Publications

2022

  • S. Ding, I. Ullah, S. Y. Gong, J. Grover, M. Mohammadi, Y. Chen, D. Vézina, G. Beaudoin-Bussières, V. T. Verma, G. Goyette, F. Gaudette, J. Richard, D. Yang, A. Smith III, M. Pazgier, M. Côté, C. Abrams, P. Kumar, W. Mothes, P. Uchil, A. Finzi, and C. Baron, “VE607 Stabilizes SARS-CoV-2 Spike In the RBD-up Conformation and Inhibits Viral Entry," iScience, vol. 25, p. 104528, 2022. doi:10.1016/j.isci.2022.104528 PMC9164512 [BibTeX]
    @Article{Ding2022,
    author={Ding, Shilei
    and Ullah, Irfan
    and Gong, Shang Yu
    and Grover, Jonathan
    and Mohammadi, Mohammadjavad
    and Chen, Yaozong
    and V{\'e}zina, Dani
    and Beaudoin-Bussi{\`e}res, Guillaume
    and Verma, Vijay Tailor
    and Goyette, Guillaume
    and Gaudette, Fleur
    and Richard, Jonathan
    and Yang, Derek
    and A. Smith III,
    and Pazgier, Marzena
    and C{\^o}t{\'e}, Marceline
    and Abrams, Cameron
    and Kumar, Priti
    and Mothes, Walther
    and Uchil, Pradeep
    and Finzi, Andr{\'e}s
    and Baron, Christian},
    title={{VE607 Stabilizes SARS-CoV-2 Spike In the RBD-up Conformation and Inhibits Viral Entry}},
    journal={{iScience}},
    volume = 25,
    pages={104528},
    year={2022},
    month={2022/06/06},
    publisher={Elsevier},
    issn={2589-0042},
    doi={10.1016/j.isci.2022.104528},
    url={https://doi.org/10.1016/j.isci.2022.104528},
    pmcid={PMC9164512}
    }

  • M. Huang, N. Alvarez, G. Palmese, and C. F. Abrams, “The effect of network topology on material properties in vinyl-ester/styrene thermoset polymers using molecular dynamics simulations and time-temperature superposition," Computational Materials Science, vol. 27, p. 111264, 2022. doi:10.1016/j.commatsci.2022.111264 [BibTeX]
    @article{Huang2022,
    author={Ming Huang and Nicolas Alvarez and Giuseppe Palmese and Cameron F. Abrams},
    title={The Effect of Network Topology on Material Properties in Vinyl-ester/Styrene Thermoset Polymers using Molecular Dynamics Simulations and Time-Temperature Superposition},
    journal={{Computational Materials Science}},
    volume=27,
    pages=111264,
    doi={10.1016/j.commatsci.2022.111264},
    url={https://doi.org/10.1016/j.commatsci.2022.111264},
    year={2022}
    }

  • S. Zarrini and C. F. Abrams, “Modeling sizing emulsion droplet deposition onto silica using all-atom molecular dynamics simulations," Composites Part B: Engineering, vol. 235, p. 109712, 2022. doi:10.1016/j.compositesb.2022.109712 [BibTeX]
    @article{Zarrini2022,
    author = {Salman Zarrini and Cameron F. Abrams},
    title = {Modeling Sizing Emulsion Droplet Deposition onto Silica Using All-Atom Molecular Dynamics Simulations},
    journal = {{Composites Part B: Engineering}},
    volume = {235},
    pages={109712},
    doi={10.1016/j.compositesb.2022.109712},
    url={https://doi.org/10.1016/j.compositesb.2022.109712},
    year = {2022}
    }

2021

  • S. Ribone, S. A. Paz, C. Abrams, and M. Villarreal, “Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking," Journal of Computer Aided Molecular Design, vol. 26, pp. 1-13, 2021. doi:10.1007/s10822-021-00432-3 PMC8616721 [BibTeX]
    @article{Ribone2021,
    author = {Sergio Ribone and Sergio Alexis Paz and Cameron Abrams and Marcos Villarreal},
    title = {Target identification for repurposed drugs active against {SARS-CoV-2}
    via high-throughput inverse docking},
    journal = {{Journal of Computer Aided Molecular Design}},
    volume = {26},
    pages = {1-13},
    year = {2021},
    doi = {10.1007/s10822-021-00432-3},
    pmcid = {PMC8616721},
    url = {https://doi.org/10.1007/s10822-021-00432-3}
    }

  • C. Fritschi, S. Liang, M. Mohammadi, S. Anang, F. Moraca, J. Chen, N. Madani, J. Sodroski, C. Abrams, W. Hendrickson, and A. B. Smith III, “Identification and Validation of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics," ACS Medicinal Chemistry Letters, vol. 12, pp. 1824-1831, 2021. doi:10.1021/acsmedchemlett.1c00437 PMC8591726 [BibTeX]
    @article{Fritschi2021,
    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 Smith III, Amos B.},
    title = {{Identification and Validation of gp120 Residue His105 as a Novel Target for HIV-1
    Neutralization by Small-Molecule CD4-Mimics}},
    journal = {{ACS Medicinal Chemistry Letters}},
    volume={12},
    pages={1824-1831},
    doi={10.1021/acsmedchemlett.1c00437},
    url={https://doi.org/10.1021/acsmedchemlett.1c00437},
    pmcid={PMC8591726},
    year={2021}
    }

  • K. Khare and C. F. Abrams, “Atomistic simulation of volumetric properties of epoxy networks: Effect of monomer length," Soft Matter, vol. 17, pp. 9957-9986, 2021. doi:10.1039/D1SM01128F [BibTeX]
    @article{Khare2021,
    author = {Ketan Khare and Cameron F. Abrams},
    title = {Atomistic Simulation of Volumetric Properties of Epoxy Networks: {E}ffect of Monomer Length},
    Journal = {{Soft Matter}},
    volume ={17},
    pages = {9957-9986},
    doi={10.1039/D1SM01128F},
    url = {https://doi.org/10.1039/D1SM01128F},
    year={2021}
    }

  • J. Prévost, J. Richard, R. Gasser, S. Ding, C. Fage, S. P. Anand, D. Adam, N. G. Vergara, A. Tauzin, M. Benlarbi, S. Y. Gong, G. Goyette, A. Privé, S. Moreira, H. Charest, M. Roger, W. Mothes, M. Pazgier, E. Brochiero, G. Boivin, C. F. Abrams, A. Schön, and A. Finzi, “Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2," Journal of Biological Chemistry, vol. 297, iss. 4, p. 11051, 2021. doi:10.1016/j.jbc.2021.101151 PMC8406544 [BibTeX]
    @article{Prevost2021,
    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},
    title = {{Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2}},
    journal = {{Journal of Biological Chemistry}},
    volume = {297},
    pages = {11051},
    number = {4},
    doi = {10.1016/j.jbc.2021.101151},
    pmcid = {PMC8406544},
    url = {https://doi.org/10.1016/j.jbc.2021.101151},
    year = {2021}
    }

  • S. Zarrini and C. F. Abrams, “The roles of coupling agent and surfactant in droplet structure in sizing emulsions: A molecular dynamics simulations study," Langmuir, vol. 37, iss. 33, pp. 10183-10190, 2021. doi:10.1021/acs.langmuir.1c01592 [BibTeX]
    @article{Zarrini2021a,
    author = {Zarrini, Salman and Abrams, Cameron F.},
    title = {The Roles of Coupling Agent and Surfactant in Droplet Structure in Sizing Emulsions: {A} Molecular Dynamics Simulations Study},
    journal = {{Langmuir}},
    volume = {37},
    pages = {10183-10190},
    number = {33},
    doi = {10.1021/acs.langmuir.1c01592},
    url = {https://doi.org/10.1021/acs.langmuir.1c01592},
    year = {2021}
    }

  • C. G. Ang, E. Carter, A. Haftl, S. Zhang, A. A. Rashad, M. Kutzler, C. F. Abrams, and I. M. Chaiken, “Peptide Triazole Thiol Irreversibly Inactivates Metastable HIV-1 Env by Accessing Conformational Triggers Intrinsic to Virus–Cell Entry," Microorganisms, vol. 9, iss. 6, 2021. doi:10.3390/microorganisms9061286 PMC8231586 [BibTeX] [Abstract]
    @article{Ang2021,
    AUTHOR = {Ang, Charles Gotuaco and Carter, Erik and Haftl, Ann and Zhang, Shiyu and Rashad, Adel A. and Kutzler, Michele and Abrams, Cameron F. and Chaiken, Irwin M.},
    TITLE = {{Peptide Triazole Thiol Irreversibly Inactivates Metastable {HIV-1 Env} by Accessing Conformational Triggers Intrinsic to Virus–Cell Entry}},
    JOURNAL = {Microorganisms},
    VOLUME = {9},
    YEAR = {2021},
    NUMBER = {6},
    ARTICLE-NUMBER = {1286},
    URL = {https://www.mdpi.com/2076-2607/9/6/1286},
    PubMedID = {34204725},
    ISSN = {2076-2607},
    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.},
    DOI = {10.3390/microorganisms9061286},
    pmcid = {PMC8231586}
    }

  • G. Shrivastav and C. F. Abrams, “Optimizing string method’s reproducibility using generalized solute tempering replica exchange," The Journal of Physical Chemistry B, vol. 125, iss. 24, pp. 6609-6616, 2021. doi:10.1021/acs.jpcb.1c02143 [BibTeX]
    @article{Shrivastav2021,
    author = {Shrivastav, Gourav and Abrams, Cameron F.},
    title = {Optimizing String Method’s Reproducibility Using Generalized Solute Tempering Replica Exchange},
    journal = {{The Journal of Physical Chemistry B}},
    volume = {125},
    number = {24},
    pages = {6609-6616},
    year = {2021},
    doi = {10.1021/acs.jpcb.1c02143},
    URL = {https://doi.org/10.1021/acs.jpcb.1c02143}
    }

  • A. Gaffney, A. Nangarlia, C. G. Ang, S. Gossert, A. A. Rashad Ahmed, M. A. Hossain, C. F. Abrams, A. B. Smith III, and I. Chaiken, “HIV-1 Env-dependent cell killing by bifunctional small-molecule/peptide conjugates," ACS Chemical Biology, vol. 16, iss. 1, pp. 193-204, 2021. doi:10.1021/acschembio.0c00888 PMC8218882 [BibTeX]
    @article{Gaffney2021,
    author = {Gaffney, Althea and Nangarlia, Aakansha and Ang, Charles G. and Gossert, Steven and
    Rashad Ahmed, Adel Ahmed and Hossain, Md Alamgir and Abrams, Cameron F. and Smith III, Amos B. and Chaiken, Irwin},
    title = {{HIV}-1 {Env}-Dependent Cell Killing by Bifunctional Small-Molecule/Peptide Conjugates},
    journal = {{ACS Chemical Biology}},
    volume = {16},
    number = {1},
    pages = {193-204},
    year = {2021},
    doi = {10.1021/acschembio.0c00888},
    pmcid = {PMC8218882},
    URL = {
    https://doi.org/10.1021/acschembio.0c00888
    },
    eprint = {
    https://doi.org/10.1021/acschembio.0c00888
    }
    }

2020

  • B. Parajuli, K. Acharya, A. Nangarlia, S. Zhang, B. Parajuli, A. Dick, B. Ngo, C. F. Abrams, and I. Chaiken, “Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate," Biochemical Journal, vol. 477, iss. 21, p. 4263–4280, 2020. doi:10.1042/BCJ20200495 [BibTeX] [Abstract]
    @article{Parajuli2020,
    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.},
    author = {Parajuli, Bibek and Acharya, Kriti and Nangarlia, Aakansha and Zhang, Shiyu and Parajuli, Bijay and Dick, Alexej and Ngo, Brendon and Abrams, Cameron F. and Chaiken, Irwin},
    doi = {10.1042/BCJ20200495},
    issn = {0264-6021},
    journal = {{Biochemical Journal}},
    month = {nov},
    number = {21},
    pages = {4263--4280},
    title = {{Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate}},
    url = {https://portlandpress.com/biochemj/article/477/21/4263/226680/Identification-of-a-glycan-cluster-in-gp120},
    volume = {477},
    year = {2020}
    }

  • S. P. Anand, Y. Chen, J. Prévost, R. Gasser, G. Beaudoin-Bussiéres, C. F. Abrams, M. Pazgier, and A. Finzi, “Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins," Viruses, vol. 12, iss. 10, p. 1104, 2020. doi:10.3390/v12101104 PMC7601831 [BibTeX]
    @article{Anand2020,
    doi = {10.3390/v12101104},
    pmcid = {PMC7601831},
    url = {https://doi.org/10.3390/v12101104},
    year = {2020},
    volume = 12,
    number = 10,
    pages = 1104,
    author = {Sai Priya Anand and Yaozong Chen and J{\'{e}}r{\'{e}}mie Pr{\'{e}}vost and Romain Gasser and Guillaume Beaudoin-Bussi{\'{e}}res and Cameron F. Abrams and Marzena Pazgier and Andr{\'{e}}s Finzi},
    title = {Interaction of human {ACE2} to membrane-bound {SARS-CoV-1} and {SARS-CoV-2} {S} glycoproteins},
    journal = {{Viruses}}
    }

  • S. Gossert, B. Parajuli, I. Chaiken, and 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 Science, vol. 29, pp. 2304-2310, 2020. doi:10.1002/pro.3949 PMC7586904 [BibTeX]
    @article{Gossert_2020,
    doi = {10.1002/pro.3949},
    pmcid = {PMC7586904},
    url = {https://doi.org/10.1002/pro.3949},
    year = {2020},
    volume = 29,
    pages = {2304-2310},
    author = {Steven Gossert and Bibek Parajuli and Irwin Chaiken and Cameron F. Abrams},
    title = {Roles of Variable Linker Length in Dual Acting Virucidal Entry Inhibitors on {HIV}-1 Potency via On-the-fly Free Energy Molecular Simulations},
    journal = {{Protein Science}}
    }

  • J. Prévost, W. D. Tolbert, H. Medjahed, R. T. Sherburn, N. Madani, D. Zoubchenok, G. Gendron-Lepage, A. E. Gaffney, M. C. Grenier, S. Kirk, N. Vergara, C. Han, B. T. Mann, A. L. Chénine, A. Ahmed, I. Chaiken, F. Kirchhoff, B. H. Hahn, H. Haim, C. F. Abrams, A. B. Smith, J. Sodroski, M. Pazgier, and A. Finzi, “The HIV-1 Env gp120 inner domain shapes the Phe43 cavity and the CD4 binding site," mBio, vol. 11, iss. 3, p. e00280-20, 2020. doi:10.1128/mbio.00280-20 PMC7251204 [BibTeX]
    @article{Prevost_2020,
    doi = {10.1128/mbio.00280-20},
    pmcid = {PMC7251204},
    url = {https://doi.org/10.1128%2Fmbio.00280-20},
    year = {2020},
    month = {may},
    publisher = {American Society for Microbiology},
    volume = {11},
    number = {3},
    author = {J{\'{e}}r{\'{e}}mie Pr{\'{e}}vost 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 Agn{\`{e}}s L. Ch{\'{e}}nine and Adel Ahmed and Irwin Chaiken and Frank Kirchhoff and Beatrice H. Hahn and Hillel Haim and Cameron F. Abrams and Amos B. Smith and Joseph Sodroski and Marzena Pazgier and Andr{\'{e}}s Finzi},
    editor = {Tongqing Zhou and Thomas E. Smithgall},
    title = {The {HIV}-1 {Env} gp120 Inner Domain Shapes the {P}he43 Cavity and the {CD}4 Binding Site},
    journal = {{mBio}},
    pages = {e00280-20}
    }

  • S. Zou, S. Zhang, A. Gaffney, H. Ding, M. Lu, J. R. Grover, M. Farrell, H. T. Nguyen, C. Zhao, S. Anang, M. Zhao, M. Mohammadi, S. C. Blanchard, C. Abrams, N. Madani, W. Mothes, J. C. Kappes, A. B. Smith, and J. Sodroski, “Long-acting BMS-378806 analogues stabilize the state-1 conformation of the human immunodeficiency virus type 1 envelope glycoproteins," Journal of Virology, vol. 94, iss. 10, p. e00148–20, 2020. doi:10.1128/jvi.00148-20 [BibTeX]
    @article{Zou_2020,
    doi = {10.1128/jvi.00148-20},
    url = {https://doi.org/10.1128%2Fjvi.00148-20},
    year = 2020,
    month = {mar},
    publisher = {American Society for Microbiology},
    volume = {94},
    number = {10},
    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 and Joseph Sodroski},
    editor = {Viviana Simon},
    title = {Long-Acting {BMS}-378806 Analogues Stabilize the State-1 Conformation of the Human Immunodeficiency Virus Type 1 Envelope Glycoproteins},
    journal = {{Journal of Virology}},
    pages = {e00148--20}
    }

  • C. G. Ang, M. A. Hossain, M. Rajpara, H. Bach, K. Acharya, A. Dick, A. A. Rashad, M. Kutzler, C. F. Abrams, and I. Chaiken, “Metastable HIV-1 surface protein env sensitizes cell membranes to transformation and poration by dual-acting virucidal entry inhibitors," Biochemistry, vol. 59, iss. 6, p. 818–828, 2020. doi:10.1021/acs.biochem.9b01008 PMC7362902 [BibTeX]
    @article{Ang_2020,
    doi = {10.1021/acs.biochem.9b01008},
    pmcid = {PMC7362902},
    url = {https://doi.org/10.1021%2Facs.biochem.9b01008},
    year = {2020},
    month = {jan},
    publisher = {American Chemical Society ({ACS})},
    volume = {59},
    number = {6},
    pages = {818--828},
    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},
    title = {Metastable {HIV}-1 Surface Protein Env Sensitizes Cell Membranes to Transformation and Poration by Dual-Acting Virucidal Entry Inhibitors},
    journal = {{Biochemistry}}
    }

2019

  • M. C. Grenier, S. Ding, D. Vézina, J. Chapleau, W. D. Tolbert, R. Sherburn, A. Schön, S. Somisetti, C. F. Abrams, M. Pazgier, A. Finzi, and A. B. Smith, “Optimization of small molecules that sensitize HIV-1 infected cells to antibody-dependent cellular cytotoxicity," ACS Medicinal Chemistry Letters, vol. 11, iss. 3, p. 371–378, 2019. doi:10.1021/acsmedchemlett.9b00445 PMC7074219 [BibTeX]
    @article{Grenier_2019,
    doi = {10.1021/acsmedchemlett.9b00445},
    pmcid = {PMC7074219},
    url = {https://doi.org/10.1021%2Facsmedchemlett.9b00445},
    year = {2019},
    month = {nov},
    publisher = {American Chemical Society ({ACS})},
    volume = {11},
    number = {3},
    pages = {371--378},
    author = {Melissa C. Grenier and Shilei Ding and Dani V{\'{e}}zina and Jean-Philippe Chapleau and William D. Tolbert and Rebekah Sherburn and Arne Sch{\"o}n and Sambasivarao Somisetti and Cameron F. Abrams and Marzena Pazgier and Andr{\'{e}}s Finzi and Amos B. Smith},
    title = {Optimization of Small Molecules That Sensitize {HIV}-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity},
    journal = {{{ACS} Medicinal Chemistry Letters}}
    }

  • J. M. Gardner and C. F. Abrams, “Energetics of flap opening in HIV-1 protease: String method calculations," The Journal of Physical Chemistry B, vol. 123, iss. 45, p. 9584–9591, 2019. doi:10.1021/acs.jpcb.9b08348 PMC7375464 [BibTeX]
    @article{Gardner_2019,
    doi = {10.1021/acs.jpcb.9b08348},
    pmcid = {PMC7375464},
    url = {https://doi.org/10.1021%2Facs.jpcb.9b08348},
    year = {2019},
    month = {oct},
    publisher = {American Chemical Society ({ACS})},
    volume = {123},
    number = {45},
    pages = {9584--9591},
    author = {Jasmine M. Gardner and Cameron F. Abrams},
    title = {Energetics of Flap Opening in {HIV}-1 Protease: {S}tring Method Calculations},
    journal = {{The Journal of Physical Chemistry B}}
    }

  • A. Bhaduri, J. Gardner, C. F. Abrams, and L. Graham-Brady, “Free energy calculation using space filled design and weighted reconstruction: A modified single sweep approach," Molecular Simulation, vol. 46, iss. 3, p. 193–206, 2019. doi:10.1080/08927022.2019.1688325 [BibTeX]
    @article{Bhaduri_2019,
    doi = {10.1080/08927022.2019.1688325},
    url = {https://doi.org/10.1080%2F08927022.2019.1688325},
    year = 2019,
    month = {nov},
    publisher = {Informa {UK} Limited},
    volume = {46},
    number = {3},
    pages = {193--206},
    author = {Anindya Bhaduri and Jasmine Gardner and Cameron F. Abrams and Lori Graham-Brady},
    title = {Free energy calculation using space filled design and weighted reconstruction: {A} modified single sweep approach},
    journal = {{Molecular Simulation}}
    }

  • S. Ding, M. C. Grenier, W. D. Tolbert, D. Vézina, R. Sherburn, J. Richard, J. Prévost, J. Chapleau, G. Gendron-Lepage, H. Medjahed, C. Abrams, J. Sodroski, M. Pazgier, A. B. Smith, and A. Finzi, “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," Journal of Virology, vol. 93, iss. 24, p. e01325–19, 2019. doi:10.1128/jvi.01325-19 [BibTeX]
    @article{Ding_2019,
    doi = {10.1128/jvi.01325-19},
    url = {https://doi.org/10.1128%2Fjvi.01325-19},
    year = 2019,
    month = {sep},
    publisher = {American Society for Microbiology},
    volume = {93},
    number = {24},
    author = {Shilei Ding and Melissa C. Grenier and William D. Tolbert and Dani V{\'{e}}zina and Rebekah Sherburn and Jonathan Richard and J{\'{e}}r{\'{e}}mie Pr{\'{e}}vost and Jean-Philippe Chapleau and Gabrielle Gendron-Lepage and Halima Medjahed and Cameron Abrams and Joseph Sodroski and Marzena Pazgier and Amos B. Smith and Andr{\'{e}}s Finzi},
    editor = {Viviana Simon},
    title = {A New Family of Small-Molecule {CD}4-Mimetic Compounds Contacts Highly Conserved Aspartic Acid 368 of {HIV}-1 gp120 and Mediates Antibody-Dependent Cellular Cytotoxicity},
    journal = {{Journal of Virology}},
    pages = {e01325--19}
    }

  • G. Shrivastav, E. Vanden-Eijnden, and C. F. Abrams, “Mapping saddles and minima on free energy surfaces using multiple climbing strings," The Journal of Chemical Physics, vol. 151, iss. 12, p. 124112, 2019. doi:10.1063/1.5120372 [BibTeX]
    @article{Shrivastav_2019,
    doi = {10.1063/1.5120372},
    url = {https://doi.org/10.1063%2F1.5120372},
    year = 2019,
    month = {sep},
    publisher = {{AIP} Publishing},
    volume = {151},
    number = {12},
    pages = {124112},
    author = {Gourav Shrivastav and Eric Vanden-Eijnden and Cameron F. Abrams},
    title = {Mapping saddles and minima on free energy surfaces using multiple climbing strings},
    journal = {{The Journal of Chemical Physics}}
    }

  • C. Zhao, A. M. Princiotto, H. T. Nguyen, S. Zou, M. L. Zhao, S. Zhang, A. Herschhorn, M. Farrell, K. Pahil, B. Melillo, S. V. Sambasivarao, C. Abrams, A. B. Smith, N. Madani, and J. Sodroski, “Strain-dependent activation and inhibition of human immunodeficiency virus entry by a specific PF-68742 stereoisomer," Journal of Virology, vol. 93, iss. 21, 2019. doi:10.1128/jvi.01197-19 [BibTeX]
    @article{Zhao_2019,
    doi = {10.1128/jvi.01197-19},
    url = {https://doi.org/10.1128%2Fjvi.01197-19},
    year = 2019,
    month = {aug},
    publisher = {American Society for Microbiology},
    volume = {93},
    number = {21},
    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 and Navid Madani and Joseph Sodroski},
    editor = {Viviana Simon},
    title = {Strain-Dependent Activation and Inhibition of Human Immunodeficiency Virus Entry by a Specific {PF}-68742 Stereoisomer},
    journal = {{Journal of Virology}}
    }

  • M. Huang and C. Abrams, “Effects of reactivity ratios on network topology and thermomechanical properties in vinyl ester/styrene thermosets: molecular dynamics simulations," Macromolecular Theory and Simulations, vol. 28, iss. 6, p. 1900030, 2019. doi:10.1002/mats.201900030 [BibTeX]
    @article{Huang_2019,
    doi = {10.1002/mats.201900030},
    url = {https://doi.org/10.1002%2Fmats.201900030},
    year = 2019,
    month = {aug},
    publisher = {Wiley},
    volume = {28},
    number = {6},
    pages = {1900030},
    author = {Ming Huang and Cameron Abrams},
    title = {Effects of Reactivity Ratios on Network Topology and Thermomechanical Properties in Vinyl Ester/Styrene Thermosets: Molecular Dynamics Simulations},
    journal = {{Macromolecular Theory and Simulations}}
    }

  • A. S. Sridhar and C. F. Abrams, “Effect of molecular packing and hydrogen bonding on the properties of epoxy-amido amine systems," Computational Materials Science, vol. 169, p. 109082, 2019. doi:10.1016/j.commatsci.2019.109082 [BibTeX]
    @article{Srikanth_2019,
    doi = {10.1016/j.commatsci.2019.109082},
    url = {https://doi.org/10.1016%2Fj.commatsci.2019.109082},
    year = 2019,
    month = {nov},
    publisher = {Elsevier {BV}},
    volume = {169},
    pages = {109082},
    author = {Arun Srikanth Sridhar and Cameron F. Abrams},
    title = {Effect of molecular packing and hydrogen bonding on the properties of epoxy-amido amine systems},
    journal = {{Computational Materials Science}}
    }

  • M. Lu, X. Ma, L. R. Castillo-Menendez, J. Gorman, N. Alsahafi, U. Ermel, D. S. Terry, M. Chambers, D. Peng, B. Zhang, T. Zhou, N. Reichard, K. Wang, J. R. Grover, B. P. Carman, M. R. Gardner, I. Nikić-Spiegel, A. Sugawara, J. Arthos, E. A. Lemke, A. B. Smith, M. Farzan, C. Abrams, J. B. Munro, A. B. McDermott, A. Finzi, P. D. Kwong, S. C. Blanchard, J. G. Sodroski, and W. Mothes, “Associating HIV-1 envelope glycoprotein structures with states on the~virus observed by smFRET," Nature, vol. 568, iss. 7752, p. 415–419, 2019. doi:10.1038/s41586-019-1101-y [BibTeX]
    @article{Lu_2019,
    doi = {10.1038/s41586-019-1101-y},
    url = {https://doi.org/10.1038%2Fs41586-019-1101-y},
    year = 2019,
    month = {apr},
    publisher = {Springer Science and Business Media {LLC}},
    volume = {568},
    number = {7752},
    pages = {415--419},
    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 Niki{\'{c}}-Spiegel and Akihiro Sugawara and James Arthos and Edward A. Lemke and Amos B. Smith and Michael Farzan and Cameron Abrams and James B. Munro and Adrian B. McDermott and Andr{\'{e}}s Finzi and Peter D. Kwong and Scott C. Blanchard and Joseph G. Sodroski and Walther Mothes},
    title = {Associating {HIV}-1 envelope glycoprotein structures with states on the~virus observed by {smFRET}},
    journal = {{Nature}}
    }

  • A. S. Sridhar and C. F. Abrams, “Yield and post-yield behavior of fatty-acid-functionalized amidoamine–epoxy systems: A molecular simulation study," Journal of Dynamic Behavior of Materials, vol. 5, iss. 2, p. 143–149, 2019. doi:10.1007/s40870-019-00193-z [BibTeX]
    @article{Srikanth_2019b,
    doi = {10.1007/s40870-019-00193-z},
    url = {https://doi.org/10.1007%2Fs40870-019-00193-z},
    year = 2019,
    month = {mar},
    publisher = {Springer Science and Business Media {LLC}},
    volume = {5},
    number = {2},
    pages = {143--149},
    author = {Arun Srikanth Sridhar and C. F. Abrams},
    title = {Yield and Post-yield Behavior of Fatty-Acid-Functionalized Amidoamine{\textendash}Epoxy Systems: {A} Molecular Simulation Study},
    journal = {{Journal of Dynamic Behavior of Materials}}
    }

2018

  • R. Gordon, S. T. Stober, and C. F. Abrams, “Counterion effects on aggregate structure of 12-hydroxystearate salts in hexane: A quantum mechanical and molecular dynamics simulation study," The Journal of Physical Chemistry B, vol. 123, iss. 2, p. 534–541, 2018. doi:10.1021/acs.jpcb.8b08477 [BibTeX]
    @article{Gordon_2018,
    doi = {10.1021/acs.jpcb.8b08477},
    url = {https://doi.org/10.1021%2Facs.jpcb.8b08477},
    year = 2018,
    month = {dec},
    publisher = {American Chemical Society ({ACS})},
    volume = {123},
    number = {2},
    pages = {534--541},
    author = {Ryan Gordon and Spencer T. Stober and Cameron F. Abrams},
    title = {Counterion Effects on Aggregate Structure of 12-Hydroxystearate Salts in Hexane: {A} Quantum Mechanical and Molecular Dynamics Simulation Study},
    journal = {{The Journal of Physical Chemistry B}}
    }

  • J. M. Gardner and C. F. Abrams, “Lipid flip-flop vs. lateral diffusion in the relaxation of hemifusion diaphragms," Biochimica et Biophysica Acta (BBA) – Biomembranes, vol. 1860, iss. 7, p. 1452–1459, 2018. doi:10.1016/j.bbamem.2018.04.007 [BibTeX]
    @article{Gardner_2018,
    doi = {10.1016/j.bbamem.2018.04.007},
    url = {https://doi.org/10.1016%2Fj.bbamem.2018.04.007},
    year = 2018,
    month = {jul},
    publisher = {Elsevier {BV}},
    volume = {1860},
    number = {7},
    pages = {1452--1459},
    author = {Jasmine M. Gardner and Cameron F. Abrams},
    title = {Lipid flip-flop vs. lateral diffusion in the relaxation of hemifusion diaphragms},
    journal = {{Biochimica et Biophysica Acta ({BBA}) - Biomembranes}}
    }

  • S. T. Gossert, B. Parajuli, I. Chaiken, and C. 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: Structure, Function, and Bioinformatics, vol. 86, iss. 7, p. 707–711, 2018. doi:10.1002/prot.25504 PMC6013385 [BibTeX]
    @article{Gossert_2018,
    doi = {10.1002/prot.25504},
    pmcid = {PMC6013385},
    url = {https://doi.org/10.1002%2Fprot.25504},
    year = 2018,
    month = {apr},
    publisher = {Wiley},
    volume = {86},
    number = {7},
    pages = {707--711},
    author = {Steven T. Gossert and Bibek Parajuli and Irwin Chaiken and Cameron F. Abrams},
    title = {Roles of conserved tryptophans in trimerization of {HIV}-1 membrane-proximal external regions: Implications for virucidal design via alchemical free-energy molecular simulations},
    journal = {{Proteins: Structure, Function, and Bioinformatics}}
    }

  • A. S. Paz, L. Maragliano, and C. F. Abrams, “Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization," Journal of Chemical Theory and Computation, vol. 14, iss. 5, p. 2743–2750, 2018. doi:10.1021/acs.jctc.8b00024 [BibTeX]
    @article{Paz_2018,
    doi = {10.1021/acs.jctc.8b00024},
    url = {https://doi.org/10.1021%2Facs.jctc.8b00024},
    year = 2018,
    month = {mar},
    publisher = {American Chemical Society ({ACS})},
    volume = {14},
    number = {5},
    pages = {2743--2750},
    author = {S. Alexis Paz and Luca Maragliano and Cameron F. Abrams},
    title = {Effect of Intercalated Water on Potassium Ion Transport through {K}v1.2 Channels Studied via On-the-Fly Free-Energy Parametrization},
    journal = {{Journal of Chemical Theory and Computation}}
    }

  • A. S. Sridhar, E. Kinaci, J. Vergara, G. Palmese, and C. F. Abrams, “The effect of alkyl chain length on mechanical properties of fatty-acid-functionalized amidoamine-epoxy systems," Computational Materials Science, vol. 150, p. 70–76, 2018. doi:10.1016/j.commatsci.2018.03.073 [BibTeX]
    @article{Srikanth_2018,
    doi = {10.1016/j.commatsci.2018.03.073},
    url = {https://doi.org/10.1016%2Fj.commatsci.2018.03.073},
    year = 2018,
    month = {jul},
    publisher = {Elsevier {BV}},
    volume = {150},
    pages = {70--76},
    author = {Arun Srikanth Sridhar and Emre Kinaci and John Vergara and Giuseppe Palmese and Cameron F. Abrams},
    title = {The effect of alkyl chain length on mechanical properties of fatty-acid-functionalized amidoamine-epoxy systems},
    journal = {{Computational Materials Science}}
    }

  • S. Paz and C. Abrams, “Testing convergence of different free-energy methods in a simple analytical system with hidden barriers," Computation, vol. 6, iss. 2, p. 27, 2018. doi:10.3390/computation6020027 [BibTeX]
    @article{Paz_2018b,
    doi = {10.3390/computation6020027},
    url = {https://doi.org/10.3390%2Fcomputation6020027},
    year = 2018,
    month = {mar},
    publisher = {{MDPI} {AG}},
    volume = {6},
    number = {2},
    pages = {27},
    author = {S. Paz and Cameron Abrams},
    title = {Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers},
    journal = {{Computation}}
    }

  • B. Parajuli, K. Acharya, H. C. Bach, B. Parajuli, S. Zhang, A. B. Smith, C. F. Abrams, and I. Chaiken, “Restricted HIV-1 env glycan engagement by lectin-reengineered DAVEI protein chimera is sufficient for lytic inactivation of the virus," Biochemical Journal, vol. 475, iss. 5, p. 931–957, 2018. doi:10.1042/bcj20170662 PMC5944358 [BibTeX]
    @article{Parajuli_2018,
    doi = {10.1042/bcj20170662},
    pmcid = {PMC5944358},
    url = {https://doi.org/10.1042%2Fbcj20170662},
    year = {2018},
    month = {mar},
    publisher = {Portland Press Ltd.},
    volume = {475},
    number = {5},
    pages = {931--957},
    author = {Bibek Parajuli and Kriti Acharya and Harry C. Bach and Bijay Parajuli and Shiyu Zhang and Amos B. Smith and Cameron F. Abrams and Irwin Chaiken},
    title = {Restricted {HIV}-1 Env glycan engagement by lectin-reengineered {DAVEI} protein chimera is sufficient for lytic inactivation of the virus},
    journal = {{Biochemical Journal}}
    }

  • F. Moraca, D. Rinaldo, A. B. Smith, and C. F. Abrams, “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," ChemMedChem, vol. 13, iss. 6, p. 627–633, 2018. doi:10.1002/cmdc.201700728 PMC5901908 [BibTeX]
    @article{Moraca_2018,
    doi = {10.1002/cmdc.201700728},
    url = {https://doi.org/10.1002%2Fcmdc.201700728},
    year = {2018},
    month = {feb},
    publisher = {Wiley},
    volume = {13},
    number = {6},
    pages = {627--633},
    author = {Francesca Moraca and David Rinaldo and Amos B. Smith and Cameron F. Abrams},
    title = {Specific Noncovalent Interactions Determine Optimal Structure of a Buried Ligand Moiety: {QM}/{MM} and Pure {QM} Modeling of Complexes of the Small-Molecule {CD}4 Mimetics and {HIV}-1 gp120},
    journal = {{ChemMedChem}},
    pmcid = {PMC5901908}
    }

2017

  • J. M. Gardner and C. F. Abrams, “Rate of hemifusion diaphragm dissipation and ability to form three-junction bound HD determined by lipid composition," The Journal of Chemical Physics, vol. 147, iss. 13, p. 134903, 2017. doi:10.1063/1.4994320 [BibTeX]
    @article{Gardner_2017,
    doi = {10.1063/1.4994320},
    url = {https://doi.org/10.1063%2F1.4994320},
    year = 2017,
    month = {oct},
    publisher = {{AIP} Publishing},
    volume = {147},
    number = {13},
    pages = {134903},
    author = {Jasmine M. Gardner and Cameron F. Abrams},
    title = {Rate of hemifusion diaphragm dissipation and ability to form three-junction bound {HD} determined by lipid composition},
    journal = {{The Journal of Chemical Physics}}
    }

  • R. Gordon, S. T. Stober, and C. F. Abrams, “Effects of optical purity and finite system size on self-assembly of 12-hydroxystearic acid in hexane: Molecular dynamics simulations," The Journal of Physical Chemistry B, vol. 121, iss. 39, p. 9223–9233, 2017. doi:10.1021/acs.jpcb.7b05246 [BibTeX]
    @article{Gordon_2017,
    doi = {10.1021/acs.jpcb.7b05246},
    url = {https://doi.org/10.1021%2Facs.jpcb.7b05246},
    year = 2017,
    month = {sep},
    publisher = {American Chemical Society ({ACS})},
    volume = {121},
    number = {39},
    pages = {9223--9233},
    author = {Ryan Gordon and Spencer T. Stober and Cameron F. Abrams},
    title = {Effects of Optical Purity and Finite System Size on Self-Assembly of 12-Hydroxystearic Acid in Hexane: {M}olecular Dynamics Simulations},
    journal = {{The Journal of Physical Chemistry B}}
    }

  • A. Herschhorn, C. Gu, F. Moraca, X. Ma, M. Farrell, A. B. Smith, M. Pancera, P. D. Kwong, A. Schön, E. Freire, C. Abrams, S. C. Blanchard, W. Mothes, and J. G. Sodroski, “The β20-β21 of gp120 is a regulatory switch for HIV-1 env conformational transitions," Nature Communications, vol. 8, iss. 1, 2017. doi:10.1038/s41467-017-01119-w [BibTeX]
    @article{Herschhorn_2017,
    doi = {10.1038/s41467-017-01119-w},
    url = {https://doi.org/10.1038%2Fs41467-017-01119-w},
    year = 2017,
    month = {oct},
    publisher = {Springer Science and Business Media {LLC}},
    volume = {8},
    number = {1},
    author = {Alon Herschhorn and Christopher Gu and Francesca Moraca and Xiaochu Ma and Mark Farrell and Amos B. Smith and Marie Pancera and Peter D. Kwong and Arne Sch{\"o}n and Ernesto Freire and Cameron Abrams and Scott C. Blanchard and Walther Mothes and Joseph G. Sodroski},
    title = {The β20-β21 of gp120 is a regulatory switch for {HIV}-1 Env conformational transitions},
    journal = {{Nature Communications}}
    }

  • K. Acharya, A. A. Rashad, F. Moraca, P. J. Klasse, J. P. Moore, C. Abrams, and I. Chaiken, “Recognition of HIV-inactivating peptide triazoles by the recombinant soluble env trimer, BG505 SOSIP.664," Proteins: Structure, Function, and Bioinformatics, vol. 85, iss. 5, p. 843–851, 2017. doi:10.1002/prot.25238 [BibTeX]
    @article{Acharya_2017,
    doi = {10.1002/prot.25238},
    url = {https://doi.org/10.1002%2Fprot.25238},
    year = 2017,
    month = {mar},
    publisher = {Wiley},
    volume = {85},
    number = {5},
    pages = {843--851},
    author = {Kriti Acharya and Adel A. Rashad and Francesca Moraca and Per Johan Klasse and John P. Moore and Cameron Abrams and Irwin Chaiken},
    title = {Recognition of {HIV}-inactivating peptide triazoles by the recombinant soluble Env trimer, {BG}505 {SOSIP}.664},
    journal = {{Proteins: Structure, Function, and Bioinformatics}}
    }

  • A. S. Sridhar, J. Vergara, G. Palmese, and C. F. Abrams, “The effect of alkyl chain length on material properties of fatty-acid-functionalized amidoamine-epoxy systems," European Polymer Journal, vol. 89, p. 1–12, 2017. doi:10.1016/j.eurpolymj.2017.01.037 [BibTeX]
    @article{Srikanth_2017,
    doi = {10.1016/j.eurpolymj.2017.01.037},
    url = {https://doi.org/10.1016%2Fj.eurpolymj.2017.01.037},
    year = 2017,
    month = {apr},
    publisher = {Elsevier {BV}},
    volume = {89},
    pages = {1--12},
    author = {Arun Srikanth Sridhar and John Vergara and Giuseppe Palmese and Cameron F. Abrams},
    title = {The effect of alkyl chain length on material properties of fatty-acid-functionalized amidoamine-epoxy systems},
    journal = {{European Polymer Journal}}
    }

  • A. S. Paz, E. Vanden-Eijnden, and C. F. Abrams, “Polymorphism at 129 dictates metastable conformations of the human prion protein n-terminal β-sheet," Chemical Science, vol. 8, iss. 2, p. 1225–1232, 2017. doi:10.1039/c6sc03275c PMC5369536 [BibTeX]
    @article{Paz_2017,
    doi = {10.1039/c6sc03275c},
    pmcid = {PMC5369536},
    url = {https://doi.org/10.1039%2Fc6sc03275c},
    year = {2017},
    publisher = {Royal Society of Chemistry ({RSC})},
    volume = {8},
    number = {2},
    pages = {1225--1232},
    author = {S. Alexis Paz and Eric Vanden-Eijnden and Cameron F. Abrams},
    title = {Polymorphism at 129 dictates metastable conformations of the human prion protein N-terminal β-sheet},
    journal = {{Chemical Science}}
    }

2016

  • J. H. Yang, A. Srikanth, C. Jang, and C. F. Abrams, “Relationships between molecular structure and thermomechanical properties of bio-based thermosetting polymers," Journal of Polymer Science Part B: Polymer Physics, vol. 55, iss. 3, p. 285–292, 2016. doi:10.1002/polb.24270 [BibTeX]
    @article{Yang_2016,
    doi = {10.1002/polb.24270},
    url = {https://doi.org/10.1002%2Fpolb.24270},
    year = 2016,
    month = {nov},
    publisher = {Wiley},
    volume = {55},
    number = {3},
    pages = {285--292},
    author = {Jung Ho Yang and Arun Srikanth and Changwoon Jang and Cameron F. Abrams},
    title = {Relationships between molecular structure and thermomechanical properties of bio-based thermosetting polymers},
    journal = {{Journal of Polymer Science Part B: Polymer Physics}}
    }

  • B. Parajuli, K. Acharya, R. Yu, B. Ngo, A. A. Rashad, C. F. Abrams, and I. M. Chaiken, “Lytic inactivation of human immunodeficiency virus by dual engagement of gp120 and gp41 domains in the virus env protein trimer," Biochemistry, vol. 55, iss. 44, p. 6100–6114, 2016. doi:10.1021/acs.biochem.6b00570 PMC5444381 [BibTeX]
    @article{Parajuli_2016,
    doi = {10.1021/acs.biochem.6b00570},
    pmcid = {PMC5444381},
    url = {https://doi.org/10.1021%2Facs.biochem.6b00570},
    year = {2016},
    month = {oct},
    publisher = {American Chemical Society ({ACS})},
    volume = {55},
    number = {44},
    pages = {6100--6114},
    author = {Bibek Parajuli and Kriti Acharya and Reina Yu and Brendon Ngo and Adel A. Rashad and Cameron F. Abrams and Irwin M. Chaiken},
    title = {Lytic Inactivation of Human Immunodeficiency Virus by Dual Engagement of gp120 and gp41 Domains in the Virus Env Protein Trimer},
    journal = {{Biochemistry}}
    }

  • F. Moraca, K. Acharya, B. Melillo, A. B. Smith, I. Chaiken, and C. 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 mimics," Journal of Chemical Information and Modeling, vol. 56, iss. 10, p. 2069–2079, 2016. doi:10.1021/acs.jcim.6b00393 PMC5206489 [BibTeX]
    @article{Moraca_2016,
    doi = {10.1021/acs.jcim.6b00393},
    pmcid = {PMC5206489},
    url = {https://doi.org/10.1021%2Facs.jcim.6b00393},
    year = {2016},
    month = {sep},
    publisher = {American Chemical Society ({ACS})},
    volume = {56},
    number = {10},
    pages = {2069--2079},
    author = {Francesca Moraca and Kriti Acharya and Bruno Melillo and Amos B. Smith and Irwin Chaiken and Cameron F. Abrams},
    title = {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 {CD}4 Mimics},
    journal = {{Journal of Chemical Information and Modeling}}
    }

  • T. Yu, J. Lu, C. F. Abrams, and E. Vanden-Eijnden, “Multiscale implementation of infinite-swap replica exchange molecular dynamics," Proceedings of the National Academy of Sciences, vol. 113, iss. 42, p. 11744–11749, 2016. doi:10.1073/pnas.1605089113 PMC5081654 [BibTeX]
    @article{Yu_2016,
    doi = {10.1073/pnas.1605089113},
    pmcid = {PMC5081654},
    url = {https://doi.org/10.1073%2Fpnas.1605089113},
    year = {2016},
    month = {oct},
    publisher = {Proceedings of the National Academy of Sciences},
    volume = {113},
    number = {42},
    pages = {11744--11749},
    author = {Tang-Qing Yu and Jianfeng Lu and Cameron F. Abrams and Eric Vanden-Eijnden},
    title = {Multiscale implementation of infinite-swap replica exchange molecular dynamics},
    journal = {{Proceedings of the National Academy of Sciences}}
    }

  • C. Jang and C. F. Abrams, “Thermal and mechanical properties of thermosetting polymers using coarse-grained simulation," The European Physical Journal Special Topics, vol. 225, iss. 8-9, p. 1775–1783, 2016. doi:10.1140/epjst/e2016-60143-0 [BibTeX]
    @article{Jang_2016,
    doi = {10.1140/epjst/e2016-60143-0},
    url = {https://doi.org/10.1140%2Fepjst%2Fe2016-60143-0},
    year = 2016,
    month = {jul},
    publisher = {Springer Science and Business Media {LLC}},
    volume = {225},
    number = {8-9},
    pages = {1775--1783},
    author = {C. Jang and C.F. Abrams},
    title = {Thermal and mechanical properties of thermosetting polymers using coarse-grained simulation},
    journal = {{The European Physical Journal Special Topics}}
    }

  • R. Gordon, S. T. Stober, and C. F. Abrams, “Aggregation of 12-hydroxystearic acid and its lithium salt in hexane: Molecular dynamics simulations," The Journal of Physical Chemistry B, vol. 120, iss. 29, p. 7164–7173, 2016. doi:10.1021/acs.jpcb.6b04193 [BibTeX]
    @article{Gordon_2016,
    doi = {10.1021/acs.jpcb.6b04193},
    url = {https://doi.org/10.1021%2Facs.jpcb.6b04193},
    year = 2016,
    month = {jul},
    publisher = {American Chemical Society ({ACS})},
    volume = {120},
    number = {29},
    pages = {7164--7173},
    author = {Ryan Gordon and Spencer T. Stober and Cameron F. Abrams},
    title = {Aggregation of 12-Hydroxystearic Acid and Its Lithium Salt in Hexane: {M}olecular Dynamics Simulations},
    journal = {{The Journal of Physical Chemistry B}}
    }

  • J. M. Gardner, M. Deserno, and C. F. Abrams, “Effect of intrinsic curvature and edge tension on the stability of binary mixed-membrane three-junctions," The Journal of Chemical Physics, vol. 145, iss. 7, p. 74901, 2016. doi:10.1063/1.4960433 [BibTeX]
    @article{Gardner_2016,
    doi = {10.1063/1.4960433},
    url = {https://doi.org/10.1063%2F1.4960433},
    year = 2016,
    month = {aug},
    publisher = {{AIP} Publishing},
    volume = {145},
    number = {7},
    pages = {074901},
    author = {Jasmine M. Gardner and Markus Deserno and Cameron F. Abrams},
    title = {Effect of intrinsic curvature and edge tension on the stability of binary mixed-membrane three-junctions},
    journal = {{The Journal of Chemical Physics}}
    }

  • A. Bucci, T. Yu, E. Vanden-Eijnden, and C. F. Abrams, “Kinetics of o2 entry and exit in monomeric sarcosine oxidase via markovian milestoning molecular dynamics," Journal of Chemical Theory and Computation, vol. 12, iss. 6, p. 2964–2972, 2016. doi:10.1021/acs.jctc.6b00071 PMC5501303 [BibTeX]
    @article{Bucci_2016,
    doi = {10.1021/acs.jctc.6b00071},
    pmcid = {PMC5501303},
    url = {https://doi.org/10.1021%2Facs.jctc.6b00071},
    year = {2016},
    month = {may},
    publisher = {American Chemical Society ({ACS})},
    volume = {12},
    number = {6},
    pages = {2964--2972},
    author = {Anthony Bucci and Tang-Qing Yu and Eric Vanden-Eijnden and Cameron F. Abrams},
    title = {Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics},
    journal = {{Journal of Chemical Theory and Computation}}
    }

  • C. Jang, M. Sharifi, G. R. Palmese, and C. 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, p. 249–255, 2016. doi:10.1016/j.polymer.2016.03.023 [BibTeX]
    @article{Jang_2016b,
    doi = {10.1016/j.polymer.2016.03.023},
    url = {https://doi.org/10.1016%2Fj.polymer.2016.03.023},
    year = 2016,
    month = {may},
    publisher = {Elsevier {BV}},
    volume = {90},
    pages = {249--255},
    author = {Changwoon Jang and Majid Sharifi and Giuseppe R. Palmese and Cameron F. Abrams},
    title = {Toughness enhancement of thermosetting polymers using a novel partially reacted substructure curing protocol: {A} combined molecular simulation and experimental study},
    journal = {{Polymer}}
    }

  • R. V. K. Sundaram, H. Li, L. Bailey, A. A. Rashad, R. Aneja, K. Weiss, J. Huynh, A. R. Bastian, E. Papazoglou, C. Abrams, S. Wrenn, and I. Chaiken, “Impact of HIV-1 membrane cholesterol on cell-independent lytic inactivation and cellular infectivity," Biochemistry, vol. 55, iss. 3, p. 447–458, 2016. doi:10.1021/acs.biochem.5b00936 [BibTeX]
    @article{Kalyana_Sundaram_2016,
    doi = {10.1021/acs.biochem.5b00936},
    url = {https://doi.org/10.1021%2Facs.biochem.5b00936},
    year = 2016,
    month = {jan},
    publisher = {American Chemical Society ({ACS})},
    volume = {55},
    number = {3},
    pages = {447--458},
    author = {Ramalingam Venkat Kalyana Sundaram and Huiyuan Li and Lauren Bailey and Adel A. Rashad and Rachna Aneja and Karl Weiss and James Huynh and Arangaserry Rosemary Bastian and Elisabeth Papazoglou and Cameron Abrams and Steven Wrenn and Irwin Chaiken},
    title = {Impact of {HIV}-1 Membrane Cholesterol on Cell-Independent Lytic Inactivation and Cellular Infectivity},
    journal = {{Biochemistry}}
    }

2015

  • M. Sharifi, C. Jang, C. F. Abrams, and G. R. Palmese, “Epoxy polymer networks with improved thermal and mechanical properties via controlled dispersion of reactive toughening agents," Macromolecules, vol. 48, iss. 20, p. 7495–7502, 2015. doi:10.1021/acs.macromol.5b00677 [BibTeX]
    @article{Sharifi_2015,
    doi = {10.1021/acs.macromol.5b00677},
    url = {https://doi.org/10.1021%2Facs.macromol.5b00677},
    year = 2015,
    month = {oct},
    publisher = {American Chemical Society ({ACS})},
    volume = {48},
    number = {20},
    pages = {7495--7502},
    author = {Majid Sharifi and Changwoon Jang and Cameron F. Abrams and Giuseppe R. Palmese},
    title = {Epoxy Polymer Networks with Improved Thermal and Mechanical Properties via Controlled Dispersion of Reactive Toughening Agents},
    journal = {{Macromolecules}}
    }

  • A. S. Paz and C. F. Abrams, “Free energy and hidden barriers of the β-sheet structure of prion protein," Journal of Chemical Theory and Computation, vol. 11, iss. 10, p. 5024–5034, 2015. doi:10.1021/acs.jctc.5b00576 [BibTeX]
    @article{Paz_2015,
    doi = {10.1021/acs.jctc.5b00576},
    url = {https://doi.org/10.1021%2Facs.jctc.5b00576},
    year = 2015,
    month = {sep},
    publisher = {American Chemical Society ({ACS})},
    volume = {11},
    number = {10},
    pages = {5024--5034},
    author = {S. Alexis Paz and Cameron F. Abrams},
    title = {Free Energy and Hidden Barriers of the β-Sheet Structure of Prion Protein},
    journal = {{Journal of Chemical Theory and Computation}}
    }

  • T. Yu, M. Lapelosa, E. Vanden-Eijnden, and C. F. Abrams, “Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations," Journal of the American Chemical Society, vol. 137, iss. 8, p. 3041–3050, 2015. doi:10.1021/ja512484q [BibTeX]
    @article{Yu_2015,
    doi = {10.1021/ja512484q},
    url = {https://doi.org/10.1021%2Fja512484q},
    year = 2015,
    month = {feb},
    publisher = {American Chemical Society ({ACS})},
    volume = {137},
    number = {8},
    pages = {3041--3050},
    author = {Tang-Qing Yu and Mauro Lapelosa and Eric Vanden-Eijnden and Cameron F. Abrams},
    title = {Full Kinetics of {CO} Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations},
    journal = {{Journal of the American Chemical Society}}
    }

  • C. Jang, T. W. Sirk, J. W. Andzelm, and C. F. Abrams, “Comparison of crosslinking algorithms in molecular dynamics simulation of thermosetting polymers," Macromolecular Theory and Simulations, vol. 24, iss. 3, p. 260–270, 2015. doi:10.1002/mats.201400094 [BibTeX]
    @article{Jang_2015,
    doi = {10.1002/mats.201400094},
    url = {https://doi.org/10.1002%2Fmats.201400094},
    year = 2015,
    month = {jan},
    publisher = {Wiley},
    volume = {24},
    number = {3},
    pages = {260--270},
    author = {Changwoon Jang and Timothy W. Sirk and Jan W. Andzelm and Cameron F. Abrams},
    title = {Comparison of Crosslinking Algorithms in Molecular Dynamics Simulation of Thermosetting Polymers},
    journal = {{Macromolecular Theory and Simulations}}
    }

2014

  • A. R. Bastian, A. Nangarlia, L. D. Bailey, A. Holmes, V. K. R. Sundaram, C. Ang, D. R. M. Moreira, K. Freedman, C. Duffy, M. Contarino, C. Abrams, M. Root, and I. Chaiken, “Mechanism of multivalent nanoparticle encounter with HIV-1 for potency enhancement of peptide triazole virus inactivation," Journal of Biological Chemistry, vol. 290, iss. 1, p. 529–543, 2014. doi:10.1074/jbc.m114.608315 [BibTeX]
    @article{Rosemary_Bastian_2014,
    doi = {10.1074/jbc.m114.608315},
    url = {https://doi.org/10.1074%2Fjbc.m114.608315},
    year = 2014,
    month = {nov},
    publisher = {American Society for Biochemistry {\&} Molecular Biology ({ASBMB})},
    volume = {290},
    number = {1},
    pages = {529--543},
    author = {Arangassery Rosemary Bastian and Aakansha Nangarlia and Lauren D. Bailey and Andrew Holmes and R. Venkat Kalyana Sundaram and Charles Ang and Diogo R. M. Moreira and Kevin Freedman and Caitlin Duffy and Mark Contarino and Cameron Abrams and Michael Root and Irwin Chaiken},
    title = {Mechanism of Multivalent Nanoparticle Encounter with {HIV}-1 for Potency Enhancement of Peptide Triazole Virus Inactivation},
    journal = {{Journal of Biological Chemistry}}
    }

  • M. K. Baker and C. F. Abrams, “Dynamics of lipids, cholesterol, and transmembrane α-helices from microsecond molecular dynamics simulations," The Journal of Physical Chemistry B, vol. 118, iss. 47, p. 13590–13600, 2014. doi:10.1021/jp507027t [BibTeX]
    @article{Baker_2014b,
    doi = {10.1021/jp507027t},
    url = {https://doi.org/10.1021%2Fjp507027t},
    year = 2014,
    month = {nov},
    publisher = {American Chemical Society ({ACS})},
    volume = {118},
    number = {47},
    pages = {13590--13600},
    author = {Michelle K. Baker and Cameron F. Abrams},
    title = {Dynamics of Lipids, Cholesterol, and Transmembrane α-Helices from Microsecond Molecular Dynamics Simulations},
    journal = {{The Journal of Physical Chemistry B}}
    }

  • M. Sharifi, C. W. Jang, C. F. Abrams, and G. R. Palmese, “Toughened epoxy polymers via rearrangement of network topology," Journal of Materials Chemistry A, vol. 2, iss. 38, p. 16071–16082, 2014. doi:10.1039/c4ta03051f [BibTeX]
    @article{Sharifi_2014,
    doi = {10.1039/c4ta03051f},
    url = {https://doi.org/10.1039%2Fc4ta03051f},
    year = 2014,
    publisher = {Royal Society of Chemistry ({RSC})},
    volume = {2},
    number = {38},
    pages = {16071--16082},
    author = {M. Sharifi and C. W. Jang and C. F. Abrams and G. R. Palmese},
    title = {Toughened epoxy polymers via rearrangement of network topology},
    journal = {{Journal of Materials Chemistry A}}
    }

  • C. Jang, M. Sharifi, G. R. Palmese, and C. F. Abrams, “Crosslink network rearrangement via reactive encapsulation of solvent in epoxy curing: A combined molecular simulation and experimental study," Polymer, vol. 55, iss. 16, p. 3859–3868, 2014. doi:10.1016/j.polymer.2014.06.022 [BibTeX]
    @article{Jang_2014,
    doi = {10.1016/j.polymer.2014.06.022},
    url = {https://doi.org/10.1016%2Fj.polymer.2014.06.022},
    year = 2014,
    month = {aug},
    publisher = {Elsevier {BV}},
    volume = {55},
    number = {16},
    pages = {3859--3868},
    author = {Changwoon Jang and Majid Sharifi and Giuseppe R. Palmese and Cameron F. Abrams},
    title = {Crosslink network rearrangement via reactive encapsulation of solvent in epoxy curing: {A} combined molecular simulation and experimental study},
    journal = {{Polymer}}
    }

  • A. Emileh, C. Duffy, A. P. Holmes, A. R. Bastian, R. Aneja, F. Tuzer, S. Rajagopal, H. Li, C. F. Abrams, and I. M. Chaiken, “Covalent conjugation of a peptide triazole to HIV-1 gp120 enables intramolecular binding site occupancy," Biochemistry, vol. 53, iss. 21, p. 3403–3414, 2014. doi:10.1021/bi500136f [BibTeX]
    @article{Emileh_2014,
    doi = {10.1021/bi500136f},
    url = {https://doi.org/10.1021%2Fbi500136f},
    year = 2014,
    month = {may},
    publisher = {American Chemical Society ({ACS})},
    volume = {53},
    number = {21},
    pages = {3403--3414},
    author = {Ali Emileh and Caitlin Duffy and Andrew P. Holmes and Arangassery Rosemary Bastian and Rachna Aneja and Ferit Tuzer and Srivats Rajagopal and Huiyuan Li and Cameron F. Abrams and Irwin M. Chaiken},
    title = {Covalent Conjugation of a Peptide Triazole to {HIV}-1 gp120 Enables Intramolecular Binding Site Occupancy},
    journal = {{Biochemistry}}
    }

  • A. Bucci and C. F. Abrams, “Oxygen pathways and allostery in monomeric sarcosine oxidase via single-sweep free-energy reconstruction," Journal of Chemical Theory and Computation, vol. 10, iss. 7, p. 2668–2676, 2014. doi:10.1021/ct500088z [BibTeX]
    @article{Bucci_2014,
    doi = {10.1021/ct500088z},
    url = {https://doi.org/10.1021%2Fct500088z},
    year = 2014,
    month = {apr},
    publisher = {American Chemical Society ({ACS})},
    volume = {10},
    number = {7},
    pages = {2668--2676},
    author = {Anthony Bucci and Cameron F. Abrams},
    title = {Oxygen Pathways and Allostery in Monomeric Sarcosine Oxidase via Single-Sweep Free-Energy Reconstruction},
    journal = {{Journal of Chemical Theory and Computation}}
    }

  • M. K. Baker, V. K. Gangupomu, and C. F. Abrams, “Characterization of the water defect at the HIV-1 gp41 membrane spanning domain in bilayers with and without cholesterol using molecular simulations," Biochimica et Biophysica Acta (BBA) – Biomembranes, vol. 1838, iss. 5, p. 1396–1405, 2014. doi:10.1016/j.bbamem.2014.01.009 [BibTeX]
    @article{Baker_2014,
    doi = {10.1016/j.bbamem.2014.01.009},
    url = {https://doi.org/10.1016%2Fj.bbamem.2014.01.009},
    year = 2014,
    month = {may},
    publisher = {Elsevier {BV}},
    volume = {1838},
    number = {5},
    pages = {1396--1405},
    author = {Michelle K. Baker and Vamshi K. Gangupomu and Cameron F. Abrams},
    title = {Characterization of the water defect at the {HIV}-1 gp41 membrane spanning domain in bilayers with and without cholesterol using molecular simulations},
    journal = {{Biochimica et Biophysica Acta ({BBA}) - Biomembranes}}
    }

2013

  • C. Abrams and G. Bussi, “Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration," Entropy, vol. 16, iss. 1, p. 163–199, 2013. doi:10.3390/e16010163 [BibTeX]
    @article{Abrams_2013,
    doi = {10.3390/e16010163},
    url = {https://doi.org/10.3390%2Fe16010163},
    year = 2013,
    month = {dec},
    publisher = {{MDPI} {AG}},
    volume = {16},
    number = {1},
    pages = {163--199},
    author = {Cameron Abrams and Giovanni Bussi},
    title = {Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration},
    journal = {{Entropy}}
    }

  • M. Contarino, A. R. Bastian, R. V. K. Sundaram, K. McFadden, C. Duffy, V. Gangupomu, M. Baker, C. Abrams, and I. Chaiken, “Chimeric cyanovirin-MPER recombinantly engineered proteins cause cell-free virolysis of HIV-1," Antimicrobial Agents and Chemotherapy, vol. 57, iss. 10, p. 4743–4750, 2013. doi:10.1128/aac.00309-13 [BibTeX]
    @article{Contarino_2013,
    doi = {10.1128/aac.00309-13},
    url = {https://doi.org/10.1128%2Faac.00309-13},
    year = 2013,
    month = {jul},
    publisher = {American Society for Microbiology},
    volume = {57},
    number = {10},
    pages = {4743--4750},
    author = {Mark Contarino and Arangassery R. Bastian and Ramalingam Venkat Kalyana Sundaram and Karyn McFadden and Caitlin Duffy and Vamshi Gangupomu and Michelle Baker and Cameron Abrams and Irwin Chaiken},
    title = {Chimeric Cyanovirin-{MPER} Recombinantly Engineered Proteins Cause Cell-Free Virolysis of {HIV}-1},
    journal = {{Antimicrobial Agents and Chemotherapy}}
    }

  • M. Lapelosa and C. F. Abrams, “Transition-path theory calculations on non-uniform meshes in two and three dimensions using finite elements," Computer Physics Communications, vol. 184, iss. 10, p. 2310–2315, 2013. doi:10.1016/j.cpc.2013.05.017 [BibTeX]
    @article{Lapelosa_2013,
    doi = {10.1016/j.cpc.2013.05.017},
    url = {https://doi.org/10.1016%2Fj.cpc.2013.05.017},
    year = 2013,
    month = {oct},
    publisher = {Elsevier {BV}},
    volume = {184},
    number = {10},
    pages = {2310--2315},
    author = {Mauro Lapelosa and Cameron F. Abrams},
    title = {Transition-path theory calculations on non-uniform meshes in two and three dimensions using finite elements},
    journal = {{Computer Physics Communications}}
    }

  • H. Vashisth and C. F. Abrams, “All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element," Proteins: Structure, Function, and Bioinformatics, vol. 81, iss. 6, p. 1017–1030, 2013. doi:10.1002/prot.24255 [BibTeX]
    @article{Vashisth_2013,
    doi = {10.1002/prot.24255},
    url = {https://doi.org/10.1002%2Fprot.24255},
    year = 2013,
    month = {feb},
    publisher = {Wiley},
    volume = {81},
    number = {6},
    pages = {1017--1030},
    author = {Harish Vashisth and Cameron F. Abrams},
    title = {All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element},
    journal = {{Proteins: Structure, Function, and Bioinformatics}}
    }

  • A. Emileh, F. Tuzer, H. Yeh, M. Umashankara, D. R. M. Moreira, J. M. LaLonde, C. A. Bewley, C. F. Abrams, and I. M. Chaiken, “A model of peptide triazole entry inhibitor binding to HIV-1 gp120 and the mechanism of bridging sheet disruption," Biochemistry, vol. 52, iss. 13, p. 2245–2261, 2013. doi:10.1021/bi400166b [BibTeX]
    @article{Emileh_2013,
    doi = {10.1021/bi400166b},
    url = {https://doi.org/10.1021%2Fbi400166b},
    year = 2013,
    month = {mar},
    publisher = {American Chemical Society ({ACS})},
    volume = {52},
    number = {13},
    pages = {2245--2261},
    author = {Ali Emileh and Ferit Tuzer and Herman Yeh and Muddegowda Umashankara and Diogo R. M. Moreira and Judith M. LaLonde and Carole A. Bewley and Cameron F. Abrams and Irwin M. Chaiken},
    title = {A Model of Peptide Triazole Entry Inhibitor Binding to {HIV}-1 gp120 and the Mechanism of Bridging Sheet Disruption},
    journal = {{Biochemistry}}
    }

  • M. Lapelosa and C. F. Abrams, “A computational study of water and CO migration sites and channels inside myoglobin," Journal of Chemical Theory and Computation, vol. 9, iss. 2, p. 1265–1271, 2013. doi:10.1021/ct300862j [BibTeX]
    @article{Lapelosa_2013b,
    doi = {10.1021/ct300862j},
    url = {https://doi.org/10.1021%2Fct300862j},
    year = 2013,
    month = {jan},
    publisher = {American Chemical Society ({ACS})},
    volume = {9},
    number = {2},
    pages = {1265--1271},
    author = {Mauro Lapelosa and Cameron F. Abrams},
    title = {A Computational Study of Water and {CO} Migration Sites and Channels Inside Myoglobin},
    journal = {{Journal of Chemical Theory and Computation}}
    }

2012

  • C. F. Abrams and E. Vanden-Eijnden, “On-the-fly free energy parameterization via temperature accelerated molecular dynamics," Chemical Physics Letters, vol. 547, p. 114–119, 2012. doi:10.1016/j.cplett.2012.07.064 [BibTeX]
    @article{Abrams_2012,
    doi = {10.1016/j.cplett.2012.07.064},
    url = {https://doi.org/10.1016%2Fj.cplett.2012.07.064},
    year = 2012,
    month = {sep},
    publisher = {Elsevier {BV}},
    volume = {547},
    pages = {114--119},
    author = {Cameron F. Abrams and Eric Vanden-Eijnden},
    title = {On-the-fly free energy parameterization via temperature accelerated molecular dynamics},
    journal = {{Chemical Physics Letters}}
    }

  • S. T. Stober and C. F. Abrams, “Energetics and mechanism of the normal-to-amyloidogenic isomerization of β2-microglobulin: On-the-fly string method calculations," The Journal of Physical Chemistry B, vol. 116, iss. 31, p. 9371–9375, 2012. doi:10.1021/jp304805v PMC3437544 [BibTeX]
    @article{Stober_2012,
    doi = {10.1021/jp304805v},
    url = {https://doi.org/10.1021%2Fjp304805v},
    year = 2012,
    month = {jul},
    publisher = {American Chemical Society ({ACS})},
    volume = {116},
    number = {31},
    pages = {9371--9375},
    author = {Spencer T. Stober and Cameron F. Abrams},
    title = {Energetics and Mechanism of the Normal-to-Amyloidogenic Isomerization of β2-Microglobulin: {O}n-the-Fly String Method Calculations},
    journal = {{The Journal of Physical Chemistry B}},
    pmcid = {PMC3437544}
    }

  • H. Vashisth, L. Maragliano, and C. Abrams, “DFG-flip in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop," Biophysical Journal, vol. 102, iss. 8, p. 1979–1987, 2012. doi:10.1016/j.bpj.2012.03.031 [BibTeX]
    @article{Vashisth_2012,
    doi = {10.1016/j.bpj.2012.03.031},
    url = {https://doi.org/10.1016%2Fj.bpj.2012.03.031},
    year = 2012,
    month = {apr},
    publisher = {Elsevier {BV}},
    volume = {102},
    number = {8},
    pages = {1979--1987},
    author = {Harish Vashisth and Luca Maragliano and Cameron~F. Abrams},
    title = {{DFG}-Flip in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop},
    journal = {{Biophysical Journal}}
    }

  • M. Zhang, C. Abrams, L. Wang, A. Gizzi, L. He, R. Lin, Y. Chen, P. Loll, J. Pascal, and J. Zhang, “Structural basis for calmodulin as a dynamic calcium sensor," Structure, vol. 20, iss. 5, p. 911–923, 2012. doi:10.1016/j.str.2012.03.019 [BibTeX]
    @article{Zhang_2012,
    doi = {10.1016/j.str.2012.03.019},
    url = {https://doi.org/10.1016%2Fj.str.2012.03.019},
    year = 2012,
    month = {may},
    publisher = {Elsevier {BV}},
    volume = {20},
    number = {5},
    pages = {911--923},
    author = {Miao Zhang and Cameron Abrams and Liping Wang and Anthony Gizzi and Liping He and Ruihe Lin and Yuan Chen and Patrick~J. Loll and John~M. Pascal and Ji-fang Zhang},
    title = {Structural Basis for Calmodulin as a Dynamic Calcium Sensor},
    journal = {{Structure}}
    }

  • S. T. Stober and C. F. Abrams, “Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors," Protein Science, vol. 21, iss. 3, p. 307–317, 2012. doi:10.1002/pro.2016 [BibTeX]
    @article{Stober_2012b,
    doi = {10.1002/pro.2016},
    url = {https://doi.org/10.1002%2Fpro.2016},
    year = 2012,
    month = {jan},
    publisher = {Wiley},
    volume = {21},
    number = {3},
    pages = {307--317},
    author = {Spencer T. Stober and Cameron F. Abrams},
    title = {Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors},
    journal = {{Protein Science}}
    }

2011

  • A. Emileh and C. 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: Structure, Function, and Bioinformatics, vol. 79, iss. 2, p. 537–546, 2011. doi:10.1002/prot.22901 [BibTeX]
    @article{Emileh_2011,
    doi = {10.1002/prot.22901},
    url = {https://doi.org/10.1002%2Fprot.22901},
    year = 2011,
    month = {nov},
    publisher = {Wiley},
    volume = {79},
    number = {2},
    pages = {537--546},
    author = {Ali Emileh and Cameron F. Abrams},
    title = {A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered {HIV}-1 gp120},
    journal = {{Proteins: Structure, Function, and Bioinformatics}}
    }

2010

  • V. K. Gangupomu and C. F. Abrams, “All-atom models of the membrane-spanning domain of HIV-1 gp41 from~metadynamics," Biophysical Journal, vol. 99, iss. 10, p. 3438–3444, 2010. doi:10.1016/j.bpj.2010.09.054 [BibTeX]
    @article{Gangupomu_2010,
    doi = {10.1016/j.bpj.2010.09.054},
    url = {https://doi.org/10.1016%2Fj.bpj.2010.09.054},
    year = 2010,
    month = {nov},
    publisher = {Elsevier {BV}},
    volume = {99},
    number = {10},
    pages = {3438--3444},
    author = {Vamshi K. Gangupomu and Cameron F. Abrams},
    title = {All-Atom Models of the Membrane-Spanning Domain of {HIV}-1 gp41 from~Metadynamics},
    journal = {{Biophysical Journal}}
    }

  • H. Vashisth and C. F. Abrams, “All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor," Journal of Molecular Biology, vol. 400, iss. 3, p. 645–658, 2010. doi:10.1016/j.jmb.2010.05.025 [BibTeX]
    @article{Vashisth_2010,
    doi = {10.1016/j.jmb.2010.05.025},
    url = {https://doi.org/10.1016%2Fj.jmb.2010.05.025},
    year = 2010,
    month = {jul},
    publisher = {Elsevier {BV}},
    volume = {400},
    number = {3},
    pages = {645--658},
    author = {Harish Vashisth and Cameron F. Abrams},
    title = {All-Atom Structural Models for Complexes of Insulin-Like Growth Factors {IGF}1 and {IGF}2 with Their Cognate Receptor},
    journal = {{Journal of Molecular Biology}}
    }

  • D. Mukherji and C. F. Abrams, “Slip-stick fracture and toughness enhancement in thermoset/thermoplastic polymer alloys under shear," EPL (Europhysics Letters), vol. 90, iss. 2, p. 26003, 2010. doi:10.1209/0295-5075/90/26003 [BibTeX]
    @article{Mukherji_2010,
    doi = {10.1209/0295-5075/90/26003},
    url = {https://doi.org/10.1209%2F0295-5075%2F90%2F26003},
    year = 2010,
    month = {apr},
    publisher = {{IOP} Publishing},
    volume = {90},
    number = {2},
    pages = {26003},
    author = {Debashish Mukherji and Cameron F. Abrams},
    title = {Slip-stick fracture and toughness enhancement in thermoset/thermoplastic polymer alloys under shear},
    journal = {{{EPL} (Europhysics Letters)}}
    }

  • N. C. Karayiannis, K. Foteinopoulou, C. F. Abrams, and M. Laso, “Modeling of crystal nucleation and growth in athermal polymers: Self-assembly of layered nano-morphologies," Soft Matter, vol. 6, iss. 10, p. 2160, 2010. doi:10.1039/b923369e [BibTeX]
    @article{Karayiannis_2010,
    doi = {10.1039/b923369e},
    url = {https://doi.org/10.1039%2Fb923369e},
    year = 2010,
    publisher = {Royal Society of Chemistry ({RSC})},
    volume = {6},
    number = {10},
    pages = {2160},
    author = {Nikos Ch. Karayiannis and Katerina Foteinopoulou and Cameron F. Abrams and Manuel Laso},
    title = {Modeling of crystal nucleation and growth in athermal polymers: {S}elf-assembly of layered nano-morphologies},
    journal = {{Soft Matter}}
    }

  • C. F. Abrams and E. Vanden-Eijnden, “Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics," Proceedings of the National Academy of Sciences, vol. 107, iss. 11, p. 4961–4966, 2010. doi:10.1073/pnas.0914540107 [BibTeX]
    @article{Abrams_2010,
    doi = {10.1073/pnas.0914540107},
    url = {https://doi.org/10.1073%2Fpnas.0914540107},
    year = 2010,
    month = {mar},
    publisher = {Proceedings of the National Academy of Sciences},
    volume = {107},
    number = {11},
    pages = {4961--4966},
    author = {C. F. Abrams and E. Vanden-Eijnden},
    title = {Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics},
    journal = {{Proceedings of the National Academy of Sciences}}
    }

  • H. L. Nyce, S. T. Stober, C. F. Abrams, and M. M. White, “Mapping spatial relationships between residues in the ligand-binding domain of the 5-HT3 receptor using a molecular ruler," Biophysical Journal, vol. 98, iss. 9, p. 1847–1855, 2010. doi:10.1016/j.bpj.2010.01.034 [BibTeX]
    @article{Nyce_2010,
    doi = {10.1016/j.bpj.2010.01.034},
    url = {https://doi.org/10.1016%2Fj.bpj.2010.01.034},
    year = 2010,
    month = {may},
    publisher = {Elsevier {BV}},
    volume = {98},
    number = {9},
    pages = {1847--1855},
    author = {Heather L. Nyce and Spencer T. Stober and Cameron F. Abrams and Michael M. White},
    title = {Mapping Spatial Relationships between Residues in the Ligand-Binding Domain of the 5-{HT}3 Receptor Using a Molecular Ruler},
    journal = {{Biophysical Journal}}
    }

  • H. Vashisth and C. F. Abrams, “Docking of insulin to a structurally equilibrated insulin receptor ectodomain," Proteins: Structure, Function, and Bioinformatics, p. NA–NA, 2010. doi:10.1002/prot.22670 [BibTeX]
    @article{Vashisth_2010b,
    doi = {10.1002/prot.22670},
    url = {https://doi.org/10.1002%2Fprot.22670},
    year = 2010,
    publisher = {Wiley},
    pages = {NA--NA},
    author = {Harish Vashisth and Cameron F. Abrams},
    title = {Docking of insulin to a structurally equilibrated insulin receptor ectodomain},
    journal = {{Proteins: Structure, Function, and Bioinformatics}}
    }

2009

  • D. Mukherji and C. F. Abrams, “Mechanical behavior of highly cross-linked polymer networks and its links to microscopic structure," Physical Review E, vol. 79, iss. 6, 2009. doi:10.1103/physreve.79.061802 [BibTeX]
    @article{Mukherji_2009,
    doi = {10.1103/physreve.79.061802},
    url = {https://doi.org/10.1103%2Fphysreve.79.061802},
    year = 2009,
    month = {jun},
    publisher = {American Physical Society ({APS})},
    volume = {79},
    number = {6},
    author = {Debashish Mukherji and Cameron F. Abrams},
    title = {Mechanical behavior of highly cross-linked polymer networks and its links to microscopic structure},
    journal = {{Physical Review E}}
    }

  • D. Mukherji and C. F. Abrams, “Anomalous ductility in thermoset/thermoplastic polymer alloys," Physical Chemistry Chemical Physics, vol. 11, iss. 12, p. 2113, 2009. doi:10.1039/b818039c [BibTeX]
    @article{Mukherji_2009b,
    doi = {10.1039/b818039c},
    url = {https://doi.org/10.1039%2Fb818039c},
    year = 2009,
    publisher = {Royal Society of Chemistry ({RSC})},
    volume = {11},
    number = {12},
    pages = {2113},
    author = {Debashish Mukherji and Cameron F. Abrams},
    title = {Anomalous ductility in thermoset/thermoplastic polymer alloys},
    journal = {{Physical Chemistry Chemical Physics}}
    }

  • D. Mukherji and C. F. Abrams, “Anomalous ductility in thermoset/thermoplastic polymer alloys: An explanation based on overlap concentration and cavity growth," EPL (europhysics letters), vol. 88, iss. 5, p. 56001, 2009. doi:10.1209/0295-5075/88/56001 [BibTeX]
    @article{Mukherji_2009c,
    doi = {10.1209/0295-5075/88/56001},
    url = {https://doi.org/10.1209%2F0295-5075%2F88%2F56001},
    year = 2009,
    month = {dec},
    publisher = {{IOP} Publishing},
    volume = {88},
    number = {5},
    pages = {56001},
    author = {Debashish Mukherji and Cameron F. Abrams},
    title = {Anomalous ductility in thermoset/thermoplastic polymer alloys: {A}n explanation based on overlap concentration and cavity growth},
    journal = {{EPL} (Europhysics Letters)}
    }

2008

  • D. Mukherji and C. F. Abrams, “Microvoid formation and strain hardening in highly cross-linked polymer networks," Physical Review E, vol. 78, iss. 5, p. 050801(R), 2008. doi:10.1103/physreve.78.050801 [BibTeX]
    @article{Mukherji_2008,
    doi = {10.1103/physreve.78.050801},
    url = {https://doi.org/10.1103%2Fphysreve.78.050801},
    year = 2008,
    month = {nov},
    publisher = {American Physical Society ({APS})},
    volume = {78},
    number = {5},
    pages = {050801(R)},
    author = {Debashish Mukherji and Cameron F. Abrams},
    title = {Microvoid formation and strain hardening in highly cross-linked polymer networks},
    journal = {{Physical Review E}}
    }

  • H. Vashisth and C. F. Abrams, “Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex," Biophysical Journal, vol. 95, iss. 9, p. 4193–4204, 2008. doi:10.1529/biophysj.108.139675 [BibTeX]
    @article{Vashisth_2008,
    doi = {10.1529/biophysj.108.139675},
    url = {https://doi.org/10.1529%2Fbiophysj.108.139675},
    year = 2008,
    month = {nov},
    publisher = {Elsevier {BV}},
    volume = {95},
    number = {9},
    pages = {4193--4204},
    author = {Harish Vashisth and Cameron F. Abrams},
    title = {Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex},
    journal = {{Biophysical Journal}}
    }

2007

  • Y. Sliozberg and C. F. Abrams, “Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations," Biophysical Journal, vol. 93, iss. 6, p. 1906–1916, 2007. doi:10.1529/biophysj.107.108043 [BibTeX]
    @article{Sliozberg_2007,
    doi = {10.1529/biophysj.107.108043},
    url = {https://doi.org/10.1529%2Fbiophysj.107.108043},
    year = 2007,
    month = {sep},
    publisher = {Elsevier {BV}},
    volume = {93},
    number = {6},
    pages = {1906--1916},
    author = {Yelena Sliozberg and Cameron F. Abrams},
    title = {Spontaneous Conformational Changes in the {E}. coli {GroEL} Subunit from All-Atom Molecular Dynamics Simulations},
    journal = {{Biophysical Journal}}
    }

  • E. Jabbarzadeh and C. F. Abrams, “Strategies to enhance capillary formation inside biomaterials: A computational study," Tissue Engineering, vol. 13, iss. 8, p. 2073–2086, 2007. doi:10.1089/ten.2006.0057 [BibTeX]
    @article{Jabbarzadeh_2007,
    doi = {10.1089/ten.2006.0057},
    url = {https://doi.org/10.1089%2Ften.2006.0057},
    year = 2007,
    month = {aug},
    publisher = {Mary Ann Liebert Inc},
    volume = {13},
    number = {8},
    pages = {2073--2086},
    author = {Ehsan Jabbarzadeh and Cameron F. Abrams},
    title = {Strategies to Enhance Capillary Formation Inside Biomaterials: {A} Computational Study},
    journal = {{Tissue Engineering}}
    }

  • D. G. Richardson and C. F. Abrams, “The effects of nanotube fillers on craze formation in simulated glassy polymers under tensile load," Molecular Simulation, vol. 33, iss. 4-5, p. 421–427, 2007. doi:10.1080/08927020601154637 [BibTeX]
    @article{Richardson_2007,
    doi = {10.1080/08927020601154637},
    url = {https://doi.org/10.1080%2F08927020601154637},
    year = 2007,
    month = {apr},
    publisher = {Informa {UK} Limited},
    volume = {33},
    number = {4-5},
    pages = {421--427},
    author = {D. G. Richardson and C. F. Abrams},
    title = {The effects of nanotube fillers on craze formation in simulated glassy polymers under tensile load},
    journal = {{Molecular Simulation}}
    }

  • E. Jabbarzadeh and C. F. Abrams, “Simulations of chemotaxis and random motility in 2D random porous domains," Bulletin of Mathematical Biology, vol. 69, iss. 2, p. 747–764, 2007. doi:10.1007/s11538-006-9153-1 [BibTeX]
    @article{Jabbarzadeh_2007b,
    doi = {10.1007/s11538-006-9153-1},
    url = {https://doi.org/10.1007%2Fs11538-006-9153-1},
    year = 2007,
    month = {jan},
    publisher = {Springer Science and Business Media {LLC}},
    volume = {69},
    number = {2},
    pages = {747--764},
    author = {Ehsan Jabbarzadeh and Cameron F. Abrams},
    title = {Simulations of Chemotaxis and Random Motility in 2{D} Random Porous Domains},
    journal = {{Bulletin of Mathematical Biology}}
    }

2006

  • C. F. Abrams, N. Lee, and A. Johner, “Diffusion/reaction in confined polymer chains," Macromolecules, vol. 39, iss. 10, p. 3655–3663, 2006. doi:10.1021/ma060044d [BibTeX]
    @article{Abrams_2006,
    doi = {10.1021/ma060044d},
    url = {https://doi.org/10.1021%2Fma060044d},
    year = 2006,
    month = {may},
    publisher = {American Chemical Society ({ACS})},
    volume = {39},
    number = {10},
    pages = {3655--3663},
    author = {Cameron F. Abrams and Nam-Kyung Lee and A. Johner},
    title = {Diffusion/Reaction in Confined Polymer Chains},
    journal = {{Macromolecules}}
    }

  • D. G. Richardson and C. F. Abrams, “Polymer chain winding in the melt," Macromolecules, vol. 39, iss. 6, p. 2330–2339, 2006. doi:10.1021/ma051985d [BibTeX]
    @article{Richardson_2006,
    doi = {10.1021/ma051985d},
    url = {https://doi.org/10.1021%2Fma051985d},
    year = 2006,
    month = {mar},
    publisher = {American Chemical Society ({ACS})},
    volume = {39},
    number = {6},
    pages = {2330--2339},
    author = {David G. Richardson and Cameron F. Abrams},
    title = {Polymer Chain Winding in the Melt},
    journal = {{Macromolecules}}
    }

2005

  • N. K. Lee, C. F. Abrams, and A. Johner, “Optimal confinement for internal polymer binding," Europhysics Letters (EPL), vol. 72, iss. 6, p. 922–928, 2005. doi:10.1209/epl/i2005-10328-3 [BibTeX]
    @article{Lee_2005,
    doi = {10.1209/epl/i2005-10328-3},
    url = {https://doi.org/10.1209%2Fepl%2Fi2005-10328-3},
    year = 2005,
    month = {dec},
    publisher = {{IOP} Publishing},
    volume = {72},
    number = {6},
    pages = {922--928},
    author = {N. K Lee and C. F Abrams and A Johner},
    title = {Optimal confinement for internal polymer binding},
    journal = {{Europhysics Letters ({EPL})}}
    }

  • C. F. Abrams, “Concurrent dual-resolution monte carlo simulation of liquid methane," The Journal of Chemical Physics, vol. 123, iss. 23, p. 234101, 2005. doi:10.1063/1.2136884 [BibTeX]
    @article{Abrams_2005,
    doi = {10.1063/1.2136884},
    url = {https://doi.org/10.1063%2F1.2136884},
    year = 2005,
    month = {dec},
    publisher = {{AIP} Publishing},
    volume = {123},
    number = {23},
    pages = {234101},
    author = {Cameron F. Abrams},
    title = {Concurrent dual-resolution Monte Carlo simulation of liquid methane},
    journal = {{The Journal of Chemical Physics}}
    }

  • Y. Sliozberg and C. F. Abrams, “Effects of confinement on the thermodynamics of a collapsing heteropolymer: An off-lattice Wang-Landau Monte Carlo simulation study," Macromolecules, vol. 38, iss. 12, p. 5321–5329, 2005. doi:10.1021/ma050443t [BibTeX]
    @article{Sliozberg_2005b,
    doi = {10.1021/ma050443t},
    url = {https://doi.org/10.1021%2Fma050443t},
    year = 2005,
    month = {jun},
    publisher = {American Chemical Society ({ACS})},
    volume = {38},
    number = {12},
    pages = {5321--5329},
    author = {Yelena Sliozberg and Cameron F. Abrams},
    title = {Effects of Confinement on the Thermodynamics of a Collapsing Heteropolymer: {A}n Off-Lattice {Wang-Landau Monte Carlo} Simulation Study},
    journal = {{Macromolecules}}
    }

  • E. Jabbarzadeh and C. F. Abrams, “Fundamental limits of efficacy of intercellular communication by diffusion," Journal of the Physical Society of Japan, vol. 74, iss. 4, p. 1139–1141", 2005. doi:10.1143/jpsj.74.1139 [BibTeX]
    @article{Jabbarzadeh_2005,
    author = {Ehsan Jabbarzadeh and Cameron F. Abrams},
    doi = {10.1143/jpsj.74.1139},
    url = {https://doi.org/10.1143\%2Fjpsj.74.1139},
    year = 2005,
    month = {apr},
    publisher = {Physical Society of Japan},
    volume = 74,
    number = 4,
    pages = {1139--1141"},
    title = {Fundamental Limits of Efficacy of Intercellular Communication by Diffusion},
    journal = {{Journal of the Physical Society of Japan}}
    }

  • E. Jabbarzadeh and C. F. Abrams, “Chemotaxis and random motility in unsteady chemoattractant fields: A computational study," Journal of Theoretical Biology, vol. 235, iss. 2, p. 221–232, 2005. doi:10.1016/j.jtbi.2005.01.005 [BibTeX]
    @article{Jabbarzadeh_2005b,
    doi = {10.1016/j.jtbi.2005.01.005},
    url = {https://doi.org/10.1016%2Fj.jtbi.2005.01.005},
    year = 2005,
    month = {jul},
    publisher = {Elsevier {BV}},
    volume = {235},
    number = {2},
    pages = {221--232},
    author = {Ehsan Jabbarzadeh and Cameron F. Abrams},
    title = {Chemotaxis and random motility in unsteady chemoattractant fields: {A} computational study},
    journal = {{Journal of Theoretical Biology}}
    }

  • Y. Sliozberg and C. F. Abrams, “Structural correlations in comb heteropolymers in good and backbone-selective solvents," Journal of Polymer Science Part B: Polymer Physics, vol. 43, iss. 8, p. 983–993, 2005. doi:10.1002/polb.20388 [BibTeX]
    @article{Sliozberg_2005,
    doi = {10.1002/polb.20388},
    url = {https://doi.org/10.1002%2Fpolb.20388},
    year = 2005,
    publisher = {Wiley},
    volume = {43},
    number = {8},
    pages = {983--993},
    author = {Yelena Sliozberg and Cameron F. Abrams},
    title = {Structural correlations in comb heteropolymers in good and backbone-selective solvents},
    journal = {{Journal of Polymer Science Part B: Polymer Physics}}
    }

2004

  • E. Jabbarzadeh and C. F. Abrams, “Simulations of chemotaxis and random motility in finite domains," MRS Proceedings, vol. 845, 2004. doi:10.1557/proc-845-aa1.9 [BibTeX]
    @article{Jabbarzadeh_2004,
    doi = {10.1557/proc-845-aa1.9},
    url = {https://doi.org/10.1557%2Fproc-845-aa1.9},
    year = 2004,
    publisher = {Cambridge University Press ({CUP})},
    volume = {845},
    author = {Ehsan Jabbarzadeh and Cameron F. Abrams},
    title = {Simulations of Chemotaxis and Random Motility in Finite Domains},
    journal = {{{MRS} Proceedings}}
    }

  • N. Lee and C. F. Abrams, “Kinetics of a polysoap collapse," The Journal of Chemical Physics, vol. 121, iss. 15, p. 7484–7493, 2004. doi:10.1063/1.1793151 [BibTeX]
    @article{Lee_2004b,
    doi = {10.1063/1.1793151},
    url = {https://doi.org/10.1063%2F1.1793151},
    year = 2004,
    month = {oct},
    publisher = {{AIP} Publishing},
    volume = {121},
    number = {15},
    pages = {7484--7493},
    author = {Nam-Kyung Lee and Cameron F. Abrams},
    title = {Kinetics of a polysoap collapse},
    journal = {{The Journal of Chemical Physics}}
    }

  • Y. Sliozberg and C. F. Abrams, “Polysoaps in backbone-selective solvents: effects of side-chain length on collapse dynamics," Soft Materials, vol. 2, iss. 1, p. 11–25, 2004. doi:10.1081/smts-120030472 [BibTeX]
    @article{Sliozberg_2004,
    doi = {10.1081/smts-120030472},
    url = {https://doi.org/10.1081%2Fsmts-120030472},
    year = 2004,
    month = {dec},
    publisher = {Informa {UK} Limited},
    volume = {2},
    number = {1},
    pages = {11--25},
    author = {Yelena Sliozberg and Cameron F. Abrams},
    title = {Polysoaps in Backbone-Selective Solvents: Effects of Side-Chain Length on Collapse Dynamics},
    journal = {{Soft Materials}}
    }

  • N. Lee, C. F. Abrams, A. Johner, and S. Obukhov, “Swelling dynamics of collapsed polymers," Macromolecules, vol. 37, iss. 2, p. 651–661, 2004. doi:10.1021/ma034808q [BibTeX]
    @article{Lee_2004,
    doi = {10.1021/ma034808q},
    url = {https://doi.org/10.1021%2Fma034808q},
    year = 2004,
    month = {jan},
    publisher = {American Chemical Society ({ACS})},
    volume = {37},
    number = {2},
    pages = {651--661},
    author = {Nam-Kyung Lee and Cameron F. Abrams and A. Johner and S. Obukhov},
    title = {Swelling Dynamics of Collapsed Polymers},
    journal = {{Macromolecules}}
    }

2003

  • N. Lee, C. F. Abrams, A. Johner, and S. Obukhov, “Arrested swelling of highly entangled polymer globules," Physical Review Letters, vol. 90, iss. 22, 2003. doi:10.1103/physrevlett.90.225504 [BibTeX]
    @article{Lee_2003,
    doi = {10.1103/physrevlett.90.225504},
    url = {https://doi.org/10.1103%2Fphysrevlett.90.225504},
    year = 2003,
    month = {jun},
    publisher = {American Physical Society ({APS})},
    volume = {90},
    number = {22},
    author = {Nam-Kyung Lee and Cameron F. Abrams and A. Johner and S. Obukhov},
    title = {Arrested Swelling of Highly Entangled Polymer Globules},
    journal = {{Physical Review Letters}}
    }

  • D. L. Site, A. Alavi, and C. F. Abrams, “Adsorption energies and geometries of phenol on the (111) surface of nickel: An ab initio study," Physical Review B, vol. 67, iss. 19, 2003. doi:10.1103/physrevb.67.193406 [BibTeX]
    @article{Delle_Site_2003,
    doi = {10.1103/physrevb.67.193406},
    url = {https://doi.org/10.1103%2Fphysrevb.67.193406},
    year = 2003,
    month = {may},
    publisher = {American Physical Society ({APS})},
    volume = {67},
    number = {19},
    author = {L. Delle Site and A. Alavi and C. F. Abrams},
    title = {Adsorption energies and geometries of phenol on the (111) surface of nickel: {A}n ab initio study},
    journal = {{Physical Review B}}
    }

  • C. F. Abrams, L. D. Site, and K. Kremer, “Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface," Physical Review E, vol. 67, iss. 2, 2003. doi:10.1103/physreve.67.021807 [BibTeX]
    @article{Abrams_2003,
    doi = {10.1103/physreve.67.021807},
    url = {https://doi.org/10.1103%2Fphysreve.67.021807},
    year = 2003,
    month = {feb},
    publisher = {American Physical Society ({APS})},
    volume = {67},
    number = {2},
    author = {Cameron F. Abrams and Luigi Delle Site and Kurt Kremer},
    title = {Dual-resolution coarse-grained simulation of the bisphenol-{A}-polycarbonate/nickel interface},
    journal = {{Physical Review E}}
    }

  • C. F. Abrams and K. Kremer, “Combined coarse-grained and atomistic simulation of liquid bisphenol-A-polycarbonate: Liquid packing and intramolecular structure," Macromolecules, vol. 36, iss. 1, p. 260–267, 2003. doi:10.1021/ma0213495 [BibTeX]
    @article{Abrams_2003b,
    doi = {10.1021/ma0213495},
    url = {https://doi.org/10.1021%2Fma0213495},
    year = 2003,
    month = {jan},
    publisher = {American Chemical Society ({ACS})},
    volume = {36},
    number = {1},
    pages = {260--267},
    author = {Cameron F. Abrams and Kurt Kremer},
    title = {Combined Coarse-Grained and Atomistic Simulation of Liquid Bisphenol-{A}-Polycarbonate: {L}iquid Packing and Intramolecular Structure},
    journal = {{Macromolecules}}
    }

2002

  • D. L. Site, C. F. Abrams, A. Alavi, and K. Kremer, “Polymers near metal surfaces: selective adsorption and global conformations," Physical Review Letters, vol. 89, iss. 15, 2002. doi:10.1103/physrevlett.89.156103 [BibTeX]
    @article{Delle_Site_2002,
    doi = {10.1103/physrevlett.89.156103},
    url = {https://doi.org/10.1103%2Fphysrevlett.89.156103},
    year = 2002,
    month = {sep},
    publisher = {American Physical Society ({APS})},
    volume = {89},
    number = {15},
    author = {L. Delle Site and C. F. Abrams and A. Alavi and K. Kremer},
    title = {Polymers near Metal Surfaces: Selective Adsorption and Global Conformations},
    journal = {{Physical Review Letters}}
    }

  • C. F. Abrams, N. -K. Lee, and S. P. Obukhov, “Collapse dynamics of a polymer chain: Theory and simulation," Europhysics Letters (EPL), vol. 59, iss. 3, p. 391–397, 2002. doi:10.1209/epl/i2002-00207-5 [BibTeX]
    @article{Abrams_2002,
    doi = {10.1209/epl/i2002-00207-5},
    url = {https://doi.org/10.1209%2Fepl%2Fi2002-00207-5},
    year = 2002,
    month = {aug},
    publisher = {{IOP} Publishing},
    volume = {59},
    number = {3},
    pages = {391--397},
    author = {C. F Abrams and N.-K Lee and S. P Obukhov},
    title = {Collapse dynamics of a polymer chain: {T}heory and simulation},
    journal = {{Europhysics Letters ({EPL})}}
    }

  • C. F. Abrams and K. Kremer, “Effects of excluded volume and bond length on the dynamics of dense bead-spring polymer melts," The Journal of Chemical Physics, vol. 116, iss. 7, p. 3162–3165, 2002. doi:10.1063/1.1445107 [BibTeX]
    @article{Abrams_2002b,
    doi = {10.1063/1.1445107},
    url = {https://doi.org/10.1063%2F1.1445107},
    year = 2002,
    month = {feb},
    publisher = {{AIP} Publishing},
    volume = {116},
    number = {7},
    pages = {3162--3165},
    author = {Cameron F. Abrams and Kurt Kremer},
    title = {Effects of excluded volume and bond length on the dynamics of dense bead-spring polymer melts},
    journal = {{The Journal of Chemical Physics}}
    }

2001

  • C. F. Abrams and K. Kremer, “The effect of bond length on the structure of dense bead-spring polymer melts," The Journal of Chemical Physics, vol. 115, iss. 6, p. 2776–2785, 2001. doi:10.1063/1.1385791 [BibTeX]
    @article{Abrams_2001,
    doi = {10.1063/1.1385791},
    url = {https://doi.org/10.1063%2F1.1385791},
    year = 2001,
    month = {aug},
    publisher = {{AIP} Publishing},
    volume = {115},
    number = {6},
    pages = {2776--2785},
    author = {Cameron F. Abrams and Kurt Kremer},
    title = {The effect of bond length on the structure of dense bead-spring polymer melts},
    journal = {{The Journal of Chemical Physics}}
    }

  • C. F. Abrams and D. B. Graves, “Atomistic simulation of fluorocarbon deposition on Si by continuous bombardment with energetic CF+ and CF2+," Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, vol. 19, iss. 1, p. 175–181, 2001. doi:10.1116/1.1322652 [BibTeX]
    @article{Abrams_2001b,
    doi = {10.1116/1.1322652},
    url = {https://doi.org/10.1116%2F1.1322652},
    year = 2001,
    month = {jan},
    publisher = {American Vacuum Society},
    volume = {19},
    number = {1},
    pages = {175--181},
    author = {Cameron F. Abrams and David B. Graves},
    title = {Atomistic simulation of fluorocarbon deposition on {Si} by continuous bombardment with energetic {CF}+ and {CF}2+},
    journal = {{Journal of Vacuum Science {\&} Technology A: Vacuum, Surfaces, and Films}}
    }

2000

  • C. F. Abrams and D. B. Graves, “Atomistic simulation of silicon bombardment by energetic CF3+: product distributions and energies," Thin Solid Films, vol. 374, iss. 2, p. 150–156, 2000. doi:10.1016/s0040-6090(00)01145-7 [BibTeX]
    @article{Abrams_2000,
    doi = {10.1016/s0040-6090(00)01145-7},
    url = {https://doi.org/10.1016%2Fs0040-6090%2800%2901145-7},
    year = 2000,
    month = {oct},
    publisher = {Elsevier {BV}},
    volume = {374},
    number = {2},
    pages = {150--156},
    author = {Cameron F Abrams and David B Graves},
    title = {Atomistic simulation of silicon bombardment by energetic {CF}3+: product distributions and energies},
    journal = {{Thin Solid Films}}
    }

  • C. F. Abrams and D. B. Graves, “Molecular dynamics simulations of Si etching with energetic F+: Sensitivity of results to the interatomic potential," Journal of Applied Physics, vol. 88, iss. 6, p. 3734–3738, 2000. doi:10.1063/1.1288701 [BibTeX]
    @article{Abrams_2000b,
    doi = {10.1063/1.1288701},
    url = {https://doi.org/10.1063%2F1.1288701},
    year = 2000,
    month = {sep},
    publisher = {{AIP} Publishing},
    volume = {88},
    number = {6},
    pages = {3734--3738},
    author = {Cameron F. Abrams and David B. Graves},
    title = {Molecular dynamics simulations of {S}i etching with energetic {F}+: {S}ensitivity of results to the interatomic potential},
    journal = {{Journal of Applied Physics}}
    }

  • J. Tanaka, C. F. Abrams, and D. B. Graves, “New c-f interatomic potential for molecular dynamics simulation of fluorocarbon film formation," Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, vol. 18, iss. 3, p. 938–945, 2000. doi:10.1116/1.582279 [BibTeX]
    @article{Tanaka_2000,
    doi = {10.1116/1.582279},
    url = {https://doi.org/10.1116%2F1.582279},
    year = 2000,
    month = {may},
    publisher = {American Vacuum Society},
    volume = {18},
    number = {3},
    pages = {938--945},
    author = {J. Tanaka and C. F. Abrams and D. B. Graves},
    title = {New C-F interatomic potential for molecular dynamics simulation of fluorocarbon film formation},
    journal = {{Journal of Vacuum Science {\&} Technology A: Vacuum, Surfaces, and Films}}
    }

  • C. F. Abrams and D. B. Graves, “On the active surface layer in CF3+ etching of Si: Atomistic simulation and a simple mass balance model," Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, vol. 18, iss. 2, p. 411–416, 2000. doi:10.1116/1.582202 [BibTeX]
    @article{Abrams_2000c,
    doi = {10.1116/1.582202},
    url = {https://doi.org/10.1116%2F1.582202},
    year = 2000,
    month = {mar},
    publisher = {American Vacuum Society},
    volume = {18},
    number = {2},
    pages = {411--416},
    author = {Cameron F. Abrams and David B. Graves},
    title = {On the active surface layer in {CF}3+ etching of {S}i: {A}tomistic simulation and a simple mass balance model},
    journal = {{Journal of Vacuum Science {\&} Technology A: Vacuum, Surfaces, and Films}}
    }

1999

  • C. F. Abrams and D. B. Graves, “Molecular dynamics simulations of Si etching by energetic CF3+," Journal of Applied Physics, vol. 86, iss. 11, p. 5938–5948, 1999. doi:10.1063/1.371637 [BibTeX]
    @article{Abrams_1999,
    doi = {10.1063/1.371637},
    url = {https://doi.org/10.1063%2F1.371637},
    year = 1999,
    month = {dec},
    publisher = {{AIP} Publishing},
    volume = {86},
    number = {11},
    pages = {5938--5948},
    author = {Cameron F. Abrams and David B. Graves},
    title = {Molecular dynamics simulations of {Si} etching by energetic {CF}3+},
    journal = {{Journal of Applied Physics}}
    }

  • C. F. Abrams and D. B. Graves, “Three-dimensional spatiokinetic distributions of sputtered and scattered products of Ar+ and Cu+ impacts onto the Cu surface: Molecular dynamics simulations," IEEE Transactions on Plasma Science, vol. 27, iss. 5, p. 1426–1432, 1999. doi:10.1109/27.799821 [BibTeX]
    @article{Abrams_1999b,
    doi = {10.1109/27.799821},
    url = {https://doi.org/10.1109%2F27.799821},
    year = 1999,
    publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
    volume = {27},
    number = {5},
    pages = {1426--1432},
    author = {C.F. Abrams and D.B. Graves},
    title = {Three-dimensional spatiokinetic distributions of sputtered and scattered products of {A}r+ and {C}u+ impacts onto the {C}u surface: {M}olecular dynamics simulations},
    journal = {{{IEEE} Transactions on Plasma Science}}
    }

  • M. A. Vyvoda, C. F. Abrams, and D. B. Grave, “Feature evolution simulations of copper seed layer deposition using atomic-level particle scattering information," IEEE Transactions on Plasma Science, vol. 27, iss. 5, p. 1433–1440, 1999. doi:10.1109/27.799822 [BibTeX]
    @article{Vyvoda_1999,
    doi = {10.1109/27.799822},
    url = {https://doi.org/10.1109%2F27.799822},
    year = 1999,
    publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
    volume = {27},
    number = {5},
    pages = {1433--1440},
    author = {M.A. Vyvoda and C.F. Abrams and D.B. Grave},
    title = {Feature evolution simulations of copper seed layer deposition using atomic-level particle scattering information},
    journal = {{{IEEE} Transactions on Plasma Science}}
    }

  • C. F. Abrams and D. B. Graves, “Cu sputtering and deposition by off-normal, near-threshold Cu+ bombardment: Molecular dynamics simulations," Journal of Applied Physics, vol. 86, iss. 4, p. 2263–2267, 1999. doi:10.1063/1.371040 [BibTeX]
    @article{Abrams_1999c,
    doi = {10.1063/1.371040},
    url = {https://doi.org/10.1063%2F1.371040},
    year = 1999,
    month = {aug},
    publisher = {{AIP} Publishing},
    volume = {86},
    number = {4},
    pages = {2263--2267},
    author = {Cameron F. Abrams and David B. Graves},
    title = {Cu sputtering and deposition by off-normal, near-threshold {C}u+ bombardment: {M}olecular dynamics simulations},
    journal = {{Journal of Applied Physics}}
    }

1998

  • C. F. Abrams and D. B. Graves, “Energetic ion bombardment of SiO2 surfaces: Molecular dynamics simulations," Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, vol. 16, iss. 5, p. 3006–3019, 1998. doi:10.1116/1.581452 [BibTeX]
    @article{Abrams_1998,
    doi = {10.1116/1.581452},
    url = {https://doi.org/10.1116%2F1.581452},
    year = 1998,
    month = {sep},
    publisher = {American Vacuum Society},
    volume = {16},
    number = {5},
    pages = {3006--3019},
    author = {Cameron F. Abrams and David B. Graves},
    title = {Energetic ion bombardment of {SiO}2 surfaces: {M}olecular dynamics simulations},
    journal = {{Journal of Vacuum Science {\&} Technology A: Vacuum, Surfaces, and Films}}
    }

1997

  • W. S. Ahn, Y. Zhong, C. F. Abrams, P. K. Lim, and P. A. Brown, “Biphasic autoxidation of tetralin catalyzed by surface-active transition metal complexes," The Journal of Physical Chemistry B, vol. 101, iss. 4, p. 596–602, 1997. doi:10.1021/jp9627234 [BibTeX]
    @article{Ahn_1997,
    doi = {10.1021/jp9627234},
    url = {https://doi.org/10.1021%2Fjp9627234},
    year = 1997,
    month = {jan},
    publisher = {American Chemical Society ({ACS})},
    volume = {101},
    number = {4},
    pages = {596--602},
    author = {Wha Seung Ahn and Yaping Zhong and Cameron F. Abrams and P. K. Lim and Phillip A. Brown},
    title = {Biphasic Autoxidation of Tetralin Catalyzed by Surface-Active Transition Metal Complexes},
    journal = {{The Journal of Physical Chemistry B}}
    }

1995

  • Y. Zhong, C. F. Abrams, and 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," Industrial & Engineering Chemistry Research, vol. 34, iss. 5, p. 1529–1535, 1995. doi:10.1021/ie00044a003 [BibTeX]
    @article{Zhong_1995,
    doi = {10.1021/ie00044a003},
    url = {https://doi.org/10.1021%2Fie00044a003},
    year = 1995,
    month = {may},
    publisher = {American Chemical Society ({ACS})},
    volume = {34},
    number = {5},
    pages = {1529--1535},
    author = {Yaping Zhong and Cameron F. Abrams and Phooi K. Lim},
    title = {Biphasic Synthesis of Poly(2,6-dimethyl-1,4-phenylene oxide) Using a Surface-Active Coupling Catalyst. 2. {P}rocess Improvements, Additional Kinetic Results, and Proposed Reaction Mechanism},
    journal = {{Industrial {\&} Engineering Chemistry Research}},
    revindex = 1
    }