Carlos F. Lopez, Ph.D.

Carlos Lopez, Ph.D.Department of Systems Biology
Harvard Medical School
200 Longwood Avenue, WAB444
Boston, MA 02115

(617) 432-6906
carlos [at] hms.harvard.edu

Research

My research focuses on developing and implementing techniques combining  mathematical modeling and experimental measurement in the study of signal transduction in mammalian cells.  The mathematical treatment of large signal transduction models is rather difficult due to the topological and mathematical complexity. To address the issue of topological complexity we have implemented a so-called rules approach to modeling signal transduction systems, whereby the model is constructed from the biochemical knowledge rather than the enumeration of differential equations.This allows us to explore hypothetical topologies in a fashion that is less manually burdensome in terms of tracking the large number of variables in a large ODE system. The systems that I have been dealing with tend to be of the order of several hundreds to thousands of equations. The calibration of such a model and application to ongoing experimental work in our laboratory is an important aspect of my work.

A second aspect of my research involves the dissemination models. Due to the multitude of approaches to modeling and the  lack of standards available for such work the classification and dissemination of models is rather complicated. I have used a  semantic‐wiki based approach for the dissemination and outreach of the apoptosis model in which I currently work with particular emphasis in annotating the assumptions of the model.

Education

Research Fellow, Harold Whitworth Pierce Fellow (2007-Present)
Harvard Medical School, Department of Systems Biology
Advisor: Peter K. Sorger

Postdoctoral Researcher (2004-2007)
University of Texas at Austin, Department of Chemistry and Biochemistry
Advisor: Peter J. Rossky

Graduate Student (1998-2004, Ph. D.)
University of Pennsylvania, Department of Chemistry
Advisor: Michael L. Klein

Undergraduate Student (1993-1998, B.S., B.L.A.)
University of Miami, Chemistry and Biochemistry Double Major/Liberal Arts
Advisor: Jeffrey D. Evanseck

Publications

  • 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 Lα 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 first year of publication).
  • 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 parametrized 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. Biphys. 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).