Curriculum Vitae

Education

• B.S., Chemical Engineering (minor: Computer Programming) — North Carolina State University (1995)
• Ph.D., Chemical Engineering — University of California, Berkeley (2000)

Professional Experience

• Drexel University, Department of Chemical and Biological Engineering
  Bartlett-Barry Professor of Chemical and Biological Engineering (2021-) · Department Head (2017-) · Professor (2012-) · Associate Professor (2008-2012) · Assistant Professor (2002-2008)
• Drexel University College of Medicine, Department of Biochemistry and Molecular Biology
  Professor (2012-)
• Max-Planck-Institute for Polymer Research
  Postdoc, Theory (2000-2002)
• University of California, Berkeley, Department of Chemical Engineering
  Graduate Research Assistant (1995-2000) · Graduate Teaching Assistant (1995-1997)
• North Carolina State University, Departments of Chemical Engineering & Computer Science
  Undergraduate Teaching Assistant (1993-1995)
• Eastman Chemical
  Summer Intern (1994)
• Dupont, Dacron Technical Research Lab
  Co-op Engineer (3 1-semester rotations) (1991-1993)

Publications

1. Shilei Ding, Derek Yang, Irfan Ullah, Ling Niu, Matthew Unger, Marco Díaz-Salinas, Monika Chandravanshi, Fei Zhou, Guillaume Beaudoin-Bussières, Mehdi Benlarbi, William Tolbert, Keon-Woong Yoon, et al., “Optimization of VE607 to generate analogs with improved neutralization activities against SARS-CoV-2 variants.” Journal of Virology, 99, e01034-25 (2025). [doi · PMID]
2. Salsabil Abou-Hatab, Cameron F. Abrams, “Minimal Collective Variables for Conformational Transitions in Steered and Temperature-Accelerated MD Simulations: A T4 Lysozyme Case Study.” Journal of Physical Chemistry B, 129, 5176-5188 (2025). [doi · PMID]
3. Bibek Parajuli, Kriti Acharya, Harry Bach, Shiyu Zhang, Cameron F. Abrams, Irwin Chaiken, “Monovalent Lectin Microvirin Utilizes Hydropathic Recognition of HIV-1 Env for Inhibition of Virus Cell Infection.” Viruses, 17, 82 (2025). [doi · PMID]
4. Mehdi Benlarbi, Shilei Ding, Étienne Bélanger, Alexandra Tauzin, Raphael Poujol, Halima Medjahed, Omar El Ferri, Yuxia Bo, Catherine Bourassa, Julie Hussin, Judith Fafard, Marzena Pazgier, et al., “Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission.” mBio, 15, e0090724 (2024). [doi · PMID]
5. Monisha Gupta, Gabriela Canziani, Charles Ang, Mohammadjavad Mohammadi, Cameron F. Abrams, Derek Yang, Amos B. Smith, III, Irwin Chaiken, “Pharmacophore Variants of the Macrocyclic Peptide Triazole Inactivator of HIV-1 Env.” Med. Chem. Res., 32, 1497-1509 (2023). [doi · PMID]
6. Shilei Ding, William D. Tolbert, Huile Zhu, Daniel Lee, Tyler Higgins, Xuchen Zhao, Dung Nguyen, Rebekah Sherburn, Jonathan Richard, Gabrielle-Gendron Lepage, Halima Medjahed, Mohammadjavad Mohammadi, et al., “Piperidine CD4-mimetic compounds expose vulnerable Env epitopes sensitizing HIV-1-infected cells to ADCC.” Viruses, 15, 1185 (2023). [doi · PMID]
7. Christopher Fritcshi, Saumya Anang, Zhen Gong, Mohammadjavad Mohammadi, Jonathan Richard, Catherine Bourassa, Kenny T. Severino, Hannah Richter, Derek Yang, Hung-Ching Chen, Ta-Jung Chiu, Michael S. Seaman, et al., “Indoline CD4-mimetic Compounds Mediate Potent and Broad HIV-1 Inhibition and Sensitization to Antibody-dependent Cellular Cytotoxicity.” Proc. Natl. Acad. Sci. USA, 120, e2222073120 (2023). [doi · PMID]
8. Giulio Alberini, S. Alexis Paz, Cameron F. Abrams, Fabio Benfenati, Luca Maragliano, “Molecular Dynamics Simulations of Ion Permeation in Human NaV Channels.” J. Chem. Theory. Comput., 19, 2953-2972 (2023). [doi · PMID]
9. Ming Huang, Cameron F. Abrams, “HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers.” SoftwareX, 21, 101303 (2023). [doi]
10. Cheyenne Chaplain, Christopher Fritschi, Saumya Anang, Zhen Gong, Jonathan Richard, Shuaiyi Yang, Mohammadjavad Mohammadi, Jun Park, Andrés Finzi, Navid Madani, Joseph Sodroski, Cameron F. Abrams, et al., “Structural and Functional Characterization of Indane-core CD4-mimetic Compounds Substituted with Heterocyclic Amines.” ACS Med. Chem. Lett., 14, 51-58 (2022). [doi · PMID]
11. Natasha Gupta Vergara, Cameron F. Abrams, “Entropic overcompensation of the N501Y mutation on SARS-CoV-2 S binding to ACE2.” J. Chem. Inform. Model., 63, 633-642 (2022). [doi · PMID]
12. Shilei Ding, Irfan Ullah, Shang Yu Gong, Jonathan R. Grover, Mohammadjavad Mohammadi, Yaozong Chen, Dani Vézina, Guillaume Beaudoin-Bussières, Vijay Tailor Verma, Guillaume Goyette, Fleur Gaudette, Jonathan Richard, et al., “VE607 stabilizes SARS-CoV-2 Spike in the `RBD-up' conformation and inhibits viral entry.” iScience, 25, 104528 (2022). [doi · PMID]
13. Ming Huang, Nicolas Alvarez, Giuseppe Palmese, Cameron Abrams, “The Effect of Network Topology on Material Properties in Vinyl-ester/Styrene Thermoset Polymers using Molecular Dynamics Simulations and Time-Temperature Superposition.” Comput. Mater. Sci., 27, 111264 (2022). [doi]
14. Salman Zarrini, Cameron Abrams, “Modeling sizing emulsion droplet deposition onto silica using all-atom molecular dynamics simulations.” Composites Part B: Engineering, 235, 109712 (2022). [doi]
15. Christopher Fritschi, Shuaiyi Liang, Mohammadjavad Mohammadi, Saumya Anang, Francesca Moraca, Junhua Chen, Navid Madani, Joseph Sodroski, Cameron Abrams, Wayne Hendrickson, Amos Smith, III, “Identification and Validation of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics.” ACS Med. Chem. Lett., 12, 1824-1831 (2021). [doi · PMID]
16. Ketan Khare, Cameron Abrams, “Atomistic Simulation of Volumetric Properties of Epoxy Networks: Effect of Monomer Length.” Soft Matter, 17, 9957-9986 (2021). [doi · PMID]
17. Sergio Ribone, Sergio Alexis Paz, Cameron Abrams, Marcos Villarreal, “Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.” J. Comput. Aided Mol. Des., 26, 1-13 (2021). [doi · PMID]
18. Jérémie Prévost, Jonathan Richard, Romain Gasser, Shilei Ding, Clément Fage, Sai Priya Anand, Damien Adam, Natasha Gupta Vergara, Alexandra Tauzin, Mehdi Benlarbi, Shang Yu Gong, Guillaume Goyette, et al., “Impact of temperature on the affinity of SARS-CoV-2 Spike for ACE2.” J. Biol. Chem., 297, 101151 (2021). [doi · PMID]
19. S. Zarrini, C. F. Abrams, “The Roles of Coupling Agent and Surfactant in Droplet Structure in Sizing Emulsions: A Molecular Dynamics Simulations Study.” Langmuir, 37, 10183-10190 (2021). [doi · PMID]
20. C. G. Ang, E. Carter, A. Haftl, S. Zhang, A. A. Rashad, M. Kutzler, C. F. Abrams, I. M. Chaiken, “Peptide triazole thiol irreversibly inactivates metastable HIV-1 Env by accessing conformational triggers intrinsic to virus-cell entry.” Microoganisms, 9, 1286 (2021). [doi · PMID]
21. G. Shrivastav, C. F. Abrams, “Optimizing string method's reproducibility using generalized solute tempering replica exchange.” J. Phys. Chem. B, 125, 6609-6616 (2021). [doi · PMID]
22. A. Gaffney, A. Nangarlia, C. G. Ang, S. Gossert, A. A. Rashad Ahmed, M. A. Hossain, C. F. Abrams, A. B. Smith III, I. Chaiken, “HIV-1 Env-dependent cell killing by bifunctional small-molecule/peptide conjugates.” ACS Chem. Biol., 16, 193-204 (2021). [doi · PMID]
23. B. Parajuli, K. Acharya, A. Nangarlia, S. Zhang, B. Parajuli, A. Dick, B. Ngo, C. F. Abrams, I. Chaiken, “Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate.” Biochem. J., 477, 4263-4280 (2020). [doi · PMID]
24. S. Gossert, B. Parajuli, I. Chaiken, C. F. Abrams, “Roles of variable linker length in dual acting virucidal entry inhibitors on HIV-1 potency via on-the-fly free energy molecular simulations.” Protein Sci., 29, 2304 (2020). [doi · PMID]
25. S. P. Anand, Y. Chen, J. Prévost, R. Gasser, G. Beaudoin-Bussiéres, C. F. Abrams, M. Pazgier, A. Finzi, “Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins.” Viruses, 12, 1104 (2020). [doi · PMID]
26. Jérémie Prévost, William D. Tolbert, Halima Medjahed, Rebekah T. Sherburn, Navid Madani, Daria Zoubchenok, Gabrielle Gendron-Lepage, Althea E. Gaffney, Melissa C. Grenier, Sharon Kirk, Natasha Gupta Vergara, Changze Han, et al., “The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site.” mBio, 11, e00280-20 (2020). [doi · PMID]
27. Shitao Zou, Shijian Zhang, Althea Gaffney, Haitao Ding, Maolin Lu, Jonathan Grover, Mark Farrell, Hanh Nguyen, Connie Zhao, Saumya Anang, Meiqing Zhao, Mohammadjavad Mohammadi, et al., “Long-Acting BMS-378806 Analogues Stabilize the State-1 Conformation of the Human Immunodeficiency Virus (HIV-1) Envelope Glycoproteins.” J. Virol., 94, e00148-20 (2020). [doi · PMID]
28. Charles Ang, Mohammed Hossain, Marg Rajpara, Harry Bach, Kriti Acharya, Alexej Dick, Adel Ahmed, Michelle Kutzler, Cameron F. Abrams, Irwin Chaiken, “Metastable HIV-1 Surface Protein Env Sensitizes Cell Membranes to Transformation and Poration by Dual-Acting Virucidal Entry Inhibitors.” Biochemistry, 59, 818-828 (2020). [doi · PMID]
29. Melissa Grenier, Shilei Ding, Dani Vézina, Jean-Philippe Chapleau, William Tolbert, Rebekah Sherburn, Arne Schon, Sambasivarao Somisetti, Cameron F. Abrams, Marzena Pazgier, Andrés Finzi, Amos B. Smith, III, “Optimization of Small Molecules for their Capacity to Sensitize HIV-1 Infected Cells to Antibody Dependent Cellular Cytotoxicity.” ACS Med. Chem. Lett., 11, 371-378 (2020). [doi · PMID]
30. Jasmine Gardner, Cameron F. Abrams, “Energetics of Flap Opening in HIV-1 Protease: String Method Calculations.” J. Phys. Chem. B, 123, 9584-9591 (2019). [doi · PMID]
31. Anindya Bhaduri, Jasmine Gardner, Cameron F. Abrams, Lori Brady, “Free energy calculation using space filled design and weighted reconstruction: A modified single sweep approach.” Mol. Sim., 46, 193-206 (2019). [doi · PMID]
32. Shilei Ding, Melissa Grenier, William Tolbert, Dani Vézina, Rebekah Sherburn, Jonathan Richard, Jérémie Prévost, Jean-Philippe Chapleau, Gabrielle Gendron-Lepage, Halima Medjahed, Cameron F. Abrams, Joseph Sodroski, et al., “A new family of small-molecule CD4-mimetic compounds contact the highly conserved aspartic acid 368 of HIV-1 gp120 and mediates ADCC.” J. Virol., 93, e01325-19 (2019). [doi · PMID]
33. Gourav Shrivastav, Eric Vanden-Eijnden, Cameron F. Abrams, “Mapping Saddles and Minima on Free Energy Surfaces using Multiple Climbing Strings.” J. Chem. Phys., 151, 124112 (2019). [doi · PMID]
34. Connie Zhao, Amy Princiotto, Hanh Nguyen, Shitao Zou, Meiqing Zhao, Shijian Zhang, Alon Herschhorn, Mark Farrell, Karanbir Pahil, Bruno Melillo, Somisetti Sambasivarao, Cameron Abrams, et al., “Strain-dependent activation and inhibition of human immunodeficiency virus (HIV-1) entry by a specific PF-68742 stereoisomer.” J. Virol., 93, 1-20 (2019). [doi · PMID]
35. Ming Huang, Cameron F. Abrams, “Effects of Reactivity Ratios on Network Topology and Thermomechanical Properties in Vinyl-Ester/Styrene Thermosets: Molecular Dynamics Simulations.” Macromol. Theory. Sim., 28, 1900030 (2019). [doi]
36. Arun Srikanth Sridhar, Cameron F. Abrams, “Effect of molecular packing and hydrogen bonding on the properties of epoxy-amido amine systems.” Comput. Mater. Sci., 169, 109082 (2019). [doi]
37. Maolin Lu, Xiaochu Ma, Luis R. Castillo-Menendez, Jason Gorman, Nirmin Alsahafi, Utz Erme, Daniel S. Terry, Michael Chambers, Dongjun Peng, Baoshan Zhang, Tongqing Zhou, Nick Reichard, et al., “Associating HIV-1 envelope glycoprotein structures with states on virus observed by smFRET.” Nature, 568, 415-419 (2019). [doi · PMID]
38. Arun Srikanth Sridhar, Cameron F. Abrams, “Yield and Post-yield Behavior of Fatty- Acid-Functionalized Amidoamine–Epoxy Systems: A Molecular Simulation Study.” J. Dyn. Behav. Mater., 5, 143-149 (2019). [doi · PMID]
39. Ryan Gordon, Spencer Stober, Cameron F. Abrams, “Counterion Effects on Aggregate Structure of 12-Hydroxystearate Salts in Hexane: A Quantum Mechanical and Molecular Dynamics Simulation Study.” J. Phys. Chem. B, 123, 534-541 (2018). [doi · PMID]
40. Jasmine Gardner, Cameron F. Abrams, “Lipid flip-flop vs. lateral diffusion in the relaxation of hemifusion diaphragms.” BBA-Biomembranes, 1860, 1452-1459 (2018). [doi · PMID]
41. Steven Gossert, Bibek Parajuli, Irwin Chaiken, Cameron F. Abrams, “Roles of Conserved Tryptophans in Trimerization of HIV-1 Membrane-Proximal External Regions: Implications for Virucidal Design via Alchemical Free-Energy Molecular Simulations.” Proteins, 86, 707-711 (2018). [doi · PMID]
42. S. Alexis Paz, Luca Maragliano, Cameron F. Abrams, “The effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parameterization.” J. Chem. Theory. Comput., 14, 2743–2750 (2018). [doi · PMID]
43. Arun Sridhar, John Vergara, Emre Kinaci, Giuseppe Palmese, Cameron F. Abrams, “The effect of alkyl chain length on mechanical properties of fatty-acid-functionalized amidoamine-epoxy system.” Comput. Mater. Sci., 150, 70-76 (2018). [doi]
44. S. Alexis Paz, Cameron F. Abrams, “Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers.” Computation, 6, 27 (2018). [doi]
45. Bibek Parajuli, Kriti Acharya, Harry C. Bach, Bijay Parajuli, Shiyu Zhang, Amos B. Smith III, Cameron F. Abrams, Irwin Chaiken, “Restricted HIV-1 Env Glycan Engagement by Lectin-Reengineered DAVEI Protein Chimera is Sufficient for Lytic Inactivation of the Virus.” Biochem. J., 475, 931-957 (2018). [doi · PMID]
46. Francesca Moraca, David Rinaldo, Amos B. Smith, III, Cameron F. Abrams, “Specific Non-Covalent Interactions Determine Optimal Structure of a Buried Ligand Moiety: QM/MM and Pure QM Modeling of Complexes of the Small-Molecule CD4 Mimetics and HIV-1 Gp120.” ChemMedChem, 13, 627-633 (2018). [doi · PMID]
47. Jasmine Gardner, Cameron F. Abrams, “Rate of hemifusion diaphragm dissipation and ability to form three-junction bound HD determined by lipid composition.” J. Chem. Phys., 147, 134903 (2017). [doi · PMID]
48. Ryan Gordon, Spencer Stober, Cameron F. Abrams, “Effects of Optical Purity and Finite System Size on Self-Assembly of 12-Hydroxystearic Acid in Hexane: Molecular Dynamics Simulations.” J. Phys. Chem. B, 121, 9223-9233 (2017). [doi · PMID]
49. Alon Herschhorn, Christopher Gu, Francesca Moraca, Xiaochu Ma, Mark Farrell, Amos B. Smith, III, Marie Pancera, Peter D. Kwong, Arne Schön, Ernesto Freire, Cameron Abrams, Scott C. Blanchard, et al., “The β20-β21 of gp120 is a regulatory switch for HIV-1 Env.” Nature Comm., 8, 1049 (2017). [doi · PMID]
50. Kriti Acharya, Adel A. Rashad, Francesca Moraca, Per Johan Klasse, John P. Moore, Cameron F. Abrams, Irwin Chaiken, “Recognition of HIV-Inactivating Peptide Triazoles by a Recombinant Soluble Trimer, BG505 SOSIP.664.” Proteins, 85, 843-851 (2017). [doi · PMID]
51. Arun Sridhar, John Vergara, Giuseppe Palmese, Cameron F. Abrams, “The Effect of Alkyl Chain Length on Material Properties of Fatty-Acid-Functionalized Amidoamine-Epoxy Systems.” Eur. Polymer J., 89, 1-12 (2017). [doi]
52. Jungho Yang, Arun Srikanth, Changwoon Jang, Cameron F. Abrams, “Relationships Between Molecular Structure and Thermomechanical Properties of Bio-Based Thermosetting Polymers.” J. Polym. Sci. B Pol. Phys., 55, 285-292 (2017). [doi]
53. S. Alexis Paz, Eric Vanden-Eijnden, Cameron F. Abrams, “Polymorphism at 129 Dictates Metastable Conformations of the Human Prion Protein N-terminal β-sheet.” Chem. Sci., 8, 1225-1232 (2017). [doi · PMID]
54. Bibek Parajuli, Kriti Acharya, Reina Yu, Adel A. Rashad, Cameron F. Abrams, Irwin M. Chaiken, “Lytic Inactivation of HIV-1 by Dual Engagement of gp120 and gp41 Domains in the Virus Env Trimer.” Biochemistry, 55, 6100-6114 (2016). [doi · PMID]
55. Francesca Moraca, Kriti Acharya, Bruno Melillo, Amos B. Smith, III, Irwin M. Chaiken, Cameron F. Abrams, “Computational Evaluation of HIV-1 gp120 Conformations of Soluble Trimeric gp140 Structures as Targets for de novo Docking of First- and Second-Generation Small-Molecule CD4 Mimetics.” J. Chem. Info. Model., 56, 2069-2079 (2016). [doi · PMID]
56. Tang-Qing Yu, Jianfeng Lu, Cameron F. Abrams, Eric Vanden-Eijnden, “A Multiscale Implementation of Infinite-Swap Replica Exchange Molecular Dynamics.” Proc. Natl. Acad. Sci. USA, 113, 11744-11749 (2016). [doi · PMID]
57. Changwoon Jang, Cameron F. Abrams, “Thermal and Mechanical Properties of Thermosetting Polymers using Coarse-grained Simulation.” Eur. Phys. J. Spec. Top., 225, 1775-1783 (2016). [doi · PMID]
58. Ryan Gordon, Spencer S. Stober, Cameron F. Abrams, “Aggregation of 12-Hydroxystearic Acid and Its Lithium Salt in Hexane: Molecular Dynamics Simulations.” J. Phys. Chem. B., 120, 7164-7173 (2016). [doi · PMID]
59. Jasmine Gardner, Markus Deserno, Cameron F. Abrams, “Effect of Intrinsic Curvature and Edge Tension on the Stability of Binary Mixed-Membrane Three-Junctions.” J. Chem. Phys., 145, 74901 (2016). [doi · PMID]
60. Anthony Bucci, Tang-Qing Yu, Eric Vanden-Eijnden, Cameron F. Abrams, “Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics.” J. Chem. Theory Comput., 12, 2964-2972 (2016). [doi · PMID]
61. Changwoon Jang, Majid Sharifi, Giuseppe Palmese, Cameron F. Abrams, “Toughness enhancement of thermosetting polymers using a novel partially reacted substructure curing protocol: A combined molecular simulation and experimental study.” Polymer, 90, 249-255 (2016). [doi · PMID]
62. Ramalingam Venkat Kalyana Sundaram, Huiyuan Li, Lauren Bailey, Adel A. Rashad, Rachna Aneja, Karl Weiss, James Huynh, Arangaserry Rosemary Bastian, Elisabeth Papazoglou, Cameron Abrams, Steven Wrenn, Irwin Chaiken, “Impact of HIV-1 Membrane Cholesterol on Cell-Independent Lytic Inactivation and Cellular Infectivity.” Biochemistry, 55, 447-458 (2016). [doi · PMID]
63. Majid Sharifi, Changwoon Jang, Cameron F. Abrams, Giuseppe Palmese, “Epoxy Polymer Networks with Improved Thermal and Mechanical Properties via Controlled Dispersion of Reactive Toughening Agents.” Macromolecules, 48, 7495-7502 (2015). [doi]
64. S. Alexis Paz, Cameron F. Abrams, “Free Energy and Hidden Barriers of the β-Sheet Structure of Prion Protein.” J. Chem. Theory Comput., 11, 5024-5034 (2015). [doi · PMID]
65. Tang-Qing Yu, Mauro Lapelosa, Eric Vanden-Eijnden, Cameron F. Abrams, “Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.” J. Amer. Chem. Soc., 137, 3041-3050 (2015). [doi · PMID]
66. Arangassery Rosemary Bastian, Aakansha Nangarlia, Lauren D. Bailey, Andrew Holmes, R. Venkat Kalyana Sundaram, Charles Ang, Diogo R. M. Moreira, Kevin Freedman, Caitlin Duffy, Mark Contarino, Cameron Abrams, Michael Root, et al., “Mechanism of Multivalent Nanoparticle Encounter with HIV-1 for Potency Enhancement of Peptide Triazole Virus Inactivation.” J. Biol. Chem., 290, 529-543 (2015). [doi · PMID]
67. Changwoon Jang, Timothy Sirk, Jan Andzelm, Cameron F. Abrams, “Comparison of Crosslinking Algorithms in Molecular Dynamics Simulations of Thermosetting Polymers.” Macromol. Theory Sim., 24, 260-270 (2015). [doi · PMID]
68. Michelle K. Baker, Cameron F. Abrams, “Dynamics of Lipids, Cholesterol, and Transmembrane α-Helices from Microsecond Molecular Dynamics Simulations.” J. Phys. Chem. B, 118, 13590-13600 (2014). [doi · PMID]
69. Changwoon Jang, Majid Sharifi, Giuseppe R. Palmese, Cameron F. Abrams., “Molecular Dynamics Simulation Study of Reactive Encapsulation of Solvent in Epoxy Curing.” Proceedings of 2014 ASC 29/US-Japan 16/ASTM D30 Conference (2014).
70. Majid Sharifi, Chang-Woon Jang, Cameron F. Abrams, Giuseppe Palmese, “Toughened epoxy polymers via rearrangement of network topology.” J. Mater. Chem. A, 2, 16071-16082 (2014). [doi]
71. Chang-Woon Jang, Majid Sharifi, Giuseppe Palmese, Cameron F. Abrams, “Crosslink Network Rearrangement via Reactive Encapsulation of Solvent in Epoxy Curing: A Combined Molecular Simulation and Experimental Study.” Polymer, 55, 3859-3868 (2014). [doi]
72. Ali Emileh, Caitlin Duffy, Andrew Holmes, Arangassery Rosemary Bastian, Rachna Aneja, Ferit Tuzer, Srivats Rajagopal, Huiyan Li, Cameron F. Abrams, Irwin Chaiken, “Covalent conjugation of a peptide triazole to HIV-1 gp120 enables intramolecular binding site occupancy.” Biochemistry, 53, 3402-3414 (2014). [doi · PMID]
73. Anthony Bucci, Cameron F. Abrams, “Oxygen pathways and allostery in monomeric sarcosine oxidase via single-sweep free-energy reconstruction.” J. Chem. Theory Comput., 10, 2668-2676 (2014). [doi · PMID]
74. Michelle K. Baker, Vamshi Gangupomu, Cameron F. Abrams, “Characterization of the water defect at the HIV-1 gp41 membrane spanning domain in bilayers with and without cholesterol using molecular simulations.” BBA-Biomembranes, 1838, 1396-1405 (2014). [doi · PMID]
75. Cameron F. Abrams, Giovanni Bussi, “Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration.” Entropy, 16, 163-199 (2014). [doi]
76. Mark Contarino, Arangassery R. Bastian, Ramalingam Venkat Kalyana Sundaram, Karyn McFadden, Caitlin Duffy, Vamshi Gangupomu, Michelle Baker, Cameron Abrams, Irwin Chaiken, “Chimeric Cyanovirin-MPER Recombinantly Engineered Proteins Cause Cell-Free Virolysis of HIV-1.” Antimicrob. Agents Ch., 57, 4743-4750 (2013). [doi · PMID]
77. Mauro Lapelosa, Cameron F. Abrams, “Transition-path theory calculations on non- uniform meshes in two and three dimensions using finite elements.” Comp. Phys. Comm., 184, 2310-2315 (2013). [doi · PMID]
78. Harish Vashisth, Cameron F. Abrams, “All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element.” Proteins, 81, 1017-1030 (2013). [doi · PMID]
79. Ali Emileh, Ferit Tuzer, Herman Yeh, Muddegowda Umashankara, Diogo Moreira, Judith LaLonde, Carole Bewley, Cameron F. Abrams, Irwin Chaiken, “A Model of the Peptide Triazole Entry Inhibitor Binding to HIV-1 gp120 and Mechanism of Bridging Sheet Disruption.” Biochemistry, 52, 2245-2261 (2013). [doi · PMID]
80. Mauro Lapelosa, Cameron F. Abrams, “A computational study of water and CO migration sites and channels inside myoglobin.” J. Chem. Theory Comput., 9, 1265-1271 (2013). [doi · PMID]
81. Cameron F. Abrams, Eric Vanden-Eijnden, “On-the-fly free energy parameterization via temperature-accelerated molecular dynamics.” Chem. Phys. Lett., 547, 114-119 (2012). [doi · PMID]
82. Spencer Stober, Cameron F. Abrams, “Energetics and mechanism of the normal-to-amyloidogenic isomerization of b2-microglobulin: On-the-fly string method calculations.” J. Phys. Chem. B, 116, 9371-9375 (2012). [doi · PMID]
83. Harish Vashisth, Luca Maragliano, Cameron F. Abrams, “DFG-flip in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop.” Biophys. J., 102, 1979-1987 (2012). [doi · PMID]
84. Miao Zhang, Cameron F. Abrams, Liping Wang, Anthony Gizzi, Liping He, Ruihe Lin, Yuan Chen, Patrick J. Loll, John M. Pascal, Ji-Fang Zhang, “Structural Basis for Calmodulin as a Dynamic Calcium Sensor.” Structure, 20, 1-13 (2012). [doi · PMID]
85. Spencer Stober, Cameron F. Abrams, “Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors.” Protein Sci., 21, 307-317 (2012). [doi · PMID]
86. Ali Emileh, Cameron F. Abrams, “A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered HIV-1 gp120.” Proteins, 79, 537-546 (2011). [doi · PMID]
87. Vamshi Gangupomu, Cameron F. Abrams, “All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics.” Biophys. J., 99, 3438-3444 (2010). [doi · PMID]
88. Harish Vashisth, Cameron F. Abrams, “All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor.” J. Mol. Biol., 400, 645-658 (2010). [doi · PMID]
89. Debashish Mukherji, Cameron F. Abrams, “Slip-stick fracture and toughness enhancement in thermoset/thermoplastic polymer alloys under shear.” Europhys. Lett., 90, 26003 (2010). [doi]
90. Nikos Ch. Karayiannis, Katerina Foteinopoulou, Cameron F. Abrams, Manuel Laso, “Modeling of crystal nucleation and growth in athermal polymers: Self-assembly of layered nano-morphologies.” Soft Matter, 6, 2160-2173 (2010). [doi]
91. Cameron F. Abrams, Eric Vanden-Eijnden, “Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.” Proc. Natl. Acad. Sci. USA, 107, 4961-4966 (2010). [doi · PMID]
92. Heather L. Nyce, Spencer Stober, Cameron F. Abrams, Michael M. White, “Mapping spatial relationships between residues in the ligand-binding domain of the 5-HT3 receptor using a molecular ruler.” Biophys. J., 98, 1847-1855 (2010). [doi · PMID]
93. Harish Vashisth, Cameron F. Abrams, “Docking of insulin to a structurally equilibrated insulin receptor ectodomain.” Proteins, 78, 1531-1543 (2010). [doi · PMID]
94. Debashish Mukherji, Cameron F. Abrams, “Mechanical behavior of highly cross-linked polymer networks and its direct links to microscopic structure.” Phys. Rev. E, 79, 61802 (2009). [doi · PMID]
95. Debashish Mukherji, Cameron F. Abrams, “Anomalous ductility in thermoset/thermoplastic polymer alloys.” Phys. Chem. Chem. Phys., 11, 2113-2115 (2009). [doi · PMID]
96. Debashish Mukherji, Cameron F. Abrams, “Anomalous ductility in thermoset/thermoplastic polymer alloys: An explanation based on overlap concentration and cavity growth.” Europhys. Lett., 88, 56001 (2009). [doi]
97. Debashish Mukherji, Cameron F. Abrams, “Microvoid formation and strain hardening in highly cross-linked polymer networks.” Phys. Rev. E, 78, 50801 (2008). [doi · PMID]
98. Harish Vashisth, Cameron F. Abrams, “Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex.” Biophys. J., 95, 4193-4204 (2008). [doi · PMID]
99. Yelena Sliozberg, Cameron F. Abrams, “Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations.” Biophys. J., 93, 1906-1916 (2007). [doi · PMID]
100. Ehsan Jabbarzadeh, Cameron F. Abrams, “Strategies to enhance capillary formation inside biomaterials: A computational study.” Tissue Eng., 13, 2073-2086 (2007). [doi · PMID]
101. David Richardson, Cameron F. Abrams, “The effects of nanotube fillers on craze formation in simulated glassy polymers under tensile load.” Mol. Sim., 33, 421-427 (2007). [doi]
102. Ehsan Jabbarzadeh, Cameron F. Abrams, “Simulations of chemotaxis and random motility in 2D random porous domains.” Bull. Math. Biol., 69, 747-764 (2007). [doi · PMID]
103. Cameron F. Abrams, Nam-Kyung Lee, Albert Johner, “Diffusion/reaction in confined polymer chains.” Macromolecules, 39, 3655-3663 (2006). [doi · PMID]
104. David Richardson, Cameron F. Abrams, “Polymer chain winding in the melt.” Macromolecules, 39, 2330-2339 (2006). [doi · PMID]
105. Cameron F. Abrams, “Molecule-Based Coarse-Graining for Polymer Simulation.” Handbook of Theoretical and Computational Nanotechnology, 4, 463-517 (2006).
106. Nam-Kyung Lee, Cameron F. Abrams, Albert Johner, “Optimal confinement for internal polymer binding.” Europhys. Lett., 72, 922-928 (2005). [doi · PMID]
107. Cameron F. Abrams, “Concurrent dual-resolution Monte Carlo simulation of liquid methane.” J. Chem. Phys., 123, 234101 (2005). [doi · PMID]
108. Yelena Sliozberg, Cameron F. Abrams, “The effects of confinement on the thermodynamics of a collapsing heteropolymer: An off-lattice Wang-Landau Monte Carlo simulation study.” Macromolecules, 38, 5321-5329 (2005). [doi]
109. Ehsan Jabbarzadeh, Cameron F. Abrams, “Fundamental limits on the efficacy of intercellular communication by diffusion.” J. Phys. Soc. Japan, 74, 1139-1141 (2005).
110. Ehsan Jabbarzadeh, Cameron F. Abrams, “Chemotaxis and random motility in unsteady chemoattractant fields: A computational study.” J. Theor. Biol., 235, 221-232 (2005). [doi · PMID]
111. Yelena Sliozberg, Cameron F. Abrams, “Structural correlations in comb heteropolymers in good and backbone-selective solvents.” J. Polym. Sci. B. Polym. Phys., 43, 983-993 (2005). [doi]
112. Ehsan Jabbarzadeh, Cameron F. Abrams, “Simulations of Chemotaxis and Random Motility in Finite Domains.” Nanoscale Materials Science in Biology and Medicine, 845, 37-48 (2005). [doi]
113. Nam-Kyung Lee, Cameron F. Abrams, “Kinetics of a polysoap collapse.” J. Chem. Phys., 121, 7484-7493 (2004). [doi · PMID]
114. Yelena Sliozberg, Cameron F. Abrams, “Polysoaps in backbone-selective solvents: Effects of side-chain length on collapse dynamics.” Soft Materials, 2, 11-25 (2004). [doi]
115. Nam-Kyung Lee, Cameron F. Abrams, Albert Johner, Sergei Obukhov, “Swelling dynamics of collapsed polymers.” Macromolecules, 37, 651-661 (2004). [doi · PMID]
116. Cameron F. Abrams, “Inhomogeneous Coarse-Graining of Polymers and Polymer/Metal Interfaces.” Computational Soft Matter: From Synthetic Polymers to Proteins, 23, 275-288 (2004).
117. Cameron F. Abrams, “Dual Resolution Molecular Simulation of Bisphenol-A Polycarbonate Adsorption onto Nickel (111): Chain Length Effects.” Multiscale Modeling and Simulation, 39, 131-142 (2004).
118. Nam-Kyung Lee, Cameron F. Abrams, Albert Johner, Sergei Obukhov, “Arrested swelling of highly entangled polymer globules.” Phys. Rev. Lett., 90, 225504 (2003). [doi · PMID]
119. Luigi Delle Site, Ali Alavi, Cameron F. Abrams, “Adsorption energies and geometries of phenol on the (111) surface of nickel: An ab initio study.” Phys. Rev. B, 67, 193406 (2003). [doi]
120. Cameron F. Abrams, Luigi Delle Site, Kurt Kremer, “Dual-resolution coarse-grained/atomistic simulation of the bisphenol-A-polycarbonate/nickel interface.” Phys. Rev. E, 67, 21807 (2003). [doi · PMID]
121. Cameron F. Abrams, Kurt Kremer, “Combined coarse-grained and atomistic simulation of liquid bisphenol-A-polycarbonate: Liquid packing and intramolecular structure.” Macromolecules, 36, 260-267 (2003). [doi · PMID]
122. Luigi Delle Site, Cameron F. Abrams, Ali Alavi, Kurt Kremer, “Polymers near metal surfaces: Selective adsorption and global conformations.” Phys. Rev. Lett., 89, 156103 (2002). [doi · PMID]
123. Cameron F. Abrams, Namkyung Lee, Sergei Obukhov, “Collapse dynamics of a homopolymer: Theory and simulation.” Europhys. Lett., 59, 391-397 (2002). [doi]
124. Cameron F. Abrams, Kurt Kremer, “Effects of excluded volume and bond length on the dynamics of dense bead-spring polymer melts.” J. Chem. Phys., 116, 3162-3165 (2002). [doi]
125. Cameron F. Abrams, Luigi "Delle Site", Kurt Kremer, “Multiscale Computer Simulations for Polymeric Materials in Bulk and near Surfaces.” Bridging Time Scales: Molecular Simulations for the Next Decade, 605, 143 (2002).
126. Cameron F. Abrams, Kurt Kremer, “The effect of bond length on the structure of dense bead-spring polymer melts.” J. Chem. Phys., 115, 2776-2785 (2001). [doi · PMID]
127. Cameron F. Abrams, David B. Graves, “Atomistic simulation of fluorocarbon deposition on Si by continuous bombardment with energetic CF+ and CF2+.” J. Vac. Sci. Technol. A, 19, 175-181 (2001). [doi]
128. Cameron F. Abrams, David B. Graves., “Atomistic simulation of Si etching by energetic CF3+: Product distributions and energies.” Thin Solid Films, 374, 150-156 (2000).
129. Cameron F. Abrams, David B. Graves., “Molecular dynamics simulations of Si etching with energetic F+: Sensitivity of results to the interatomic potential.” J. Appl. Phys., 88, 3734-3738 (2000). [doi · PMID]
130. Junichi Tanaka, Cameron F. Abrams, David B. Graves., “New C-F interatomic potential for molecular dynamic simulation of fluorocarbon film formation.” J. Vac. Sci. Technol. A, 18, 938-945 (2000). [doi]
131. Cameron F. Abrams, David B. Graves, “On the active surface layer in CF3+ etching of Si: Atomistic simulation and a simple mass balance model.” J. Vac. Sci. Technol. A, 18, 411-416 (2000). [doi]
132. Cameron F. Abrams, David B. Graves, “Molecular dynamics simulations of Si etching by energetic CF3+ ions.” J. Appl. Phys., 86, 5938-5948 (1999). [doi]
133. Cameron F. Abrams, David B. Graves, “Three-dimensional spatiokinetic distributions of sputtered and scattered products of Ar+ and Cu+ impacts onto the Cu surface: Molecular dynamics simulations.” IEEE Trans. Plas. Sci., 27, 1426-1432 (1999). [doi]
134. Michael A. Vyvoda, Cameron F. Abrams, David B. Graves, “Feature evolution simulation of copper seed layer deposition: Using atomic level particle scattering information.” IEEE Trans. Plas. Sci., 27, 1433-1440 (1999). [doi]
135. Cameron F. Abrams, David B. Graves, “Cu sputtering and deposition by off-normal, near-threshold Cu+ bombardment: Molecular dynamics simulations.” J. Appl. Phys., 86, 2263-2267 (1999). [doi]
136. Cameron F. Abrams, David B. Graves, “Energetic ion bombardment of SiO2 surfaces: Molecular dynamics simulations.” J. Vac. Sci. Technol. A, 16, 3006-3019 (1998). [doi]
137. W. S. Ahn, Yaping Zhong, Cameron F. Abrams, P. K. Lim, P. A. Brown, “Biphasic autoxidation of tetralin catalyzed by surface-active transition metal complexes.” J. Phys. Chem. B, 101, 596-602 (1997). [doi]
138. Yaping Zhong, Cameron F. Abrams, P. K. Lim., “Biphasic synthesis of poly(2,6-dimethyl-1,4-phenylene oxide) using a surface-active coupling catalyst. 2. Process improvements, additional kinetic results, and proposed reaction mechanism.” Ind. Eng. Chem. Res., 34, 1529-1535 (1995). [doi · PMID]

Seminars & Presentations

Invited Lectures

• “Molecular Simulations of Thermosetting Polymers”, Chemical and Biomolecular Engineering, North Carolina State University, 3 April 2026
• “Molecular Simulations of Thermosetting Polymers”, Chemical Engineering, University of Virginia, 2 October 2024
• “Modern Molecular Simulations Using Extended Lagrangian Approaches”, National Institute of Chemistry, 18 June 2024
• “Modern Molecular Simulations Using Extended Lagrangian Approaches”, National University of Cordoba, 25 March 2024
• “Molecular Simulations of Thermosetting Polymers”, Chemical Engineering, Northeastern University, 5 December 2023
• “Molecular Simulations of Thermosetting Polymers”, Chemical and Biomolecular Engineering, Lehigh University, 9 November 2022
• “Recent simulation methods for resolving molecular details in thermodynamics and kinetics”, Chemical Engineering, University of South Florida, 3 March 2021
• “Recent simulation methods for resolving molecular details in thermodynamics and kinetics”, Chemical and Biological Engineering, University at Buffalo, 23 October 2019
• “Recent simulation methods for resolving molecular details in thermodynamics and kinetics”, Chemical Engineering, University of California, 10 October 2019
• “Recent simulation methods for resolving molecular details in thermodynamics and kinetics”, Chemical Engineering, University of Rhode Island, 18 October 2018
• “On-the-fly free-energy parameterization: Better statistics in biomolecular simulations from enhanced sampling”, Simons Foundation, 13 November 2017
• “New Rare-Event Methods in Molecular Simulations: Some Recent Progress”, 15 October 2017
• “New Rare-Event Methods in Molecular Simulations: Applications to Ligand Entry Kinetics and Protein Conformational Changes”, 9 September 2017
• “Rare-Event Methods in Molecular Simulations: Some Recent Progress”, 4 August 2017
• “Thermodynamics and kinetics of biomolecular interactions using molecular simulations”, 17 March 2017
• “Thermodynamics and kinetics of biomolecular interactions using molecular simulations”, 1 March 2017
• “Determining protein conformational statistics using molecular dynamics simulations”, 31 October 2016
• “Recent Advances in Molecular Simulations of Complex Materials and Biomolecules”, ExxonMobil Research and Engineering, 25 October 2016
• “Determining conformational statistics of proteins via replica-exchange on-the-fly free-energy parameterization”, 252nd National Meeting of the American Chemical Society, 25 August 2016
• “The Roles of Intrinsic Curvature and Lipid Sorting on the Stability of Hemifusions via Coarse-Grained Molecular Simulations”, CECAM International Workshop on Biomembranes: The Consequences of Complexity, 19 August 2016
• “New rare-event methods in molecular simulations: Applications to ligand entry kinetics and protein conformational changes”, Center for Biophysics and Computational Biology Seminar, 27 April 2016
• “New rare-event methods in molecular simulations: Applications to ligand entry kinetics and protein conformational changes”, AMCS/PICS Colloquium, 15 April 2016
• “Markovian Milestoning MD Simulations for Computing On- and Off-Rates”, 251st National Meeting of the American Chemical Society, 12 March 2016
• “Markovian Milestoning MD Simulations for Computing On- and Off-Rates”, Mathematical Challenges in Protein and Drug Design
• “Small-Molecule Entry and Exit Kinetics in Proteins Computed Using Markovian Milestoning”, Plenary Session, 11 November 2015
• “Metastabilities and Kinetics in Proteins and Viruses”, Mainz Molecular Simulation Days, 11 June 2015
• “Metastabilities and Kinetics in Proteins and Viruses”, Biological Physics Seminar Series, 28 April 2015
• “Understanding and harnessing biomolecular metastabilities”, Patten Seminar Series, 16 September 2014
• “Markovian Milestoning for Computing Diffusion Rates of Ligands in Proteins”, Telluride Science Research Center Workshop: Searching for Reaction Coordinates and Order Parameters, 11 July 2014
• “Understanding and harnessing biomolecular metastabilities”, UW Molecular Science and Engineering Center Seminar, 22 April 2014
• “Markovian Milestoning for Computing Diffusion Rates of Ligands in Proteins”, March meeting of the American Physical Society, 7 March 2014
• “Understanding and harnessing biomolecular metastabilities”, Special Seminar, 9 January 2014
• “HIV-1 Envelope Structure and Function”, Faculty Fellows Symposium, 11 November 2013
• “Exploring and Mapping Free Energy Surfaces using Temperature-Acceleration, the String Method, and Single-Sweep”, Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics, 19 July 2013
• “MD of Soft-Matter Systems”, 2013 MACH Conference, 13 April 2013
• “Novel Microbicides against HIV”, Drexel University College of Engineering, 13 February 2013
• “Observing Rare Events in Biomolecular Simulations using Temperature-Acceleration and the String Method”, Drexel University College of Medicine, 26 November 2012
• “Observing Rare Events in Biomolecular Simulations using Temperature-Acceleration and the String Method”, Chemistry, Physical Chemistry Seminar, 24 September 2012
• “Observing Rare Events in Biomolecular Simulations using Temperature-Acceleration and the String Method”, Institut Pasteur, 3 September 2012
• “Collective-Variable-Enhanced Biomolecular Simulations”, Kavli Institute of Theoretical Physics, 26 April 2012
• “Animating the Protein Data Bank with Modern Molecular Simulations”, Rutgers-Camden Center for Computational and Integrative Biology, 28 November 2011
• “Collective Variables and Conformational Sampling in Biomolecular Simulations”, 2011 von Neumann Symposium of the American Mathematical Society, 7 July 2011
• “Animating the Protein Data Bank with Modern Molecular Simulations”, Department of Chemical and Biomolecular Engineering, 6 April 2011
• “Target-Blind Conformational Sampling in All-Atom Protein Simulations with Temperature-Accelerated Molecular Dynamics”, 240th ACS National Meeting & Exposition, 25 August 2010
• “The Receptors for Insulin and Insulin-Like Growth Factors: All-Atom Molecular Simulations”, Hagedorn Research Institute (Novo Nordisk), 6 August 2010
• “Large-Scale Conformational Sampling in All-Atom Protein Simulations using Temperature-Accelerated Molecular Dynamics”, Courant Institute Biophysics Seminar, 29 January 2010
• “Molecular Simulation Studies of Insulin and its Receptor”, Department of Physics, 11 November 2008
• “Molecular Simulation Studies of Insulin and its Receptor”, Department of Biochemistry and Molecular Biology, 28 January 2008
• “Molecular Simulation Studies of Chaperonin”, Department of Chemical and Biomolecular Engineering, 4 October 2007
• “Computer Simulation Studies of Chaperonin”, Department of Chemical and Environmental Engineering, 28 August 2007
• “Some Recent Developments in Monte Carlo Simulations of Soft Condensed Matter”, Department of Applied Mathematics, 25 October 2006
• “Systematic Coarse-Graining and Concurrent Multiresolution Simulation of Molecular Liquids”, ORNL/CNRS NanoFocUL, 30 August 2006
• “Entanglement Effects in the Plastic Deformation of Glassy Polymers and Nanocomposites”, US-Poland Workshop on Nanoscience and Nanostructured Materials, 29 June 2006
• “Simulation Studies of Chemotaxis and Random Motility”, CCNY Chemical Engineering Department, 30 January 2006
• “Simulation Studies of Chemotaxis and Random Motility”, University of New Mexico Department of Chemical and Nuclear Engineering, 6 December 2005
• “Simulation Studies of Chemotaxis and Random Motility”, Lehigh University Department of Chemical Engineering, 16 November 2005
• “Systematic Coarse-Graining and Concurrent Multiresolution Simulation of Molecular Liquids”, University of Minnesota Institute for Mathematics and its Applications (IMA) workshop: Effective Theories of Materials and Macromolecules, 11 June 2005
• “Simulations of Chemotaxis and Random Motility in Finite Domains”, Materials Research Society Fall Meeting
• “Resolution Focusing in Simulations of Molecular Liquids”, American Chemical Society National Meeting, 22 August 2004
• “Resolution Focusing in Simulations of Molecular Liquids”, NYU Courant Institute Applied Mathematics Seminar
• “Inhomogeneous Coarse-Graining of Polymers and Polymer/Metal Interfaces”, FZ Jülich Workshop on Computational Soft Matter
• “Multiresolution Simulation of Polymers”, ETHZ Summer School on Multiscale Modeling and Simulation
• “Atomistic Simulation of Energetic Fluorocarbon Ion Bombardment of Silicon”, Department of Chemistry
• “Comparison of Coarse-Graining Schemes for Structural Investigation of Polycarbonate Liquids via Simulation”, Division of Engineering and Applied Science
• “Theory and Simulation of the Fractal Stages of Homopolymer Collapse”, Department of Physics, 13 Nov 2001
• “Molecular Dynamics Simulations of Reactive Ion Bombardment of Silicon Surfaces”, Department of Physics
• “Molecular Dynamics Simulations of Reactive Ion Bombardment of Silicon Surfaces”, Ph.D. Colloquium

Contributed Presentations

• Gourav Shrivastav, Eric Vanden-Eijnden, Cameron F. Abrams, “Mapping Saddles and Minima on Free Energy Surfaces Using Multiple Climbing Strings”, Annual Meeting of the American Institute of Chemical Engineers, Orlando, Florida
• Ming Huang, Cameron F. Abrams, “Interrelating Relative Reactivity, Network Topologies, and Thermochemical Properties in Vinyl-Ester Thermosets Using All-Atom Molecular Simulations”, Annual Meeting of the American Institute of Chemical Engineers, Orlando, Florida
• Salman Zarrini, Cameron F. Abrams, “Multi-scale Modeling of Fiber-Matrix Interphase”, Annual Meeting of the American Institute of Chemical Engineers, Orlando, Florida
• Steven Gossert, Bibek Parajuli, Irwin Chaiken, Cameron 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”
• Jasmine Gardner, Cameron F. Abrams, “Flap-Opening Dynamics and Ligand Unbinding of HIV-1 Protease Studied using Accelerated MD Simulations”
• Natasha Gupta, Ryan Gordon, Samba Somisetti, Cameron F. Abrams, “Identifying unique HIV-1 entry inhibitor leads using virtual screening and docking techniques”
• Steven Gossert, Cameron F. Abrams, “Roles of Conserved Tryptophans in Trimerization of HIV-1 Membrane-Proximal External Regions: Implications for Virucidal Design via Alchemical Free-Energy Molecular Simulations”
• Jasmine Gardner, Cameron F. Abrams, “Line Tension and Lipid Sorting Modulate Dynamics of Hemifusion Diaphragm Dissipation”
• Jasmine Gardner, Cameron F. Abrams, “Intrinsic curvature and lipid sorting modulate dynamics of hemifusion diaphragm dissipation”
• Changwoon Jang, Cameron F. Abrams, “Optimizing coarse-grained potentials to improve the prediction of thermoset epoxy polymer properties”
• S. Alexis Paz, Eric Vanden-Eijnden, Cameron F Abrams, “Free energy and hidden barriers: The β-sheet structure of the prion protein”, 61st Annual Meeting of the Biophysical Society, New Orleans, Louisiana
• Alexis Paz, Cameron F. Abrams, “Replica-Exchange on-the-Fly Parameterization: Application of a High-Precision Free-Energy Method to Understanding the Roles of the M129V/D178N Polymorphisms in the Conformational Thermodynamics of Human Prion Protein”
• Jung-ho Yang, Cameron F. Abrams, “Understanding Relationships Between Molecular Structures and Thermomechanical Properties of Thermosetting Polymers with Novel Bio-Based Building Blocks”
• Francesca Moraca, Adel A. Rashad, Kriti Acharya, Irwin Chaiken, Cameron F. Abrams, “Cyclic peptide triazoles docking and Molecular Dynamics simulation in three different gp120 states: selection of the best target for future peptide triazole’s optimization”
• S. Alexis Paz, Matthew Cameron, Cameron F. Abrams, “On the Role of the V3 Loop in the Conformational Thermodynamics of Bridging Sheet Formation in HIV-1 gp120: On-the-fly parameterization Free-Energy Calculations of the BG505 SOSIP.664 protomer”
• Changwoon Jang, Cameron F. Abrams, “Coarse-Grained Molecular Dynamics Simulations of DGEBA/POP-DA Crosslinked Thermosets”
• S. Alexis Paz, Cameron F Abrams, “Free energy and hidden barriers: The β-sheet structure of the prion protein”, 251st National Meeting of the American Chemical Society, San Diego, California
• Francesca Moraca, Adel A. Rashad, Kriti Acharya, Irwin Chaiken, Cameron F. Abrams, “Binding of the cyclic peptide triazole AAR029F to the HIV-1 envelope glycoprotein gp120 in 3 different conformations to explore its mechanism of action and the possible competition with the 17b antibody”
• S. Alexis Paz, Cameron F Abrams, “Prion protein conformational statistics via on-the-fly free-energy parameterization”, Annual Meeting of the American Institute of Chemical Engineers, Salt Lake City, Utah
• Tang-Qing Yu, Mauro Lapelosa, Eric Vanden-Eijnden, Cameron F Abrams, “Markovian Milestoning for Computing Rates of Entry, Exit, and Internal Diffusion of Ligands in Proteins”, Biophysical Society Annual Meeting, Baltimore, Maryland
• Anthony Bucci, Cameron F Abrams, “Identification and Allosteric Regulation of Oxygen Pathways in Monomeric Sarcosine Oxidase Via Single-Sweep Free Energy Reconstruction”, Annual Meeting of the American Institute of Chemical Engineers, Atlanta, Georgia
• Mauro Lapelosa, Tang-Qing Yu, Eric Vanden-Eijnden, Cameron F Abrams, “Markovian Milestoning for Computing Diffusion Rates of Ligands in Proteins”, Annual Meeting of the American Institute of Chemical Engineers, San Francisco, California
• Harish Vashisth, Cameron F Abrams, “Understanding the activation mechanism of the insulin receptor kinase domain using enhanced conformational sampling and free-energy calculations”, Annual Meeting of the American Institute of Chemical Engineers, Pittsburgh, Pennsylvania
• Cameron F Abrams, Eric Vanden-Eijnden, “On the fly free energy parameterization using temperature accelerated molecular dynamics”, Annual Meeting of the American Institute of Chemical Engineers, Pittsburgh, Pennsylvania
• Debashish Mukherji, Majid Sharifi, Giuseppe R Palmese, Cameron F Abrams, “Toughness enhancement in neat epoxies by microsurface drawing”, International Workshop on Computational Mechanics of Materials (IWCMM XXII), Baltimore, Maryland
• Cameron F Abrams, “Unbiased Folding of alpha-Helices using Temperature Accelerated Molecular Dynamics”
• Harish Vashisth, Cameron F Abrams, “Temperature-accelerated molecular dynamics reveals that insulin can undergo large-scale conformational reorganization on binding to its receptor”
• Spencer Stober, Cameron F Abrams, “Enhanced Meta-Analysis of Acetylcholine Binding Protein Structures Reveals Conformational Signatures of Agonism in Nicotinic Receptors”
• Ali Emileh, Ferit Tuzer, Diogo R. Moreira, Irwin Chaiken, Cameron F Abrams, “A model for binding of peptide-triazole dual-site antagonist entry inhibitors to HIV gp120”
• Ali Emileh, Cameron F. Abrams, “HIV-1 gp120: Atomic Insight into a Layered Topology and Plasticity of the Inner Domain”
• Harish Vashisth, Cameron F. Abrams, “A temperature-accelerated molecular dynamics study of the insulin receptor kinase”
• Ali Emileh, Cameron F. Abrams, “Investigation of the layered structure of HIV-1 gp120 using temperature-accelerated molecular dynamics”, 24th Annual Symposium of the Protein Society
• Vamshi Gangupomu, Cameron F. Abrams, “Conformational prediction of the HIV-1 gp41 membrane-spanning domain”, 240th ACS National Meeting & Exposition
• Harish Vashisth, Cameron F. Abrams, “DFG-flip in the insulin receptor kinase is facilitated by a helical intermediate”, 5th Protein Kinases in Drug Discovery, Boston, Massachusetts
• Debashish Mukherji, Cameron F. Abrams, “Anomalous ductility in thermoset/thermoplastic polymer alloys: An explanation based on overlap concentration and cavity growth”
• Debashish Mukherji, Cameron F. Abrams, “Possible explanation of anomalous ductility inthermoset/thermoplastic polymer alloys”
• Harish Vashisth, Cameron F. Abrams, “How insulin-like growth factor hormones IGF1 and IGF2 engage their cognate receptor”, Biophysical Society Annual Meeting, San Francisco, CA
• Debashish Mukherji, Cameron F. Abrams, “Strain Hardening in Highly Cross-Linked Polymer Networks: An Explanation Based on Microvoid Formation”
• Debashish Mukherji, Cameron F. Abrams, “Anomalous Ductility in Thermoset/Thermoplastic Polymer Alloys”
• Ali Emileh, Cameron F. Abrams, “Investigation of geometrical constraints on α1 helix folding in b12-bound HIV-1 gp120 core through targeted molecular dynamics”
• Harish Vashisth, Cameron F. Abrams, “Molecular Simulation Studies of Insulin Binding to the Insulin Receptor”, Annual Meeting of the American Institute of Chemical Engineers, Nashville, TN
• Harish Vashisth, Cameron F. Abrams, “Millisecond Time-scale Ligand (Un)binding Event Studied using Accelerated Molecular Dynamics Simulations”, Foundations of Molecular Modeling and Simulation (FOMMS-2009), Blaine, WA
• Harish Vashisth, Cameron F. Abrams, “Thermodynamics of Ligand (Un)binding in the Insulin Hexamer and the Insulin Receptor”, Gordon Research Conference on Computer Aided Drug Design, Tilton, NH
• Debashish Mukherji, Cameron F. Abrams, “Microvoid formation and strain hardening in highly cross-linked polymer networks, American Physical Society March Meeting”
• Harish Vashisth, Cameron F. Abrams, “A Thermodynamic Study of Ligand Access/escape from Protein Cavities”, Biophysical Society Annual Meeting, Boston, MA
• Harish Vashisth, Cameron F. Abrams, “Docking of Insulin to its Receptor”, Biophysical Society Annual Meeting, Boston, MA
• Harish Vashisth, Cameron F. Abrams, “Thermodynamics of Multiple Phenol Dissociation Pathways in the R6 Insulin Hexamer”, Annual Meeting of the American Institute of Chemical Engineers, Philadelphia, PA
• Harish Vashisth, Cameron F. Abrams, “Thermodynamics of Multiple Phenol Dissociation Pathways in the R6 Insulin Hexamer”, Annual Meeting of the American Institute of Chemical Engineers, Philadelphia, PA
• Harish Vashisth, Cameron F. Abrams, “Ligand escape pathways and free energy calculations from nonequilibrium simulations: A computational study of the insulin-phenol complex”
• Cameron F. Abrams, “Molecular dynamics simulations of the GroEL heptamer”, Annual Meeting of the American Institute of Chemical Engineers, Salt Lake City, UT
• Harish Vashisth, Cameron F. Abrams, “Escape pathways of phenolic ligands from the insulin-phenol complex”, Annual Meeting of the American Institute of Chemical Engineers, Salt Lake City, UT
• Yelena Sliozberg, Cameron F. Abrams, “Spontaneous conformational transitions in unbiased all-atom molecular dynamics simulations of the GroEL subunit”, Biophysical Society Annual Meeting, Baltimore, MD
• Yelena Sliozberg, Cameron F. Abrams, “Nucleotide-dependent allostery in the GroEL subunit”
• Cameron F. Abrams, “Crazing and Entanglements in Glassy Polymers”
• Nam-Kyung Lee, Cameron F. Abrams, Albert Johner, “Optimal Confinement for Internal Polymer Binding”, American Physical Society March Meeting, Baltimore, MD
• David Richardson, Cameron F. Abrams, “Entanglement Effects in Plastic Deformation of Linear Polymer Glasses”, American Physical Society March Meeting, Baltimore, MD
• Ehsan Jabbarzadeh, Cameron F. Abrams, “Strategies to Enhance Capillary Formation inside Biomaterials: A Computational Study”
• Yelena Sliozberg, Cameron F. Abrams, “Density-of-States Simulation of Collapse of Confined Heteropolymers”
• David Richardson, Cameron F. Abrams, “Entanglement Effects in the Plastic Deformation of Filled Polymer Glasses: A Simulation Study”
• Yelena Sliozberg, Cameron F. Abrams, “Density-of-States Simulation of Collapse of Confined Heteropolymers”
• Ehsan Jabbarzadeh, Cameron F. Abrams, “Simulation of cell chemotaxis in 2D random porous domains”
• Cameron F. Abrams, “Resolution Focusing in Molecular Simulation of Liquids”
• Ehsan Jabbarzadeh, Cameron F. Abrams, “Chemotaxis and random motility in unsteady chemoattractant fields: A computational study”
• Yelena Sliozberg, Cameron F. Abrams, “Molecular simulation of branched amphiphilic heteropolymers in confined geometries”
• Ehsan Jabbarzadeh, Cameron F. Abrams, “Chemotactic Cell Migration in Inhomogeneous Domains: A Computational Study”, 2004 BMES Annual Fall Meeting, Philadelphia
• Ehsan Jabbarzadeh, Cameron F. Abrams, “Computational Studies of Cell Migration”
• Ehsan Jabbarzadeh, Cameron F. Abrams, “Computational Studies of Cell Migration”
• Yelena Sliozberg, Nam-Kyung Lee, Cameron F. Abrams, “Molecular Dynamics Simulation of Intramolecular Self-Assembly in Polysoaps”
• Cameron F. Abrams, Luigi Delle Site, Kurt Kremer, “Multiscale Molecular Dynamics Simulation of the Liquid Polycarbonate/Nickel (111) Interface”
• Cameron F. Abrams, Nam-Kyung Lee, Sergei Obukhov, “A Combined Simulation and Theoretical Study of Homopolymer Collapse”
• Cameron F. Abrams, Kurt Kremer, “Multiscale Simulation of Bisphenol-A-Polycarbonate”
• Cameron F. Abrams, Kurt Kremer, “Structure and Dynamics of Polycarbonate Melts via Novel Coarse-Grained Molecular Dynamics Simulation”
• Cameron F. Abrams, David B. Graves, “Product Formation Mechanisms in Fluorocarbon Ion Etching of Silicon via Atomistic Simulation”
• V. V. Serikov, S. Kawamoto, Cameron F. Abrams, David B. Graves, “Atomic scale simulation of plasma-assisted deposition of diamond-like carbon films”
• Cameron F. Abrams, David B. Graves, “Deposition and Etching Using Fluorocarbon Ions:  Molecular Dynamics Simulations”
• Cameron F. Abrams, David B. Graves, “Deposition and Etching Using Fluorocarbon Ions: Molecular Dynamics Simulations”
• Junichi Tanaka, Cameron F. Abrams, David B. Graves, “Molecular Dynamics Simulations of Fluorocarbon Films”
• Cameron F. Abrams, David B. Graves, “Scattering and Sputtering Processes of Energetic Ar+ and Cu+ Ions on Cu Surfaces: Molecular Dynamics Simulations”
• Cameron F. Abrams, David B. Graves, “Scattering and Sputtering Processes of Energetic Ar+ and Cu+ Ions on Cu Surfaces: Molecular Dynamics Simulations”
• Cameron F. Abrams, David B. Graves, “Molecular Dynamics Simulations of Ar+ and Cu+ Impacts onto Cu Surfaces: Product Spatiokinetic Distributions”, Northern California Chapter of the American Vacuum Society Thin Films User Symposium, Foster City, California
• Cameron F. Abrams, David B. Graves, “Scattering and Sputtering Processes of Energetic Ar+ and Cu+ Ions on Cu Surfaces: Molecular Dynamics Simulations”
• Cameron F. Abrams, David B. Graves, “Energy and Angular Distributions of Argon Ions Reflected from SiO2 Surfaces: Molecular Dynamics Simulations”

Funded Proposals

Funded

• “Combining Molecular Simulations and Biophysical Methods to Characterize Conformational Dynamics of the HIV-1 Envelope Glycoprotein” NIH, R01 AI178833, $4,091,232, 7/10/2023-6/30/2028. Co-PIs: Joe Sodroski, Dana Farber Cancer Institute/Harvard Medical School; Walther Mothes, Yale
• “Transition Path Theory and Markovian Milestoning for Prediction of Protein-Ligand Binding Kinetics in Molecular Simulations” NIH, R01 GM100472 (1st renewal), 9/1/17-5/31/21, $1,300,000, 9/1/17-5/31/21. Co-I: Eric Vanden-Eijnden, NYU
• “Thermosets for Agile Manufacturing,” Army Research Lab, W911NF-17-2-0227, $3,000,000, 9/1/17-12/31/23. Co-I (PI: G. R. Palmese)
• “Biobased Thermosetting Polymers for Composite, Adhesive, and Coating Applications,” Army Research Lab, W911NF-12-R-0011, $2,400,000, 1/1/17-12/31/19. Co-I (PI: G. R. Palmese) Abrams' share supported one FTE PhD student.
• “Dual-action virolytic entry inhibitors against HIV-1” NIH, R01 GM115249, 1,700,000, 7/1/15-6/30/19. Multiple-PI grant; other Co-PI is Irwin Chaiken, DUCOM. Abrams' share supports one FTE PhD student.
• “Structure-based antagonism of HIV-1 envelope function in cell entry” NIH, $10,000,000, 9/30/13-8/31/23. Co-I (PI: I. Chaiken) 9/30/13-8/31/23. Abrams is the leader of the Computational Core of this program project, directly supervising one postdoc and an annual direct cost of $136,000.
• “Drexel/ExxonMobil Sponsored Research Agreement: Advanced Studies of Self-Assembly” ExxonMobil, $460,000, 1/1/14-12/31/17.
• “Center for Sustainable Corrosion Protection” Army Research Lab, W911NF-13-2-0046, $3,000,000, 9/1/13-8/31/18. Co-I (PI: G. R. Palmese)
• “Collaborative Research: Multiscale molecular simulations of protein-mediated bilayer fusion,” NSF, MCB-1330205, $350,000, 9/1/13-8/31/18. This is a collaboration with M. Deserno at CMU; CMU budget is also $350,000, but does not pass through Drexel.
• “Collaborative Research: On-the-fly free energy parameterization in molecular simulations” NSF, DMR-1207389', $286,455, 9/1/12-8/31/15. NYU (Vanden-Eijnden) is the secondary institution, receiving about the same amount.
• “Materials in Extreme Dynamic Environments: The Johns Hopkins Consortium” Army Research Lab (through U. Del./JHU), $300,000, 4/2012-3/2020. (PI: KT Ramesh, JHU)
• “Approaches to computing diffusion rates in proteins from transition path theory” NIH, R01 GM100472, $1,100,000, 9/1/11-5/31/16. (Co-I: Eric Vanden-Eijnden, NYU)
• “PASI: Molecular-Based Multiscale Modeling and Simulation; Montevideo, Uruguay; September 1-14, 2012” NSF, OISE-1124480', $100,000, 9/2024. (PI: Jim Pfaendtner, UW)
• “HIV-1 gp120 conformational transitions in activation and antagonism” NIH, R21 AI093248, $450,000, 4/1/11-3/31/13. Multiple-PI grant; other Co-PI is Irwin Chaiken, DUCOM Biochemistry
• “Conformational signatures of Neurotransmitter-Induced Gating and Desensitization of Nicotinic Ion Channels: A Collaborative Simulation and Experimental Approach” Commonwealth of Pennsylvania, Tobacco Settlement Funds, GRID/CURE', $55,000, 1/1/11-12/31/11. (Co-I: Mike White, DUCOM Biochemistry)
• “MRI: Acquisition of a GPU-Accelerated High Performance Computing Cluster” NSF, AST-0959884, $440,000, 3/1/10-2/28/11.
• “Chimeric Virucides Based on a Novel Theory of Viral Metastability” NIH, R01 AI084117, $1,300,000, 9/1/09-8/31/13. (Co-I Irwin Chaiken, DUCOM Biochemistry)
• “DURIP: Acquisition of a High-Performance Computer Cluster” Army Research Lab, W911NF-07-1-0301, $120,000, 6/15/07-6/14/08.
• “Drexel-ARL Materials Center of Excellence in Polymeric Materials” Army Research Lab, W911NF-06-2-0013, $1,350,000, 3/30/2006-3/31/2011. (PI: Giuseppe Palmese; Co-Is Yossef Elabd and Chris Li)
• “CAREER: Multiscale simulation of solute transport in hydrogels” NSF, CBET-0544933, $400,000, 2/1/2006-1/31/2010.
• “Thermodynamics of Heteropolymers in Confinement” American Chemical Society, PRF 42368-G7, $35,000, 2/2005-1/2007.
• “ITR: Inhomogeneously Resolved Simulation of Protein Assembly Dynamics” NSF, DMR-0427643, $420,000, 9/2004-8/2008.
• “ONR-YIP: Predicting Failure in Carbon Nanotube Reinforced Polymer Composites: A Novel Multiscale Simulation Approach” Office of Naval Research, N00014-03-1-0655', $332,313, 6/2003-5/2006.
• “QSB: Quantitative Simulation of Cell Migration in Porous Biomaterials” NSF, CBET-0331191', $96,129, 11/2003-10/2005.

Supercomputer Time

• “Molecular Dynamics Studies of Epoxies,” DoD HPCMP, 9M hours, through 10/31/2024.
• “Molecular Dynamics Studies of Various Protein Systems” NSF ACCESS, MCB080073N, 7/1/2007-present.
• “Molecular Simulation of Mechanical Deformation of Filled Epoxies” NSF TeraGrid, 30,000 hours, 9/1/2006-9/1/2007.

Pending / Planned

• “New CD4 mimetics targeting conformational vulnerabilities of the HIV-1 envelope glycoprotein” NIH, $700,00. (MPI: Co-PIs’s Andrés Finzi (UMontreal) and Amos Smith III (UPenn))

Patents

• Recombinant Chimeric Cyanovirin-MPER Constructs for Inactivating HIV-1. US Patent #10,603,545 B2, March 31, 2020. Inventors: Irwin M. Chaiken, Cameron F. Abrams, Mark A. Contarino, Arangassery R. Bastian.

Students & Postdocs Supervised

Doctoral

• Prince Gyasi — MD Simulations of HIV-1 Env (9/24-)
• Imran Yasin — Molecular Simulations of Thermoset Additive Manufacturing (3/20-3/21)
• Dr. Ming Huang — Molecular Simulations of Thermoset Additive Manufacturing (11/17-8/22)
• Matthew Cameron — Milestoning MD of Ligand Binding Kinetics (11/16-8/17)
• Donald Seaman — Molecular Simulations of Bio-based Thermosets (11/16-6/19)
• Dr. Natasha Vergara — Computational Design of HIV-1 Entry Inhibitors (11/16-8/22)
• Dr. Steven Gossert — Novel HIV-1 Virucides (11/15-6/20)
• Dr. Jasmine Gardner — Lipid and protein contributions to viral proliferation as studied using MD simulations and advanced MD techniques (11/14-6/19)
• Dr. Arun Srikanth — Molecular simulations of thermosets (11/13-06/18)
• Dr. Ryan Gordon — Molecular Simulation Studies Self-Assembly
• Dr. Anthony Bucci — Approaches to computing diffusion rates in proteins using transition-path theory (10/11-5/16)
• Dr. Michelle Baker — Molecular Simulation Studies of HIV-1 Structural Biology
• Dr. Ali Emileh — Molecular Simulation of HIV-1 gp120 (10/07-12/12)
• Dr. Spencer Stober — Protein Conformational Changes (1/08-9/12)
• Dr. Vamshi Gangupomu. “Molecular Simulations Studies of HIV-1 gp41 Protein-Membrane Interactions — Dates of supervision: 7/09-10/10 (previously supervised by Franco Capaldi (7/09-10/10 (previously supervised by Franco Capaldi, MEM))
• Dr. Harish Vashisth. “Molecular Dynamics Studies of Insulin.” Dates of Supervision: 9/05-6/10. Graduated — June 2010. Supported on NSF CBET-0544933 (CAREER). Currently a full professor in the Chemical Engineering Department and the University of New Hampshire.
• Daniel Rundle. Dates of supervision: 9/05-6/06. Left PhD program. (9/05-6/06)
• David G. Richardson (co-advisor: W. Krandick — Drexel CS). Dissertation title unknown. Dates of supervision: 10/03-10/06. Supported on ONR N00014-03-1-0655. Graduation date unknown. (10/03-10/06)
• Dr. Yelena Sliozberg. “Molecular Simulation of Chaperonins — Dates of Supervision: 9/02-9/07. Graduated
• Dr. Ehsan Jabbarzadeh (co-advisor: C. Laurencin — UVA). “Theoretical and Experimental Approaches to Vascularization of Tissue Engineered Bone (1/03-6/07; Graduated, June 2007)

Postdoctoral

• *Dr. Salsabil Abou-Hatab — MD Simulations of HIV-1 Env
• Dr. Ketan Khare — Dynamics of Thermosetting Polymers
• Dr. Mohammadjavad Mohammadi — Computational Drug Design of HIV-1 Entry Inhibitors (2019-present)
• Dr. Gourav Shrivastav — Markovian Milestoning (2018-2022)
• Dr. Salman Zarrini — Molecular Simulation Studies of Thermosets (2018-2022)
• Dr. Samba Venkatasomisetti — Computational Drug Design of HIV-1 Entry Inhibitors (2017-2019)
• Dr. Jungho Yang — Computational Studies of Corrosion (2015-2017)
• Dr. Francesca Moraca — Computational Drug Design of HIV-1 Entry Inhibitors (2014-2016)
• Dr. Sergio Alexis Paz — On-the-fly free energy parameterization (2014-2016)
• Dr. Chang-Woon Jang — Molecular Simulations of Epoxies (2012-2017)
• Dr. Mauro Lapelosa — Transition-Path Theory (2011-2013)
• Dr. Debashish Mukherji — Molecular simulations of epoxies (2008-2010)

Masters

• *Matthew Gilpin. “Studies of Protein Conformational Dynamics” — Dates of supervision: 7/21-. (7/21-)
• Shyno Mathew. “Studies of O2 diffusion in monomeric sarcosine oxidase” — Dates of supervision: 6/08-6/10. Graduated BS/MS June 2010. (6/08-6/10)

Undergraduate

• Megan Gatchel (REU) — SARS-CoV-2 Variants Studied using Molecular Simulations
• Theodore Houser — Classification of HIV-1 Entry Inhibitors
• Marta Martinez — Classification of HIV-1 Spike Glycoprotein Structures
• Nicholas Carpentieri — Classification of HIV-1 Entry Inhibitors
• Noor Al-Nazal — Thermoset Molecular Simulations
• Ian O’Donnell — Cheminformatics Website and Database in PHP/MariaDB
• Zach Lloyd (REU) — Molecular Simulations in Thermoset Materials
• Ai Vi Truong — Molecular Simulations in Thermoset Materials
• Yen La — Molecular Simulations in Thermoset Materials
• Ariel Yeung — Molecular Simulations in HIV
• Tapiwanahse Ndlovu — Computational exploration of EGFRK
• Stephanie Edwards — Computational exploration of HIV-1 Env drug design targets
• Matthew Cameron — Computational drug design of HIV-1 entry inhibitors
• Priya Ramachandrula — Enhanced Sampling MD of Calmodulin
• Charles Bender — 2-D Wang-Landau Monte Carlo
• Christopher Petersen — 2-D Wang-Landau Monte Carlo
• Suroor Manzoor — Bitwise Voxelized 3D Domains: Toward Efficient Simulation of Diffusion in Porous Media

Honors & Awards

• Inaugural Bartlett '81 -- Barry '81 Professor of Chemical and Biological Engineering — Drexel University, 2022
• Provost Award for Outstanding Career Scholarly Achievement — Drexel University, 2020
• College of Engineering Outstanding Career Research Award — Drexel University, 2020
• Department of Chemical and Biological Engineering Research Award — Drexel University, 2017
• Impact Award in Computational Molecular Science and Engineering — American Institute of Chemical Engineers, 2015
• Fellow — American Institute of Medical and Biological Engineering, 2015
• College of Engineering Research Award — Drexel University, 2014
• Invited Participant, “Physical Principles of Multiscale Modeling, Analysis and Simulation in Soft Condensed Matter,” — Kavli Institute for Theoretical Physics, UCSB, 2012
• General Participant, “German-American Frontiers of Engineering” Symposium — National Academy of Engineering, 2008
• Graduate Mentor of the Year — Drexel University, 2007
• CAREER Awardee — NSF, 2006
• General Participant, ``Frontiers of Engineering'' Symposium — National Academy of Engineering, 2004
• Young Investigator Awardee — Office of Naval Research, 2006
• Chevron Graduate Fellow — University of California, Berkeley, Dept. Chem. Engr., 1998
• 2nd Place, Poster Competition, N — Northern California AVS Thin Films User Group, 1997
• 1st Place, Southern Regional Undergraduate Paper Contest — American Institute of Chemical Engineers, 1995
• 3rd Place, Southern Regional Undergraduate Paper Contest — American Institute of Chemical Engineers, 1994
• Phi Kappa Phi Inductee — NCSU, 1991
• Eastman Scholar — NCSU, 1991

Service

Department of Chemical and Biological Engineering, Drexel University

• Chair, Graduate Committee, 2008-2014, Member 2008-present
• Member, Undergraduate Committee, 2008-present
• Member, Committee on Academic Standing, 2008-2017; Chair, 2014-2017
• Graduate Advisor, 2008-2014
• Standing Member, Faculty Search Committee
• Standing Member, Faculty Evaluation Committee
• Faculty Advisor, AIChE Student Chapter, 2004-2006
• Seminar series organizer, 2003-2006
• Department Head, 2017-

College of Engineering, Drexel University

• Member, Junior Advisory Committee, 2006-2008
• Member, Senior Advisory Committee, 2008-2010
• Member, Tenure and Promotion Committee, 2015-2017
• Member, Task Force on Computational Engineering Minor, 2015-2016
• Chair, Electrical and Computer Engineering Department Head Search Committee, 2018
• Chair, Materials Science and Engineering Department Head Review Committee, 2019

University

• Workshop tutor, Drexel Center for Academic Excellence, 2002-2003
• Scholars Day Interviewer, 2003 & 2005
• Open Houses, several
• Member of the Faculty Senate representing COE, 2010-2013
• Member, COE Dean’s Search Committee, 2010-2011, Search failed
• Member, Senate Committee on Research and Scholarly Activities, 2010-2013. Chair, 2011-2013
• Member, Strategic Initiative #4 Implementation Task Force, 2012-2013
• Member, Computing Task Force, 2012-2013
• Chair, Board of Governance of the University Research Computing Facility, 2013-2017
• Member, Lebow College of Business Dean’s Search Committee, 2012-2014; Hired Frank Linnehan
• Member, CIO Search Committee, 2015; Hired Tom DiChiaro.
• Provost’s Fellow, CY 2016, under SVPR Aleister Saunders.
• Member, Review Committee for CoE Dean Joseph Hughes, 2016
• Member, Return to Campus Oversight Committee, 2020-2022

Profession

• National member: AIChE, ACS, AIMBE
• Session Chair, AIChE Annual Meetings, 2004-2011
• Session Chair, ACS Annual Meeting, 2016
• Session Co-organizer, APS March Meeting, 2004
• Session Organizer, APS March Meeting, 2005:
• “Theory and Simulation of Polymers I: General”
• “Theory and Simulation of Polymers II: Surfaces and Confinement”
• Ad-hoc Proposal Reviewer (counts): NSF (18), ACS , NIH , ESF , DTRA , AVH , ISF, counts
• Review Panelist (counts): NSF (9), NIH, counts
• Site visit panel: NSF-STC (1, Chair), 1, Chair
• Referee for the following journals :, counts as of June 2024; 236 total

New Courses Developed

• CHE 800-002: Molecular Simulation (2003-04 Spring Term, 2020-21 Spring Term), 2003-04 Spring Term, 2020-21 Spring Term
• Fundamentals of statistical mechanics, simulation programming and execution, Molecular Dynamics and Monte Carlo methods, free energy techniques, and advanced special topics were all covered in this course. Extensive course web pages were developed and continue to be maintained as a reference . Students were evaluated based on individual term projects., transition path sampling and Wang-Landau MC, metadynamics
• CHE 206: Basic Chemical Engineering Thermodynamics, 2007-08 Winter and all Winter/Summer terms
• This is the first of a two-course sequence in thermodynamics for chemical engineering majors, and it replaces general engineering thermodynamics . Text is Chemical, Biochemical and Engineering Thermodynamics by S. Sandler., TDEC 210 or “Energy II”
• CHE 614: Advanced Graduate Chemical Engineering Thermodynamics, 2010-11 Fall Term
• This is a new course in statistical mechanics for PhD students in Chemical Engineering. Students were evaluated based on homework assignments, two exams, and a term project. Text is Introduction to Modern Statistical Mechanics by D. Chandler.
• ENGR 131: Introductory Programming for Engineers, 2018-19 Winter Term
• This course used a zyBooks platform to teach Python to freshman engineering students. The lead instructor was Naga Kandasamy . Abrams lectured to one of four sections and developed the two take-home programming assignments. Abrams led instruction in the next academic year., Drexel ECE