investigation of DLI function, we derived the simplified prototype microvirin (MVN)-DLI, containing an MVN domain that binds high-mannose glycans in Env, connected to a DKWASLWNW sequence (denoted ‘Trp3') derived from the membrane-associated region of gp41. The relatively much stronger affinity of the lectin component than Trp3 argues that the lectin functions to capture Env to enable Trp3 engagement and consequent Env membrane disruption and virolysis. The relatively simplified engagement pattern of MVN with Env opened up the opportunity, pursued here, to use recombinant glycan knockout gp120 variants to identify the precise Env binding site for MVN that drives DLI engagement and lysis. Using mutagenesis combined with a series of biophysical and virological experiments, we identified a restricted set of residues, N262, N332 and N448, all localized in a cluster on the outer domain of gp120, as the essential epitope for MVN binding. By generating these mutations in the corresponding HIV-1 virus, we established that the engagement of this glycan cluster with the lectin domain of MVN*-DLI is the trigger for DLI-derived virus and cell inactivation. Beyond defining the initial encounter step for lytic inactivation, this study provides a guide to further elucidate DLI mechanism, including the stoichiometry of Env trimer required for function, and downstream DLI optimization.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Prevost_2020,

title = {The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site},

author = {Jérémie Prévost and William D. Tolbert and Halima Medjahed and Rebekah T. Sherburn and Navid Madani and Daria Zoubchenok and Gabrielle Gendron-Lepage and Althea E. Gaffney and Melissa C. Grenier and Sharon Kirk and Natasha Vergara and Changze Han and Brendan T. Mann and Agnès L. Chénine and Adel Ahmed and Irwin Chaiken and Frank Kirchhoff and Beatrice H. Hahn and Hillel Haim and Cameron F. Abrams and Amos B. Smith III and Joseph Sodroski and Marzena Pazgier and Andrés Finzi},

editor = {Tongqing Zhou and Thomas E. Smithgall},

url = {https://doi.org/10.1128%2Fmbio.00280-20},

doi = {10.1128/mbio.00280-20},

year  = {2020},

date = {2020-05-01},

urldate = {2020-05-01},

journal = {mBio},

volume = {11},

number = {3},

pages = {e00280-20},

publisher = {American Society for Microbiology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zou_2020,

title = {Long-Acting BMS-378806 Analogues Stabilize the State-1 Conformation of the Human Immunodeficiency Virus Type 1 Envelope Glycoproteins},

author = {Shitao Zou and Shijian Zhang and Althea Gaffney and Haitao Ding and Maolin Lu and Jonathan R. Grover and Mark Farrell and Hanh T. Nguyen and Connie Zhao and Saumya Anang and Meiqing Zhao and Mohammadjavad Mohammadi and Scott C. Blanchard and Cameron Abrams and Navid Madani and Walther Mothes and John C. Kappes and Amos B. Smith III and Joseph Sodroski},

editor = {Viviana Simon},

url = {https://doi.org/10.1128%2Fjvi.00148-20},

doi = {10.1128/jvi.00148-20},

year  = {2020},

date = {2020-03-01},

urldate = {2020-03-01},

journal = {Journal of Virology},

volume = {94},

number = {10},

pages = {e00148--20},

publisher = {American Society for Microbiology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Anand2020,

title = {Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins},

author = {Sai Priya Anand and Yaozong Chen and Jérémie Prévost and Romain Gasser and Guillaume Beaudoin-Bussiéres and Cameron F. Abrams and Marzena Pazgier and Andrés Finzi},

url = {https://doi.org/10.3390/v12101104},

doi = {10.3390/v12101104},

year  = {2020},

date = {2020-01-01},

journal = {Viruses},

volume = {12},

number = {10},

pages = {1104},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gossert_2020,

title = {Roles of Variable Linker Length in Dual Acting Virucidal Entry Inhibitors on HIV-1 Potency via On-the-fly Free Energy Molecular Simulations},

author = {Steven Gossert and Bibek Parajuli and Irwin Chaiken and Cameron F. Abrams},

url = {https://doi.org/10.1002/pro.3949},

doi = {10.1002/pro.3949},

year  = {2020},

date = {2020-01-01},

journal = {Protein Science},

volume = {29},

pages = {2304-2310},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ang_2020,

title = {Metastable HIV-1 Surface Protein Env Sensitizes Cell Membranes to Transformation and Poration by Dual-Acting Virucidal Entry Inhibitors},

author = {Charles G. Ang and Md. Alamgir Hossain and Marg Rajpara and Harry Bach and Kriti Acharya and Alexej Dick and Adel A. Rashad and Michele Kutzler and Cameron F. Abrams and Irwin Chaiken},

url = {https://doi.org/10.1021%2Facs.biochem.9b01008},

doi = {10.1021/acs.biochem.9b01008},

year  = {2020},

date = {2020-01-01},

journal = {Biochemistry},

volume = {59},

number = {6},

pages = {818--828},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Grenier_2019,

title = {Optimization of Small Molecules That Sensitize HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity},

author = {Melissa C. Grenier and Shilei Ding and Dani Vézina and Jean-Philippe Chapleau and William D. Tolbert and Rebekah Sherburn and Arne Schön and Sambasivarao Somisetti and Cameron F. Abrams and Marzena Pazgier and Andrés Finzi and Amos B. Smith III},

url = {https://doi.org/10.1021%2Facsmedchemlett.9b00445},

doi = {10.1021/acsmedchemlett.9b00445},

year  = {2019},

date = {2019-11-01},

urldate = {2019-11-01},

journal = {ACS Medicinal Chemistry Letters},

volume = {11},

number = {3},

pages = {371--378},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bhaduri_2019,

title = {Free energy calculation using space filled design and weighted reconstruction: A modified single sweep approach},

author = {Anindya Bhaduri and Jasmine Gardner and Cameron F. Abrams and Lori Graham-Brady},

url = {https://doi.org/10.1080%2F08927022.2019.1688325},

doi = {10.1080/08927022.2019.1688325},

year  = {2019},

date = {2019-11-01},

journal = {Molecular Simulation},

volume = {46},

number = {3},

pages = {193--206},

publisher = {Informa UK Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikanth_2019,

title = {Effect of molecular packing and hydrogen bonding on the properties of epoxy-amido amine systems},

author = {Arun Srikanth Sridhar and Cameron F. Abrams},

url = {https://doi.org/10.1016%2Fj.commatsci.2019.109082},

doi = {10.1016/j.commatsci.2019.109082},

year  = {2019},

date = {2019-11-01},

journal = {Computational Materials Science},

volume = {169},

pages = {109082},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gardner_2019,

title = {Energetics of Flap Opening in HIV-1 Protease: String Method Calculations},

author = {Jasmine M. Gardner and Cameron F. Abrams},

url = {https://doi.org/10.1021%2Facs.jpcb.9b08348},

doi = {10.1021/acs.jpcb.9b08348},

year  = {2019},

date = {2019-10-01},

journal = {The Journal of Physical Chemistry B},

volume = {123},

number = {45},

pages = {9584--9591},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ding_2019,

title = {A New Family of Small-Molecule CD4-Mimetic Compounds Contacts Highly Conserved Aspartic Acid 368 of HIV-1 gp120 and Mediates Antibody-Dependent Cellular Cytotoxicity},

author = {Shilei Ding and Melissa C. Grenier and William D. Tolbert and Dani Vézina and Rebekah Sherburn and Jonathan Richard and Jérémie Prévost and Jean-Philippe Chapleau and Gabrielle Gendron-Lepage and Halima Medjahed and Cameron Abrams and Joseph Sodroski and Marzena Pazgier and Amos B. Smith III and Andrés Finzi},

editor = {Viviana Simon},

url = {https://doi.org/10.1128%2Fjvi.01325-19},

doi = {10.1128/jvi.01325-19},

year  = {2019},

date = {2019-09-01},

urldate = {2019-09-01},

journal = {Journal of Virology},

volume = {93},

number = {24},

pages = {e01325--19},

publisher = {American Society for Microbiology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shrivastav_2019,

title = {Mapping saddles and minima on free energy surfaces using multiple climbing strings},

author = {Gourav Shrivastav and Eric Vanden-Eijnden and Cameron F. Abrams},

url = {https://doi.org/10.1063%2F1.5120372},

doi = {10.1063/1.5120372},

year  = {2019},

date = {2019-09-01},

journal = {The Journal of Chemical Physics},

volume = {151},

number = {12},

pages = {124112},

publisher = {AIP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhao_2019,

title = {Strain-Dependent Activation and Inhibition of Human Immunodeficiency Virus Entry by a Specific PF-68742 Stereoisomer},

author = {Connie Zhao and Amy M. Princiotto and Hanh T. Nguyen and Shitao Zou and Meiqing Lily Zhao and Shijian Zhang and Alon Herschhorn and Mark Farrell and Karanbir Pahil and Bruno Melillo and Somisetti V. Sambasivarao and Cameron Abrams and Amos B. Smith III and Navid Madani and Joseph Sodroski},

editor = {Viviana Simon},

url = {https://doi.org/10.1128%2Fjvi.01197-19},

doi = {10.1128/jvi.01197-19},

year  = {2019},

date = {2019-08-01},

urldate = {2019-08-01},

journal = {Journal of Virology},

volume = {93},

number = {21},

publisher = {American Society for Microbiology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huang_2019,

title = {Effects of Reactivity Ratios on Network Topology and Thermomechanical Properties in Vinyl Ester/Styrene Thermosets: Molecular Dynamics Simulations},

author = {Ming Huang and Cameron Abrams},

url = {https://doi.org/10.1002%2Fmats.201900030},

doi = {10.1002/mats.201900030},

year  = {2019},

date = {2019-08-01},

journal = {Macromolecular Theory and Simulations},

volume = {28},

number = {6},

pages = {1900030},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lu_2019,

title = {Associating HIV-1 envelope glycoprotein structures with states on the~virus observed by smFRET},

author = {Maolin Lu and Xiaochu Ma and Luis R. Castillo-Menendez and Jason Gorman and Nirmin Alsahafi and Utz Ermel and Daniel S. Terry and Michael Chambers and Dongjun Peng and Baoshan Zhang and Tongqing Zhou and Nick Reichard and Kevin Wang and Jonathan R. Grover and Brennan P. Carman and Matthew R. Gardner and Ivana Nikić-Spiegel and Akihiro Sugawara and James Arthos and Edward A. Lemke and Amos B. Smith III and Michael Farzan and Cameron Abrams and James B. Munro and Adrian B. McDermott and Andrés Finzi and Peter D. Kwong and Scott C. Blanchard and Joseph G. Sodroski and Walther Mothes},

url = {https://doi.org/10.1038%2Fs41586-019-1101-y},

doi = {10.1038/s41586-019-1101-y},

year  = {2019},

date = {2019-04-01},

urldate = {2019-04-01},

journal = {Nature},

volume = {568},

number = {7752},

pages = {415--419},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikanth_2019b,

title = {Yield and Post-yield Behavior of Fatty-Acid-Functionalized Amidoamine–Epoxy Systems: A Molecular Simulation Study},

author = {Arun Srikanth Sridhar and C. F. Abrams},

url = {https://doi.org/10.1007%2Fs40870-019-00193-z},

doi = {10.1007/s40870-019-00193-z},

year  = {2019},

date = {2019-03-01},

journal = {Journal of Dynamic Behavior of Materials},

volume = {5},

number = {2},

pages = {143--149},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gordon_2018,

title = {Counterion Effects on Aggregate Structure of 12-Hydroxystearate Salts in Hexane: A Quantum Mechanical and Molecular Dynamics Simulation Study},

author = {Ryan Gordon and Spencer T. Stober and Cameron F. Abrams},

url = {https://doi.org/10.1021%2Facs.jpcb.8b08477},

doi = {10.1021/acs.jpcb.8b08477},

year  = {2018},

date = {2018-12-01},

journal = {The Journal of Physical Chemistry B},

volume = {123},

number = {2},

pages = {534--541},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gardner_2018,

title = {Lipid flip-flop vs. lateral diffusion in the relaxation of hemifusion diaphragms},

author = {Jasmine M. Gardner and Cameron F. Abrams},

url = {https://doi.org/10.1016%2Fj.bbamem.2018.04.007},

doi = {10.1016/j.bbamem.2018.04.007},

year  = {2018},

date = {2018-07-01},

journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes},

volume = {1860},

number = {7},

pages = {1452--1459},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikanth_2018,

title = {The effect of alkyl chain length on mechanical properties of fatty-acid-functionalized amidoamine-epoxy systems},

author = {Arun Srikanth Sridhar and Emre Kinaci and John Vergara and Giuseppe Palmese and Cameron F. Abrams},

url = {https://doi.org/10.1016%2Fj.commatsci.2018.03.073},

doi = {10.1016/j.commatsci.2018.03.073},

year  = {2018},

date = {2018-07-01},

journal = {Computational Materials Science},

volume = {150},

pages = {70--76},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gossert_2018,

title = {Roles of conserved tryptophans in trimerization of HIV-1 membrane-proximal external regions: Implications for virucidal design via alchemical free-energy molecular simulations},

author = {Steven T. Gossert and Bibek Parajuli and Irwin Chaiken and Cameron F. Abrams},

url = {https://doi.org/10.1002%2Fprot.25504},

doi = {10.1002/prot.25504},

year  = {2018},

date = {2018-04-01},

journal = {Proteins: Structure, Function, and Bioinformatics},

volume = {86},

number = {7},

pages = {707--711},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Paz_2018,

title = {Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization},

author = {S. Alexis Paz and Luca Maragliano and Cameron F. Abrams},

url = {https://doi.org/10.1021%2Facs.jctc.8b00024},

doi = {10.1021/acs.jctc.8b00024},

year  = {2018},

date = {2018-03-01},

journal = {Journal of Chemical Theory and Computation},

volume = {14},

number = {5},

pages = {2743--2750},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Paz_2018b,

title = {Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers},

author = {S. Paz and Cameron Abrams},

url = {https://doi.org/10.3390%2Fcomputation6020027},

doi = {10.3390/computation6020027},

year  = {2018},

date = {2018-03-01},

journal = {Computation},

volume = {6},

number = {2},

pages = {27},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Parajuli_2018,

title = {Restricted HIV-1 Env glycan engagement by lectin-reengineered DAVEI protein chimera is sufficient for lytic inactivation of the virus},

author = {Bibek Parajuli and Kriti Acharya and Harry C. Bach and Bijay Parajuli and Shiyu Zhang and Amos B. Smith III and Cameron F. Abrams and Irwin Chaiken},

url = {https://doi.org/10.1042%2Fbcj20170662},

doi = {10.1042/bcj20170662},

year  = {2018},

date = {2018-03-01},

urldate = {2018-03-01},

journal = {Biochemical Journal},

volume = {475},

number = {5},

pages = {931--957},

publisher = {Portland Press Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Moraca_2018,

title = {Specific Noncovalent 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},

author = {Francesca Moraca and David Rinaldo and Amos B. Smith III and Cameron F. Abrams},

url = {https://doi.org/10.1002%2Fcmdc.201700728},

doi = {10.1002/cmdc.201700728},

year  = {2018},

date = {2018-02-01},

urldate = {2018-02-01},

journal = {ChemMedChem},

volume = {13},

number = {6},

pages = {627--633},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gardner_2017,

title = {Rate of hemifusion diaphragm dissipation and ability to form three-junction bound HD determined by lipid composition},

author = {Jasmine M. Gardner and Cameron F. Abrams},

url = {https://doi.org/10.1063%2F1.4994320},

doi = {10.1063/1.4994320},

year  = {2017},

date = {2017-10-01},

journal = {The Journal of Chemical Physics},

volume = {147},

number = {13},

pages = {134903},

publisher = {AIP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Herschhorn_2017,

title = {The β20-β21 of gp120 is a regulatory switch for HIV-1 Env conformational transitions},

author = {Alon Herschhorn and Christopher Gu and Francesca Moraca and Xiaochu Ma and Mark Farrell and Amos B. Smith III and Marie Pancera and Peter D. Kwong and Arne Schön and Ernesto Freire and Cameron Abrams and Scott C. Blanchard and Walther Mothes and Joseph G. Sodroski},

url = {https://doi.org/10.1038%2Fs41467-017-01119-w},

doi = {10.1038/s41467-017-01119-w},

year  = {2017},

date = {2017-10-01},

urldate = {2017-10-01},

journal = {Nature Communications},

volume = {8},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gordon_2017,

title = {Effects of Optical Purity and Finite System Size on Self-Assembly of 12-Hydroxystearic Acid in Hexane: Molecular Dynamics Simulations},

author = {Ryan Gordon and Spencer T. Stober and Cameron F. Abrams},

url = {https://doi.org/10.1021%2Facs.jpcb.7b05246},

doi = {10.1021/acs.jpcb.7b05246},

year  = {2017},

date = {2017-09-01},

journal = {The Journal of Physical Chemistry B},

volume = {121},

number = {39},

pages = {9223--9233},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikanth_2017,

title = {The effect of alkyl chain length on material properties of fatty-acid-functionalized amidoamine-epoxy systems},

author = {Arun Srikanth Sridhar and John Vergara and Giuseppe Palmese and Cameron F. Abrams},

url = {https://doi.org/10.1016%2Fj.eurpolymj.2017.01.037},

doi = {10.1016/j.eurpolymj.2017.01.037},

year  = {2017},

date = {2017-04-01},

journal = {European Polymer Journal},

volume = {89},

pages = {1--12},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Acharya_2017,

title = {Recognition of HIV-inactivating peptide triazoles by the recombinant soluble Env trimer, BG505 SOSIP.664},

author = {Kriti Acharya and Adel A. Rashad and Francesca Moraca and Per Johan Klasse and John P. Moore and Cameron Abrams and Irwin Chaiken},

url = {https://doi.org/10.1002%2Fprot.25238},

doi = {10.1002/prot.25238},

year  = {2017},

date = {2017-03-01},

journal = {Proteins: Structure, Function, and Bioinformatics},

volume = {85},

number = {5},

pages = {843--851},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Paz_2017,

title = {Polymorphism at 129 dictates metastable conformations of the human prion protein N-terminal β-sheet},

author = {S. Alexis Paz and Eric Vanden-Eijnden and Cameron F. Abrams},

url = {https://doi.org/10.1039%2Fc6sc03275c},

doi = {10.1039/c6sc03275c},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Chemical Science},

volume = {8},

number = {2},

pages = {1225--1232},

publisher = {Royal Society of Chemistry (RSC)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Yang_2016,

title = {Relationships between molecular structure and thermomechanical properties of bio-based thermosetting polymers},

author = {Jung Ho Yang and Arun Srikanth and Changwoon Jang and Cameron F. Abrams},

url = {https://doi.org/10.1002%2Fpolb.24270},

doi = {10.1002/polb.24270},

year  = {2016},

date = {2016-11-01},

journal = {Journal of Polymer Science Part B: Polymer Physics},

volume = {55},

number = {3},

pages = {285--292},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}