Publications

135 entries « 2 of 3 »

2016

Bibek Parajuli; Kriti Acharya; Reina Yu; Brendon Ngo; Adel A. Rashad; Cameron F. Abrams; Irwin M. Chaiken

Lytic Inactivation of Human Immunodeficiency Virus by Dual Engagement of gp120 and gp41 Domains in the Virus Env Protein Trimer Journal Article

In: Biochemistry, vol. 55, no. 44, pp. 6100–6114, 2016.

Links | BibTeX

Tang-Qing Yu; Jianfeng Lu; Cameron F. Abrams; Eric Vanden-Eijnden

Multiscale implementation of infinite-swap replica exchange molecular dynamics Journal Article

In: Proceedings of the National Academy of Sciences, vol. 113, no. 42, pp. 11744–11749, 2016.

Links | BibTeX

Francesca Moraca; Kriti Acharya; Bruno Melillo; Amos B. Smith; Irwin 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 Mimics Journal Article

In: Journal of Chemical Information and Modeling, vol. 56, no. 10, pp. 2069–2079, 2016.

Links | BibTeX

Jasmine M. Gardner; Markus Deserno; Cameron F. Abrams

Effect of intrinsic curvature and edge tension on the stability of binary mixed-membrane three-junctions Journal Article

In: The Journal of Chemical Physics, vol. 145, no. 7, pp. 074901, 2016.

Links | BibTeX

C. Jang; C. F. Abrams

Thermal and mechanical properties of thermosetting polymers using coarse-grained simulation Journal Article

In: The European Physical Journal Special Topics, vol. 225, no. 8-9, pp. 1775–1783, 2016.

Links | BibTeX

Ryan Gordon; Spencer T. Stober; Cameron F. Abrams

Aggregation of 12-Hydroxystearic Acid and Its Lithium Salt in Hexane: Molecular Dynamics Simulations Journal Article

In: The Journal of Physical Chemistry B, vol. 120, no. 29, pp. 7164–7173, 2016.

Links | BibTeX

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 Journal Article

In: Journal of Chemical Theory and Computation, vol. 12, no. 6, pp. 2964–2972, 2016.

Links | BibTeX

Changwoon Jang; Majid Sharifi; Giuseppe R. Palmese; Cameron F. Abrams

Toughness enhancement of thermosetting polymers using a novel partially reacted substructure curing protocol: A combined molecular simulation and experimental study Journal Article

In: Polymer, vol. 90, pp. 249–255, 2016.

Links | BibTeX

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 Journal Article

In: Biochemistry, vol. 55, no. 3, pp. 447–458, 2016.

Links | BibTeX

2015

Majid Sharifi; Changwoon Jang; Cameron F. Abrams; Giuseppe R. Palmese

Epoxy Polymer Networks with Improved Thermal and Mechanical Properties via Controlled Dispersion of Reactive Toughening Agents Journal Article

In: Macromolecules, vol. 48, no. 20, pp. 7495–7502, 2015.

Links | BibTeX

S. Alexis Paz; Cameron F. Abrams

Free Energy and Hidden Barriers of the β-Sheet Structure of Prion Protein Journal Article

In: Journal of Chemical Theory and Computation, vol. 11, no. 10, pp. 5024–5034, 2015.

Links | BibTeX

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 Journal Article

In: Journal of the American Chemical Society, vol. 137, no. 8, pp. 3041–3050, 2015.

Links | BibTeX

Changwoon Jang; Timothy W. Sirk; Jan W. Andzelm; Cameron F. Abrams

Comparison of Crosslinking Algorithms in Molecular Dynamics Simulation of Thermosetting Polymers Journal Article

In: Macromolecular Theory and Simulations, vol. 24, no. 3, pp. 260–270, 2015.

Links | BibTeX

2014

Changwoon Jang; Majid Sharifi; Giuseppe R. Palmese; Cameron F. Abrams

Molecular Dynamics Simulation Study of Reactive Encapsulation of Solvent in Epoxy Curing Proceedings Article

In: Proceedings of the American Society for Composites - 29th Technical Conference, ASC 2014; 16th US-Japan Conference on Composite Materials; ASTM-D30 Meeting, DEStech Publications, 2014, ISBN: 9781605951249.

BibTeX

Arangassery Rosemary Bastian; Aakansha Nangarlia; Lauren D. Bailey; Andrew Holmes; R. Venkat Kalyana Sundaram; Charles Ang; Diogo R. M. Moreira; Kevin Freedman; Caitlin Duffy; Mark Contarino; Cameron Abrams; Michael Root; Irwin Chaiken

Mechanism of Multivalent Nanoparticle Encounter with HIV-1 for Potency Enhancement of Peptide Triazole Virus Inactivation Journal Article

In: Journal of Biological Chemistry, vol. 290, no. 1, pp. 529–543, 2014.

Links | BibTeX

Michelle K. Baker; Cameron F. Abrams

Dynamics of Lipids, Cholesterol, and Transmembrane α-Helices from Microsecond Molecular Dynamics Simulations Journal Article

In: The Journal of Physical Chemistry B, vol. 118, no. 47, pp. 13590–13600, 2014.

Links | BibTeX

Changwoon Jang; Majid Sharifi; Giuseppe R. Palmese; Cameron F. Abrams

Crosslink network rearrangement via reactive encapsulation of solvent in epoxy curing: A combined molecular simulation and experimental study Journal Article

In: Polymer, vol. 55, no. 16, pp. 3859–3868, 2014.

Links | BibTeX

Ali Emileh; Caitlin Duffy; Andrew P. Holmes; Arangassery Rosemary Bastian; Rachna Aneja; Ferit Tuzer; Srivats Rajagopal; Huiyuan Li; Cameron F. Abrams; Irwin M. Chaiken

Covalent Conjugation of a Peptide Triazole to HIV-1 gp120 Enables Intramolecular Binding Site Occupancy Journal Article

In: Biochemistry, vol. 53, no. 21, pp. 3403–3414, 2014.

Links | BibTeX

Michelle K. Baker; Vamshi K. 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 Journal Article

In: Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1838, no. 5, pp. 1396–1405, 2014.

Links | BibTeX

Anthony Bucci; Cameron F. Abrams

Oxygen Pathways and Allostery in Monomeric Sarcosine Oxidase via Single-Sweep Free-Energy Reconstruction Journal Article

In: Journal of Chemical Theory and Computation, vol. 10, no. 7, pp. 2668–2676, 2014.

Links | BibTeX

M. Sharifi; C. W. Jang; C. F. Abrams; G. R. Palmese

Toughened epoxy polymers via rearrangement of network topology Journal Article

In: Journal of Materials Chemistry A, vol. 2, no. 38, pp. 16071–16082, 2014.

Links | BibTeX

2013

Cameron Abrams; Giovanni Bussi

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration Journal Article

In: Entropy, vol. 16, no. 1, pp. 163–199, 2013.

Links | BibTeX

Mauro Lapelosa; Cameron F. Abrams

Transition-path theory calculations on non-uniform meshes in two and three dimensions using finite elements Journal Article

In: Computer Physics Communications, vol. 184, no. 10, pp. 2310–2315, 2013.

Links | BibTeX

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 Journal Article

In: Antimicrobial Agents and Chemotherapy, vol. 57, no. 10, pp. 4743–4750, 2013.

Links | BibTeX

Ali Emileh; Ferit Tuzer; Herman Yeh; Muddegowda Umashankara; Diogo R. M. Moreira; Judith M. LaLonde; Carole A. Bewley; Cameron F. Abrams; Irwin M. Chaiken

A Model of Peptide Triazole Entry Inhibitor Binding to HIV-1 gp120 and the Mechanism of Bridging Sheet Disruption Journal Article

In: Biochemistry, vol. 52, no. 13, pp. 2245–2261, 2013.

Links | BibTeX

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 Journal Article

In: Proteins: Structure, Function, and Bioinformatics, vol. 81, no. 6, pp. 1017–1030, 2013.

Links | BibTeX

Mauro Lapelosa; Cameron F. Abrams

A Computational Study of Water and CO Migration Sites and Channels Inside Myoglobin Journal Article

In: Journal of Chemical Theory and Computation, vol. 9, no. 2, pp. 1265–1271, 2013.

Links | BibTeX

2012

Cameron F. Abrams; Eric Vanden-Eijnden

On-the-fly free energy parameterization via temperature accelerated molecular dynamics Journal Article

In: Chemical Physics Letters, vol. 547, pp. 114–119, 2012.

Links | BibTeX

Spencer T. Stober; Cameron F. Abrams

Energetics and Mechanism of the Normal-to-Amyloidogenic Isomerization of β2-Microglobulin: On-the-Fly String Method Calculations Journal Article

In: The Journal of Physical Chemistry B, vol. 116, no. 31, pp. 9371–9375, 2012.

Links | BibTeX

Miao Zhang; Cameron 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 Journal Article

In: Structure, vol. 20, no. 5, pp. 911–923, 2012.

Links | BibTeX

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 Journal Article

In: Biophysical Journal, vol. 102, no. 8, pp. 1979–1987, 2012.

Links | BibTeX

Spencer T. Stober; Cameron F. Abrams

Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors Journal Article

In: Protein Science, vol. 21, no. 3, pp. 307–317, 2012.

Links | BibTeX

2011

Ali Emileh; Cameron F. Abrams

A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered HIV-1 gp120 Journal Article

In: Proteins: Structure, Function, and Bioinformatics, vol. 79, no. 2, pp. 537–546, 2011.

Links | BibTeX

2010

Vamshi K. Gangupomu; Cameron F. Abrams

All-Atom Models of the Membrane-Spanning Domain of HIV-1 gp41 from Metadynamics Journal Article

In: Biophysical Journal, vol. 99, no. 10, pp. 3438–3444, 2010.

Links | BibTeX

Harish Vashisth; Cameron F. Abrams

All-Atom Structural Models for Complexes of Insulin-Like Growth Factors IGF1 and IGF2 with Their Cognate Receptor Journal Article

In: Journal of Molecular Biology, vol. 400, no. 3, pp. 645–658, 2010.

Links | BibTeX

Heather L. Nyce; Spencer T. 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 Journal Article

In: Biophysical Journal, vol. 98, no. 9, pp. 1847–1855, 2010.

Links | BibTeX

Debashish Mukherji; Cameron F. Abrams

Slip-stick fracture and toughness enhancement in thermoset/thermoplastic polymer alloys under shear Journal Article

In: EPL (Europhysics Letters), vol. 90, no. 2, pp. 26003, 2010.

Links | BibTeX

C. F. Abrams; E. Vanden-Eijnden

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics Journal Article

In: Proceedings of the National Academy of Sciences, vol. 107, no. 11, pp. 4961–4966, 2010.

Links | BibTeX

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 Journal Article

In: Soft Matter, vol. 6, no. 10, pp. 2160, 2010.

Links | BibTeX

Harish Vashisth; Cameron F. Abrams

Docking of insulin to a structurally equilibrated insulin receptor ectodomain Journal Article

In: Proteins: Structure, Function, and Bioinformatics, pp. NA–NA, 2010.

Links | BibTeX

2009

Debashish Mukherji; Cameron F. Abrams

Anomalous ductility in thermoset/thermoplastic polymer alloys: An explanation based on overlap concentration and cavity growth Journal Article

In: EPL (Europhysics Letters), vol. 88, no. 5, pp. 56001, 2009.

Links | BibTeX

Debashish Mukherji; Cameron F. Abrams

Mechanical behavior of highly cross-linked polymer networks and its links to microscopic structure Journal Article

In: Physical Review E, vol. 79, no. 6, 2009.

Links | BibTeX

Debashish Mukherji; Cameron F. Abrams

Anomalous ductility in thermoset/thermoplastic polymer alloys Journal Article

In: Physical Chemistry Chemical Physics, vol. 11, no. 12, pp. 2113, 2009.

Links | BibTeX

2008

Debashish Mukherji; Cameron F. Abrams

Microvoid formation and strain hardening in highly cross-linked polymer networks Journal Article

In: Physical Review E, vol. 78, no. 5, pp. 050801(R), 2008.

Links | BibTeX

Harish Vashisth; Cameron F. Abrams

Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex Journal Article

In: Biophysical Journal, vol. 95, no. 9, pp. 4193–4204, 2008.

Links | BibTeX

2007

Yelena Sliozberg; Cameron F. Abrams

Spontaneous Conformational Changes in the E. coli GroEL Subunit from All-Atom Molecular Dynamics Simulations Journal Article

In: Biophysical Journal, vol. 93, no. 6, pp. 1906–1916, 2007.

Links | BibTeX

Ehsan Jabbarzadeh; Cameron F. Abrams

Strategies to Enhance Capillary Formation Inside Biomaterials: A Computational Study Journal Article

In: Tissue Engineering, vol. 13, no. 8, pp. 2073–2086, 2007.

Links | BibTeX

D. G. Richardson; C. F. Abrams

The effects of nanotube fillers on craze formation in simulated glassy polymers under tensile load Journal Article

In: Molecular Simulation, vol. 33, no. 4-5, pp. 421–427, 2007.

Links | BibTeX

Ehsan Jabbarzadeh; Cameron F. Abrams

Simulations of Chemotaxis and Random Motility in 2D Random Porous Domains Journal Article

In: Bulletin of Mathematical Biology, vol. 69, no. 2, pp. 747–764, 2007.

Links | BibTeX

2006

Cameron F. Abrams; Nam-Kyung Lee; A. Johner

Diffusion/Reaction in Confined Polymer Chains Journal Article

In: Macromolecules, vol. 39, no. 10, pp. 3655–3663, 2006.

Links | BibTeX

135 entries « 2 of 3 »