Publications

CFL ORCID: http://orcid.org/0000-0003-3668-7468

CFL Google Scholar Citations: LINK

Publications:

An unbiased metric of antiproliferative drug effect in vitro. Harris, L. A., Frick, P.L., Garbett, S. P., Hardeman,K. N., Paudel B. B., Lopez, C. F., Quaranta, V. Q., and Tyson, D. R. Nature Methods (Early Edition, doi:10.1038/nmeth.3852) (2016)

Fischer AW, Heinze S, Putnam DK, Li B, Pino JC, Xia Y, Lopez CF, Meiler J.  CASP11 – An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline. PloS one. 11(4). e0152517.PMID: 27046050

Competition and allostery govern substrate selectivity of cyclooxygenase-2. Mitchener, M. M., Hermanson, D. J., Shockley, E. M., Brown, H. A., Lindsley, C. W., Reese, J., Rouzer, C. A., Lopez, C. F., and Marnett, L. J. Proc. Nat. Acad. Sci. USA (Early Edition, doi:10.1073/pnas.1507307112) (2015).

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Chylek, L. A., Harris, L. A., Tung, C.-S., Faeder, J. R., Lopez, C. F. and Hlavacek, W. S., WIREs Syst Biol Med. doi: 10.1002/wsbm.1245 (2014).

Programming biological models in Python using PySB C. F. Lopez*, J. L. Muhlich*, J. A. Bachman*, P. K. Sorger. Mol. Syst. Biol. Vil. 9, Art. 646 (2013).

vGap in publications due in part to needed recovery time from a major traffic accident.v

Hydrophobicity of protein surfaces: Separating geometry from chemistry. N. Giovambattista, C. F. Lopez, P. G. Debenedetti, and P. J. Rossky.  Proc. Nat. Acad. Sci. USA Vol. 105 Iss. 7 pp. 2274-2279 (2008).

Mechanistic Elements of Protein Cold Denaturation. C. F. Lopez, Richard K. Darst, and P. J. Rossky J. Phys. Chem. B Vol. 112 Iss 19 pp. 5961-5967 (2008).

Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics. C. F. Lopez, S. O. Nielsen, G. Srinivas, W. F. DeGrado, and M. L. Klein J. Chem. Theory Comput. Vol. 2 Iss. 3 pp. 649-655 (2006).

Modeling surfactant adsorption on hydrophobic surfaces. S. O. Nielsen, G. Srinivas, C. F. Lopez, and M. L. Klein.  Phys. Rev. Lett. Vol. 94 Iss. 22 pp. 228301 (2005).

Structure and dynamics of model pore insertion into a membrane. C. F. Lopez, S. O. Nielsen, B. Ensing, P. B. Moore, and M. L. Klein. Biophys. J. Vol. 88, Iss. 5, pp. 3083-3094 (2005).

Transmembrane peptide-induced lipid sorting and dynamical mechanism of La to inverse cubic phase transition using coarse grain molecular dynamics. S. O. Nielsen, C. F. Lopez, P. B. Moore, I. Ivanov, J. C. Shelley, and M. L. Klein. Biophys. J. Vol. 87, Iss. 4, pp. 2107-2115 (2004).

Hydrogen bonding structure and dynamics of water at the dimyristoylphosphatidylcholine lipid bilayer surface from a molecular dynamics simulation. C. F. Lopez, S. O. Nielsen, and M. L. Klein, P. B. Moore. J. Phys. Chem. B Vol. 108, Iss. 21, pp. 6603-6610 (2004).

Coarse grain models and the computer simulation of soft materials. S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein J. Phys.: Condens. Matter Vol. 16, Iss. 15, pp. R481-R512 (2004). (Featured in Top papers 2004 showcase, downloaded over 1000 times in one year).

Membrane bound hydraphiles facilitate cation translocation. G. Srinivas, C. F. Lopez, and M. L. Klein. J. Phys. Chem. B Vol. 108, Iss. 14, pp 4231-4235 (2004).

Understanding nature’s design for a nanosyringe. C. F. Lopez, S. O. Nielsen, P. B. Moore, and M. L. Klein. Proc. Nat. Acad. Sci. USA, Vol. 101, Iss. 13, pp. 4431-4434 (2004). (Featured cover article, with commentary by A. Aksimentiev and K. Schulten).

Molecular dynamics investigations of lipid Langmuir monolayers using a coarse grain model. S. O. Nielsen, C. F. Lopez, P. B. Moore, J. C. Shelley, and M. L. Klein. J. Phys. Chem. B Vol. 107., Iss. 50, pp. 13911-13917 (2003).

A coarse grain model for n-alkanes parameterized from surface tension data. S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein. J. Chem. Phys. Vol. 119, Iss. 14, pp. 7043-7049 (2003).

Self-assembly of a phospholipid Langmuir monolayer using coarse-grained molecular dynamics simulations. C. F. Lopez,  S. O. Nielsen, P. B. Moore, J. C. Shelley, and M. L. Klein.  J. Phys.: Condens. Matter, Vol. 14, Iss 40, pp 9431-9444 (2002) (Special issue on liquid state theory in honor of professor J. P. Hansen)

Computer simulation studies of biomembranes using a coarse grain model. C. F. Lopez, P. B. Moore, J. C. Shelley, M. Y. Shelley, and M. L. Klein. Comput. Phys. Commun. Vol 147, Iss 1-2, pp 1-6 (2002) (Special issue on computational modeling and simulation of complex systems).

Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the human immunodeficiency virus HIV-1. C. F. Lopez, M. Montal, J. K. Blasie, M. L. Klein, and P. B. Moore. Biophys. J. Vol 83, Iss 3, pp 1259-1267 (2002).

Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation. P. B. Moore, C. F. Lopez, and M. L. Klein. Biophys. J. Vol 81, Iss 5, pp 2484-2494 (2001).

Patents

08/2003    Tubular Nanostructures, (design for a Nanosyringe). US Patent Number 10/446,622.

08/2003    Methods, Systems and Computer Program Products for Simulating Biomembranes Using Coarse Grain Models. US Patent Number 10/459,698

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