Carlos F. Lopez, Ph.D.

Assistant Professor

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Faculty Appointments
Assistant Professor of Cancer Biology Assistant Professor of Biomedical EngineeringAssistant Professor of Biomedical Informatics
Ph.D., CHEMISTRY, University of Pennsylvania, Philadelphia, PennsylvaniaB.S., University of Miami, Coral Gables, Florida
Office Address
Vanderbilt Univ. Dept of Cancer Bio.
2220 Pierce Ave, 496 PRB
Nashville, TN 37232
Research Description
The goal of my work is the development and application of numerical methods to understand signal transduction cascades in cells and their dysregulation in cancer. My group efforts comprise a tri-partite approach to study molecular cancer cell biology: (1) Development of modelling and simulation tools necessary to study signalling events across multiple spatiotemporal time-scales. To this end we use techniques of statistical mechanics, molecular simulation, mesoscale modelling, reaction kinetics, and cell-population modelling to develop a systems-level description of cellular environments. (2) Use developed tools to study signalling processes relevant to cancer phenotypes. (3) Collaborate with experimental and theoretical groups to test and expand our hypotheses to develop a fundamental understanding of the rules that govern functional genomics and systems biology. My group currently co-develops and contributes to the PySB ( modelling platform, which uses a novel modelling-with-programs paradigm to biological signalling pathway simulations. With this approach, the biological knowledge is encoded into executable programs that enhance our capabilities to express, share, and revise our understanding of complex interactions at a large signalling network scale. We have employed a combination of this modelling framework along with in-house developed numerical methods to explore proposed mechanistic hypotheses in the literature about cell death regulation. With our work we were able to elucidate important aspects of signalling, identify gaps in our knowledge, and bring a consensus to the field about extrinsic apoptosis regulation. [Lopez et al. Submitted] My lab is located at the Vanderbilt-Ingram Cancer Center in Vanderbilt University School of Medicine; one of the leading institutions for cancer research in the world and consistently ranked in the top five for NIH funding in the USA. My work provides a theoretical perspective to experimental and clinical efforts in the department and university with the goal of developing a better understanding of cancer development and treatment.
Research Keywords
modeling, simulation, kinetics, molecular simulation, molecular dynamics, multi scale, computation, computational, signaling, cancer
Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med [print-electronic]. 2014 Jan; 6(1): 13-36. PMID: 24123887, PMCID: PMC3947470, DOI: 10.1002/wsbm.1245, ISSN: 1939-005X.

Lopez CF, Muhlich JL, Bachman JA, Sorger PK. Programming biological models in Python using PySB. Mol. Syst. Biol. 2013; 9: 646. PMID: 23423320, PMCID: PMC3588907, PII: msb20131, DOI: 10.1038/msb.2013.1, ISSN: 1744-4292.

Lopez CF, Darst RK, Rossky PJ. Mechanistic elements of protein cold denaturation. J Phys Chem B [print-electronic]. 2008 May 5/15/2008; 112(19): 5961-7. PMID: 18181599, DOI: 10.1021/jp075928t, ISSN: 1520-6106.

Giovambattista N, Lopez CF, Rossky PJ, Debenedetti PG. Hydrophobicity of protein surfaces: Separating geometry from chemistry. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2008 Feb 2/19/2008; 105(7): 2274-9. PMID: 18268339, PMCID: PMC2268126, PII: 0708088105, DOI: 10.1073/pnas.0708088105, ISSN: 1091-6490.

Lopez CF, Nielsen SO, Srinivas G, Degrado WF, Klein ML. Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics. J Chem Theory Comput. 2006 May; 2(3): 649-55. PMID: 18985168, PMCID: PMC2577386, DOI: 10.1021/ct050298p, ISSN: 1549-9626.

Nielsen SO, Srinivas G, Lopez CF, Klein ML. Modeling surfactant adsorption on hydrophobic surfaces. Phys. Rev. Lett [print-electronic]. 2005 Jun 6/10/2005; 94(22): 228301. PMID: 16090439, DOI: 10.1103/PhysRevLett.94.228301, ISSN: 0031-9007.

Lopez CF, Nielsen SO, Ensing B, Moore PB, Klein ML. Structure and dynamics of model pore insertion into a membrane. Biophys. J [print-electronic]. 2005 May; 88(5): 3083-94. PMID: 15722425, PMCID: PMC1305460, PII: S0006-3495(05)73362-2, DOI: 10.1529/biophysj.104.053769, ISSN: 0006-3495.

Nielsen SO, Lopez CF, Ivanov I, Moore PB, Shelley JC, Klein ML. Transmembrane peptide-induced lipid sorting and mechanism of Lalpha-to-inverted phase transition using coarse-grain molecular dynamics. Biophys. J. 2004 Oct; 87(4): 2107-15. PMID: 15454415, PMCID: PMC1304638, PII: S0006-3495(04)73690-5, DOI: 10.1529/biophysj.104.040311, ISSN: 0006-3495.

Lopez CF, Nielsen SO, Moore PB, Klein ML. Understanding nature's design for a nanosyringe. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2004 Mar 3/30/2004; 101(13): 4431-4. PMID: 15070735, PMCID: PMC384764, PII: 0400352101, DOI: 10.1073/pnas.0400352101, ISSN: 0027-8424.

Lopez CF, Montal M, Blasie JK, Klein ML, Moore PB. Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the human immunodeficiency virus HIV-1. Biophys. J. 2002 Sep; 83(3): 1259-67. PMID: 12202353, PMCID: PMC1302226, PII: S0006-3495(02)73898-8, DOI: 10.1016/S0006-3495(02)73898-8, ISSN: 0006-3495.

Moore PB, Lopez CF, Klein ML. Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation. Biophys. J. 2001 Nov; 81(5): 2484-94. PMID: 11606264, PMCID: PMC1301718, PII: S0006-3495(01)75894-8, DOI: 10.1016/S0006-3495(01)75894-8, ISSN: 0006-3495.

Available Postdoctoral Position Details
Posted: 12/6/2013
The laboratory of Carlos F. Lopez at Vanderbilt University, Department of Cancer Biology, seeks applicants for a postdoctoral fellow position. The overall goal of work at the Lopez Lab is the understanding of cue-response mechanisms in cellular signaling and their link to cancer phenotypes. We also aim to develop and implement novel modeling and simulation tools to understand complex results from experiments. Ongoing work investigates the mechanisms of molecular signal regulation leading to mitochondrial outer membrane permeabilization in extrinsic apoptosis and its role in cancer. We aim to distinguish key mechanistic elements among the known apoptosis regulation interactions, understand pathway cross-talk within the cell, and use this data to rationalize mechanism controversies currently found in the literature. The goal of this work is to formulate a novel understanding of regulation and dysregulation in cancer and significantly contribute toward advances in cancer treatments.

The successful candidate will participate in research projects related to modeling, simulation, and quantitative biology to study different aspects of signal transduction. Expertise with numerical methods, chemical theory, physics, chemical engineering, systems biology, or other quantitative disciplines is desirable. Candidates should have a Ph.D. in one of the physical or life sciences related to the proposed work, a strong record of successful research, and experience with related quantitative techniques. The candidate can expect to acquire experience with numerical methods for cell biology, programming (e.g. C or Python), and the development of novel tools to study cancer biology.

The Lopez lab maintains a comfortable and well-outfitted laboratory with access to computational resources both in the lab and on a University-maintained ~4000 core cluster with high throughput Infiniband connectivity. The department is housed in the Vanderbilt-Ingram cancer center, which provides a rich environment for research, collaboration, and scientific exploration. The city of Nashville is a medium-sized (pop 1.4 million), vibrant, city with a low urban cost of living (ranked 90 in the US, 100 is average) and a very heterogeneous independent arts and culture scene. The city of Nashville is consistently ranked among the top-ten cities in the country for young professionals and possesses one of the most vibrant music cultures (not just Country music) in the nation.