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Publications

Publications using work performed on Proteus (in reverse chronological order):

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, Francesca Moraca, Kriti Acharya, Bruno Melillo, Amos B. Smith III, Irwin Chaiken, and Cameron F. Abrams, J. Chem. Inf. Model., 201656 (10), pp 2069–2079 DOI:10.1021/acs.jcim.6b00393

Effect of intrinsic curvature and edge tension on the stability of binary mixed-membrane three-junctions, Jasmine M. Gardner,   Markus Deserno, and   Cameron F. Abrams, The Journal of Chemical Physics 145, 074901 (2016); DOI:10.1063/1.4960433

Aggregation of 12-Hydroxystearic Acid and Its Lithium Salt in Hexane: Molecular Dynamics Simulations, Ryan Gordon, Spencer T. Stober, and Cameron F. Abrams, J. Phys. Chem. B, 2016, 120 (29), pp 7164–7173 DOI:10.1021/acs.jpcb.6b04193

Thermal and mechanical properties of thermosetting polymers using coarse-grained simulation, Changwoon Jang and Cameron F. Abrams, Eur. Phys. J. Spec. Top. (2016) 225: 1775 DOI:10.1140/epjst/e2016-60143-0

Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics, Anthony Bucci, Tang-Qing Yu, Eric Vanden-Eijnden, and Cameron F. Abrams, J. Chem. Theory Comput., 2016, 12 (6), pp 2964–2972 DOI:10.1021/acs.jctc.6b00071

Toughness enhancement of thermosetting polymers using a novel partially reacted substructure curing protocol: A combined molecular simulation and experimental study, Changwoon Jang, Majid Sharifi, Giuseppe R. Palmese, Cameron F. Abrams, Polymer 90:249-255 (2016) DOI:10.1016/j.polymer.2016.03.023

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains, Yemin Lan, Gail Rosen and Ruth Hershberg, Microbiome 2016 4:18 DOI:10.1186/s40168-016-0162-5 

Epoxy Polymer Networks with Improved Thermal and Mechanical Properties via Controlled Dispersion of Reactive Toughening Agents, Majid Sharifi, Changwoon Jang, Cameron F. Abrams, and Giuseppe R. Palmese, Macromolecules, 2015, 48 (20), pp 7495–7502 DOI: 10.1021/acs.macromol.5b00677

Mechanical properties of nanocrystalline nanoporous platinum, Ran Liu, Jacob Gruber, Dhriti Bhattacharyya, Garritt J. Tucker, Antonia Antoniou, Acta Materialia, 103 pp.624–632 (2016) DOI:10.1016/j.actamat.2015.10.050

Uncore RPD: Rapid Design Space Exploration of the Uncore via Regression Modeling, Karthik Sangaiah, Mark Hempstead, Baris Taskin, Proceedings of IEEE/ACM International Conference on Computer-Aided Design (ICCAD '15), November 2015, pp. 365-372. URL: http://dl.acm.org/citation.cfm?id=2840819.2840871

Fizzy: feature subset selection for metagenomics, Gregory Ditzler, J. Calvin Morrison, Yemin Lan, Gail L. Rosen, BMC Bioinformatics 2015 16:358 (2015). DOI:10.1186/s12859-015-0793-8

Giant enhancement in the ferroelectric field effect using a polarization gradient, Zongquan Gu, Mohammad A. Islam, Jonathan E. Spanier, Appl. Phys. Lett. 107, 162901 (2015). DOI:10.1063/1.4933095

Full Kinetics of CO Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations, Tang-Qing Yu, Mauro Lapelosa, Eric Vanden-Eijnden, and Cameron F. Abrams, J. Am. Chem. Soc., 2015, 137 (8), pp 3041–3050 DOI:10.1021/ja512484q

Free Energy and Hidden Barriers of the β‑Sheet Structure of Prion Protein, S. Alexis Paz and Cameron F. Abrams, J. Chem. Theory Comput. (accepted; 2015). DOI: 10.1021/acs.jctc.5b00576

Quantifying the influence of twin boundaries on the deformation of nanocrystalline copper using atomistic simulations, G.J. Tucker, S.M. Foiles, International Journal of Plasticity, 65, 191-205 (2015). DOI: 10.1016/j.ijplas.2014.09.006

Band structure and optical transitions in LaFeO3: Theory and Experiment, M.D. Scafetta, A.M. Cordi, J.M. Rondinelli, and S.J. May, J. Phys.: Condens. Matter, 26, 505502 (2014). DOI:10.1088/0953-8984/26/50/505502

Role of Acentric Displacements on the Crystal Structure and Second-Harmonic Generating Properties of RbPbCO3F and CsPbCO3F, T. Tran, P.S. Halasyamani, and J.M. Rondinelli, Inorganic Chemistry, 53, 6241-6251 (2014). DOI:10.1021/ic500778n