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Scholarly Interest Report
         
Cecilia Clementi
Professor
Professor of Chemistry and Chemical and Biomolecular Engineering
 
e-mail:cecilia@rice.edu
 
  • B.S. Physics (1995) University of Florence, Firenze, Italy
  • M.Sc. Physics (1996) Int'l School for Advanced Studies, Trieste, Italy
  • Ph.D. Physics (1998) Int'l School for Advanced Studies, Trieste, Italy
 
Primary Department
   Department of Chemistry
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Department Affiliations
 
  • Department of Chemical and Biomolecular Engineering
  • Institute of Biosciences and Bioengineering
  • Keck Center for Quantitative Biomedical Sciences
  • Ken Kennedy Institute for Information Technology
  • Rice Quantum Institute
  • Smalley Institute for Nanoscale Science and Technology
  •  
    Websites
     Clementi Research Group
     
    Research Areas
     Physical Chemistry; Theoretical Biophysics; Statistical Mechanics; Protein Folding; Computational Molecular Biology
     

    Research Statement

     


    "Anyone who has ever struggled to fold a roadmap should have an extra measure of respect for protein molecules, which fold up all on their own and practically put themselves away in the glove box" - (by Brian Hayes, from a paper published on American Scientist, 1998)



    Virtually all biological activities are regulated by proteins. Combined in diverse cellular assemblies that vary with cell cycle, tissue type and in response to external stimuli, proteins constitute the  nanomachines of biology. Understanding how proteins move and interact with neighboring molecules is necessary for solving critical puzzles in molecular biology, as for instance the so called "protein misfolding diseases" such as Alzheimer's and certain types of cancers. Yet, our understanding of protein mechanisms at the molecular level is still in its relative infancy.  Research has long focused on grasping the "sequence-to-structure" relationship, but structure can only give a cursory understanding of a protein's function.  


    Filling the sizeable gaps in our knowledge of protein dynamics and function (or malfunction) is increasingly crucial in the nanotechnology era. The possibility now exists of engineering bio-nano conjugates which promise novel therapies, such as tunable nanoparticles designed to interact with certain proteins to ablate tumor tissue. These opportunities can be fully exploited only if technological progress is paired with a major step forward in our understanding of the detailed physical and chemical factors regulating protein mechanisms (encompassing dynamics, folding, interactions, and assembly) and consequently in our ability to model and predict these processes.

    The study of protein dynamics and interactions at the molecular level of detail still poses outstanding challenges both for theory and experiment. No single technique can at present span the whole range of typical time and length scales relevant for a protein biological function. New theoretical and computational approaches need to be developed in order to address this challenge. It is our belief that this goal can be achieved by reconciling biological and biochemical approaches with a physical and mathematical perspective of the problem.

    The results of Clementi's research group in the past few years have paved the way to create a new theoretical scaffold,  blending
    theory, simulation and experiment to address the characterization of protein systems at multiple length and time scales.


    Please visit our group web page to find more information on the ongoing research projects: http://leonardo.rice.edu/~cecilia


     

     
    Teaching Areas
     Physical Chemistry; Quantum Chemistry; Thermodynamics and Statistical Mechanics, Molecular Biophysics
     
    Selected Publications
     Refereed articles
     

    M. A. Rohrdanz, W. Zheng, C. Clementi "Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions." Ann. Rev. Phys. Chem., 64 (2013) : 295-316.


    DOI: 10.1146/annurev-physchem-040412-110006
     
     

    W. Zheng, A. V. Vargiu, M. A. Rohrdanz, P. Carloni, and C. Clementi "Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile." J. Chem. Phys., 139 (2013) : 145102.

     
     

    W. Zheng, M. A. Rohrdanz, C. Clementi "Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics." J. Phys. Chem. B, 117 (2013) : 12769-12776.

     
     

    A. Davtyan, N. P. Schaefer, W. Zheng, C. Clementi, P. G. Wolynes, G. A. Papoian "Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing." J. Phys. Chem. B, 116 (2012) : 8494-8503.

     
     

    M. A. Rohrdanz, W. Zheng, M. Maggioni, C. Clementi "Determination of reaction coordinates via locally scaled diffusion map." J. Chem. Phys., 134 (2011) : 124116.

     
     

    P. Das, T. A. Frewen, I. G. Kevrekidis, C. Clementi "Think Globally, Move Locally: Coarse Graining of Effective Free Energy Surfaces." Lecture Notes in Computational Science and Engineering, 35 (2011)

     
     

    P.J. Ledbetter, C. Clementi "A new perspective on transition states: chi(1) separatrix." J. Chem. Phys., 135 (2011) : 044116-1:044116-13.

     
     

    P.J. Ledbetter, C. Clementi "A new perspective on transition states: chi(1) separatrix." J. Chem. Phys., 135 (2011) : 044116-1:044116-13.

     
     

    W. Zheng, B. Qi, M. A. Rohrdanz, A. Caflisch, A. R. Dinner, C. Clementi "Delineation of folding pathways of a beta-sheet miniprotein." J. Phys. Chem. B, 115 (2011) : 13065-13074.

     
     

    W. Zheng, M. A. Rohrdanz, M. Maggioni, C. Clementi "Polymer reversal rate calculated via locally scaled diffusion map." J. Chem. Phys., 134 (2011) : 144109.

     
     

    B. P. Lambeth, Jr., C. Junghans, K. Kremer, C. Clementi, L. Delle Site "Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces." J. Chem. Phys., 133 (2010) : 221101.

     
     

    H. Stamati, C. Clementi, L. E. Kavraki "Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides." Proteins Struct. Funct. Bioinf., 78 (2010) : 223-235.

     
     

    A. Shehu, L. E. Kavraki, C. Clementi "Multiscale characterization of protein conformational ensembles." Proteins: Structure, Function and Bioinformatics , 76 (2009) : 837-851.

     
     

    J. A. Hegler, J. Latzer, A. Shehu, C. Clementi, P. G. Wolynes "Restriction vs. guidance: Fragment assembly and associative memory Hamiltonians for protein structure prediction." Proc. Natl. Acad. Sci. USA, 106 (2009) : 15302-15307.

     
     

    M. Praprotnik, S. Matysiak, L. Delle Site, K. Kremer, C. Clementi "Adaptive resolution simulation of liquid water" [Erratum to document cited in CA147:529061], J.Phys.: Condens. Matter, 21, 499801/1 (2009)

     
     

    A. Shehu, L. E. Kavraki, C. Clementi "Unfolding the Fold of Cyclic Systeine-rich Peptides." Protein Sci., 17 (2008) : 482-493.

     
     

    C. Clementi "Coarse-Grained Models of Protein Folding." Curr. Opin. Struct. Biol., 18 (2008) : 10-15.

     
     

    H. Stamati, L. E. Kavraki, C. Clementi "Applications of Non-Linear Dimensionality Reduction to Characterize the Conformational Landscape of Small Peptides." Proteins: Structure, Function and Bioinformatics (2008) Submitted

     
     

    S. Matysiak C. Clementi "Mapping Folding Energy Landscapes with Theory and Experiment." Arc. Biochem. Biophys., 469 (2008) : 29-33.

     
     

    S. Matysiak, C. Clementi, M. Praprotnik, K. Kremer, L. delle Site "Modeling diffusive dynamics in adaptive resolution simulation of liquid water." J. Chem. Phys., 128 (2008) : 024503.

     
     

    Heath, A.P., Kavraki, L.E. & Clementi, C. "From Coarse-Grain to All-Atom: Toward Multiscale Analysis of Protein Landscapes." Proteins, 68 (2007) : 646-661.

     
     

    Mossa, A. & Clementi, C. "Supersymmetric Langevin equation to explore free energy landscapes." Phys. Rev. E, 75 (2007) : 046707.

     
     

    Plaku, E., Stamati, H., Clementi, C. & Kavraki, L.E. "Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction." Proteins, 67 (2007) : 897-907.

     
     

    Praprotnik, M., Matysiak, S., Delle Site, L. Kremer, K., & Clementi, C. "Adaptive resolution simulation of liquid water." J. Phys.: Condens. Matter, 19 (2007) : 292201.

     
     

    Shehu, A., Clementi, C. & Kavraki, L.E. "Sampling Conformational Space to Model Equilibrium Fluctuations in Proteins." Algorithmica, 48 (2007) : 303-307.

     
     

    Shehu, A., Kavraki, L.E. & Clementi, C. "On the Characterization of Protein Native State Ensembles." Biophysical Journal, 92 (2007) : 1503-1511.

     
     

    A. Mossa, M. Pettini, C. Clementi "Hamiltonian dynamics of homopolymer chain models." Phys. Rev. E., 74 (2006) : 041805.

     
     

    A. Shehu, C. Clementi, L. E. Kavraki "Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations." Proteins: Structure, Function and Bioinformatics, 65 (2006) : 164-179.

     
     

    A. Shehu, C. Clementi, L. E. Kavraki "Sampling conformation space to model equilibrium fluctuations in proteins." Algorithmica (2006) In Press

     
     

    P. Das, M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi "Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction." Proc. Natl. Acad. Sci. USA, 103 (2006) : 9885-9890.

     
     

    S. Matysiak, A. Montesi, M. Pasquali, A. B. Kolomeisky, and C. Clementi "Dynamics of Polymer Translocation through Nanopores: Theory Meets Experiment." PHys. Rev. Lett., 96 (2006) : 118130.

     
     

    S. Matysiak, C. Clementi "Minimalist protein model as a diagnostic tool for misfolding and aggregation." J. Mol. Biol., 363 (2006) : 297-308.

     
     

    Das, P., Matysiak, S. & Clementi, C. "Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes." Proceedings of the National Academy of Science, 102(29) (2005) : 10141-10146.

     
     

    Das, P., Wilson, C.J., Fossati, G., Wittung-Stafshede, P., Matthews, K.S. and Clementi, C. "Characterization of the folding landscape of monomeric lactose repressor: Quantitative comparison of theory and experiment." Proceedings of the National Academy of Science, 102(41) (2005) : 14569-14574.

     
     

    Matysiak, S., Montesi, A., Pasquali, M., Kolomeisky, A.B., Clementi, C. "Dynamics of polymer translocation through nanopores: Theory meets experiment." Physical Review Letters, accepted for publication (2005) In Press

     
     

    Wilson,C.J., Das, P., Clementi, C., Matthews, K.S. and Wittung-Stafshede, P. "The experimental folding landscape of monomeric lactose repressor, a large two-domain protein, involves two kinetic intermediates ." Proceedings of the National Academy of Science, 102(41) (2005) : 14563-14568.

     
     

    C. Clementi, S.S. Plotkin "The effects of non-native interactions on protein folding rates: Theory and simulation." Protein Science, 13 (7) (2004) : 1750-1766.

     
     

    L. L. Chaves, J. N. Onuchic and C. Clementi "Quantifying the Roughness on the Free Energy Landscape: Entropic Bottlenecks and Protein Folding Rates." J. Am. Chem. Soc., 126(27) (2004) : 8426-8432.

     
     

    S. Matysiak and C. Clementi "Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: How far can a minimalist model go?." J. Mol Biol., 343 (1) (2004) : 235-248.

     
     Book chapters
     

    S. Matysiak, C. Clementi "Characterization of protein folding landscapes by coarse-grained models incorporating experimental data", Coarse-Graining of Condensed Phase and Biomolecular Systems, G. A. Voth Ed, Taylor & Francis/CRC press, Chapter 11 (2009): 157-170

     
     

    S. Matysiak, C. Clementi "Characterization of Protein-Folding Landscapes by Coarse-Grained Models Incorporating Experimental Data." Coarse-graining in Condensed Phase and Biomolecular Systems (2008) : 157-170.

     
    Presentations
     Conference Committee Member
     

    "XV Texas Protein Folders Meeting." Texas Protein Folders Annual research conference, Navasota, Texas. (March 30-April 1 2007)

     
     

    "Multiscale Modeling in Soft Matter and Bio-Physics." Bridging Time and Length Scales in Materials Science and Bio-Physics, IPAM/UCLA, Los Angeles, CA. (September 26 - 30, 2005)

     
     Invited Talks
     

    "A multiscale approach to characterize macromolecular dynamics and functions." International Conference on Molecular Dynamics: Computation Meets Experiment, King Abdullah University of Science and Technology (KAUST), Saudi Arabia. (February, 2013)

     
     

    "Multiscale characterization of the photocycle of Photoactive Yellow Protein." 246th National Meeting of the American Chemical Society, Indianapolis, Indiana. (September, 2013)

     
     

    "Multiscale characterization of the photocycle of Photoactive Yellow Protein." 69th Southwestern Regional Meeting of the American Chemical Society, Waco, Texas. (November, 2013)

     
     

    "Multiscale modeling of macromolecular dynamics." Telluride Science Research Center Workshop on The Complexity of Dynamics and Kinetics in Many Dimensions, Telluride, Colorado. (June 16-20, 2013)

     
     

    "Multiscale modeling of macromolecular dynamics." American Physical Society March Meeting, Baltimore, Maryland. (March, 2013)

     
     

    "Multiscale modeling of macromolecular dynamics." Conference on Industrial and Applied Mathematics Conference on Mathematical Aspects of Materials Science, Philadelphia, Pennsylvania. (June 8-12 2013)

     
     

    "Multiscale modeling of macromolecular dynamics." Molecular Kinetics 2013 Conference, Berlin, Germany. (September, 2013)

     
     

    "Multiscale modeling of macromolecular dynamics." Symposium honoring Prof. Peter Wolynes on the occasion of his 60th birthday, Chinese Academy of Sciences, Beijing, China. (August, 2013)

     
     

    "A multiscale appraoch to characterize macromolecular dynamics and functions." Lorenz Center International Center for Workshops in the Sciences, Modeling the Dynamics of Complex Molecular Systems Workshop , Leiden, The Netherlands. (August, 2012)

     
     

    "A multiscale appraoch to characterize macromolecular dynamics and functions." 6th International Conference on Multiscale Materials Modeling, Biopolis, Singapore. (October, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." International Society of Quantum Biology and Pharmacology Meeting , Stockholm, Sweden. (June 17, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." European Science Foundation Conference on Energy Landscapes, Amsterdam, The Netherlands. (July, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Institute for Complex Adaptive Matter 2012 Annual Conference, New York, New York. (May 23-26, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Telluride Science Research Center "Searching for Reaction Coordinates and Order Parameters" Workshop, Telluride, Colorado. (June 18-22, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." German Research School for Simulation Sciences, University of Jülich, Jülich, Germany. (February 29, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Institute for Computational and Experimental Research in Mathematics Workshop on Bridging Scales in Computational Chemistry, Brown University, Providence, Rhode Island. (August, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Centre Eurpoéen de Calcul Atomic et Moléculaire Workshop on Machine Learning in Atomistic Simulations, Lugano, Switzerland. (September, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Telluride Science Research Center Workshop on the Structure and Dynamics of Complex Macromolecular Systems of Biological and Synthetic Origin, Telluride, Colorado. (July 1-6, ,2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and function." Biocomputation Workshop, Asia University, Taichun, Taiwan. (October 27-28, 2011)

     
     

    "A multiscale approach to characterize macromolecular dynamics and function." Collective Variable Methods in Biomolecular Simulation - Principles and Applications Workshop, University of Nottingham, Nottingham UK. (November 4-6, 2011)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Cyber-enhanced Discovery and Innovation (CDI) Distinguished Lecture at the National Science Foundation, Arlington, Virginia. (September 1, 2011)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Department of Chemistry, Indiana University, Bloomington, Indiana. (September 28, 2011)

     
     

    "Prediction of protein functional states by multi-resolution protein." Navigating Chemical Compound Space for Materials and Bio Design Workshop 1: Design of Drugs and Chemicals that Influence Biology, Los Angeles, California. (April 4-8, 2011)

     
     

    "Prediction of protein functional states by multi-resolution protein modeling." 2011 Protein Stability Conference, Breckenridge, Colorado. (July 18-20, 2011)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." BioScience 2010 Workshop on Expanding the Frontiers of Biomolecular Science, Julich, Germany. (November, 2010)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Telluride Science Research Center Workshop on Searching for Reaction Coordinates and Order Parameters, Telluride, Colorado. (June 20-26)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." International Society of Quantum Biology and Pharmacology 2010 Meeting, Cetraro, Italy. (June 15, 2010)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." 10th Anniversary Conference of the Institute for Pure & Applied Mathematics, University of California, Los Angeles, Los Angeles, California. (November 1-4, 2010)

     
     

    "A multiscale approach to characterize macromolecular dynamics and functions." Chemistry Colloquium, Penn State University, State College, Pennsylvania. (May 1, 2010)

     
     

    "Location and Identification of Reaction Paths and Barriers on Protein Free Energy Landscapes Using Supersymmetric Langevin Dynamics." Department of Chemistry, University of Texas, Austin, Texas. (February 15, 2010)

     
     

    "Prediction of functional states by multi-domain protein modeling." Department of Chemistry, Arizona State University, Tempe, Arizona. (March 3, 2010)

     
     

    "Prediction of functional states by multi-resolution protein modeling." Department of Chemistry, University of Maryland, College Park, Maryland. (April 12, 2010)

     
     

    "Prediction of functional states by multi-resolution protein modeling." 239th National Meeting of the American Chemical Society, San Francisco, California. (March 23, 2010)

     
     

    "Location and Identification of Reaction Paths and Barriers on Protein Free Energy Landscapes Using Supersymmetric Langevin Dynamics ." IPAM/UCLA Workshop on Rare Events, Los Angeles, California. (February, 2009)

     
     

    "Prediction of Protein Functional States by Multi-Resolution Protein Modeling." American Physical Society March Meeting, Pittsburgh, Pennsylvania. (March, 2009)

     
     

    "Prediction of Protein Functional States by Multi-Resolution Protein Modeling." 9th International Conference on Femtochemistry, Femtobiology, and Femtophysics, Beijing, China. (August, 2009)

     
     

    "Prediction of Protein Functional States by Multi-Resolution Protein Modeling." Volkswagen 2009 Symposium, (September 21, 2009)

     
     

    "Prediction of Protein Functional States by Multi-Resolution Protein Modeling." Keystone Symposia on Molecular and Cellular Biology, Keystone, Colorado. (June 6, 2009)

     
     

    "Prediction of Protein Functional States by Multi-Resolution Protein Modeling." 53rd Annual Meeting of the Biophysical Society, Boston, Massachusetts. (March, 2009)

     
     

    "Prediction of Protein Functional States by Multi-Resolution Protein Modeling." 2009 Frontier in Macromolecular Simulations Symposium, Atlanta, Georgia. (November 16, 2009)

     
     

    "Multiresolution protein modeling by combining theory and experiment." Multiscale Methods for the Design of Biofunctional Molecules Workshop, University of Duisburg-Essen, Duisburg-Essen, Germany. (April 2-5, 2008)

     
     

    "Multiresolution protein modeling by combining theory and experiment." 236th National Meeting of The American Chemical Society, Philadelphia, Pennsylvania. (August, 2008)

     
     

    "Multiresolution protein modeling by combining theory and experiment." Reunion Workshop of the IPAM semester-long program Bridging Time and Length Scales in Materials Science and Biophysics, Lake Arrowhead, California. (June, 2008)

     
     

    "Multiresolution protein modeling by combining theory and experiment." International Workshop on Searching for Reaction Coordinates and Order Parameters, Telluride, Colorado. (June, 2008)

     
     

    "Multiscale framework for the characterization of protein native states." 235th National Meeting, The American Chemical Society, New Orleans, Louisiana. (April 6-10, 2008) With A. Shehu

     
     

    "Prediction of protein functional states by multi-resolution protein modeling." Gordon Research Conference on Protein Folding Dynamics, Ventura, California. (January 6-11, 2008)

     
     

    "Multiresolution Protein Modeling by combining theory and experiment." Multiscale Modelling in Biomolecular Systems, Imperial College, London, UK. (September 12-14, 2007)

     
     

    "Multiresolution modeling of biophysical systems." Bridging Time and Length Scales in Materials Science and Biophysics, Lake Arrowhead, CA. (June 11-16, 2007)

     
     

    "Multiresolution protein modeling by combining theory and experiment." 6th International Conference on Biological Physics, Montevideo, Uruguay. (August 27-31, 2007)

     
     

    "Multiresolution protein modeling by combining theory and experiment." 234th National Meeting of the American Chemical Society, Boston, MA. (August 19-23, 2007)

     
     

    "Novel approach to protein flexibility." Colorado Protein Stability Conference, Breckenridge, CO. (July 18-21, 2007)

     
     

    "Reaction coordinates to characterize macromolecular motions." NSF workshop on: Cyber-Enabled Discovery and Innovation, Institute for Pure and Applied Mathematics, UCLA, Los Angeles, CA. (October 29, 2007)

     
     

    "A Novel Approach toward a Complete Characterization of Protein Flexibility." “Trends in Enzymology” meeting, Como, Italy. (June 7-10, 2006)

     
     

    "Multiscale modeling of water molecules." International Workshop on “Mesoscale and Multiscale Description of Complex Fluids”, Prato, Italy. (July 4-8, 2006)

     
     

    "Multiscale modeling of water molecules." 62nd SouthWest Regional Meeting of the American Chemical Society, Houston, TX. (October 19-22, 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." International meeting on “Theory and simulation of biomolecular nano-machines”, Kobe, Japan. (Dec 12-16 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." 23rd Annual Houston Conference on “Biomedical Engineering Research”, Houston, Texas. (February 10 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." 62nd SouthWest Regional Meeting of the American Chemical Society, Houston, TX. (October 19-22, 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." 20th Annual Symposium of The Protein Society, San Diego, CA. (August 5-8, 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." WE-Heraeus-Seminar on “Biomolecular Simulation: From Physical Principles to Biological Function”, Bad Honnef (Germany). (May 22-24 2006)

     
     

    "Minimalist protein modeling as a diagnostic tool for misfolding and aggregation." 13th Texas Protein Folders Meeting, Camp Allen, Navasota, Texas. (June 3-5, 2005)

     
     

    "Optimal combination of theory and experiment for the characterization of protein folding landscapes." Colorado Protein Stability Conference, Breckenridge, CO. (July 14-16, 2005)

     
     

    "Optimal combination of theory and experiment for the characterization of protein folding landscapes." US-Japan symposium on Protein Folding and Design, Philadelphia, PA. (May 2-5, 2005)

     
     

    "Sampling Biomolecular Conformations with Spatial and Energetic Constraints." Bridging Time and Length Scales in Materials Science and Bio-Physics, Lake Arrowhead, CA. (December 12-16, 2005)

     
     Lectures
     

    "Series of Lectures on Protein Folding and Conformational Diseases." Institute for Complex Adaptive Matter/Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janerio Summer School on Biological Physics, Rio de Janeiro, Brazil. (September 29 - October 6, 2012)

     
     

    "Computational studies of biological molecules." Biological Physics at the Molecular/Cellular Interfacer ICAM/FAPERJ School, Rio de Janeiro, Brazil. (March 16-23, 2008)

     
     

    "Introduction to Molecular Biophysics: Protein motion, folding and function." IPAM program on: "Bridging Time and Length Scales in Materials and Bio-Physics", UCLA, Los Angeles, CA. (September 14 2005)

     
     Panelist
     

    "National Science Foundation Program Review Panel on CDI - cyber-enhanced discovery and innovations - Type II - Physical." Arlington, Virginia. (May 6-8, 2010)

     
     Posters
     

    "Computational evidence for a proposed photoactive yellow protein signaling state." 235th National Meeting, The American Chemical Society, New Orleans, Louisiana. (April 6-10, 2008)

     
     

    "Experimental and Theoretical Studies of Collagen Mimetic Peptides." 235th National Meeting, The American Chemical Society, New Orleans, Louisiana. (April 6-10, 2008) With J. Fallas

     
     Seminar Speaker
     

    "Multiscale characterization of the photocycle of Photoactive Yellow Protein." Bioinformatics Institute Workshop, Matrix, Singapore. (May 25-31, 2013)

     
     

    "Multiscale modeling of macromolecular dynamics." Bioinformatics Institute Workshop, Matrix, Singapore. (May 25-31, 2013)

     
     

    "A multiscale approach to characterize macromolecular dynamics and function." Department of Mathematics, Duke University, Durham, North Carolina. (February 3, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and function." Department of Physics, CNR, Marseille, France. (January 13, 2012)

     
     

    "A multiscale approach to characterize macromolecular dynamics and function." Department of Chemistry, New York University, New York, New York. (March 11, 2011)

     
     

    "A multiscale approach to characterize macromolecular dynamics and function." Department of Physics, University of Houston, Houston, Texas. (October 4, 2011)

     
     

    "Prediction of Protein Functional States by Multi-Resolution Protein Modeling." Department of Physics, University of Florence, Florence, Italy. (December 23, 2009)

     
     

    "Prediction of protein functional states by multi-resolution protein modeling." Max-Planck Institute for Polymer Research, Mainz, Germany. (March 31, 2008)

     
     

    "Chemistry Department Seminar." University of Buenos Aires, Buenos Aires, Argentina. (September 5, 2007)

     
     

    "Chemistry Department Seminar." California Insitute of Technology. (January 18, 2007)

     
     

    "Department of Chemical Engineering Seminar." Buenos Aires Institute of Technology (ITBA), Buenos Aires, Argentina. (September 6, 2007)

     
     

    "Department of Computational Biology Seminar." University of Pittsburgh. (May 1, 2007)

     
     

    "Multiresolution protein modeling by combining theory and experiment." Computational and Applied Mathematics Department Seminar, Duke University, Durham, NC. (November 14, 2007)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." Max-Planck Institut für Polymerforschung, Mainz (Germany). (June 13 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." University of Texas at Austin, Department of Chemistry and Biochemistry. (November 30 2006)

     
     

    January 19 2006.  "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." Biophysics Department, UT Southwestern Medical Center Dallas.

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." University of Florence (Italy), Department of Physics. (June 21 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." Baylor College of Medicine, Department of Biochemistr. (March 23 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." Stanford University, Department of Chemistry. (April 3 2006)

     
     

    "Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." Washington University in St. Louis, Center for Computational Biology. (April 28 2006)

     
     

    "Chemical Biology seminar." University of Southern California, Los Angeles, CA. (October 25 2005)

     
     

    "Exploring the Protein Folding landscape by combining theory and experiment." Texas A&M University, Department of Physics, College Station, TX. (February 16, 2005)

     
     

    "Minimalist protein modeling as a diagnostic tool for misfolding and aggregation." University of California San Diego, Center for Theoretical Biological Physics, San Diego, CA. (October 28 2005)

     
     

    "Optimal combination of theory and experiment for the characterization of protein fodling landscapes." University of California Santa Barbara, Department of Chemistry, (December 5 2005)

     
     

    "Optimal combination of theory and experiment for the characterization of protein folding landscapes." University of California Los Angeles, Department of Chemical Engineering, Los Angeles, CA. (October 14 2005)

     
     

    "Theoretical and Computational Biophysics seminar." University of Illinois at Urbana-Champaign, Beckman Institute, Urbana, IL. (April 11, 2005)

     
     Session Chair
     

    "Human Frontier Science Program." Tokyo, Japan. (June, 2009)

     
     

    "Symposium on "Protein Folding"." 62nd SouthWest Regional Meeting of the American Chemical Society, Houston, TX. (October 19-22, 2006)

     
     Workshops
     

    "Multiscale characterization of the photocycle of Photoactive Yellow Protein." International Workshop on 'Connecting electrochemical and water simulations: Status and future challenges' , Tegernsee, Germany. (April, 2013)

     
    Editorial Positions
     Member of the Editorial Board, Multiscale Modeling and Simulation. Society for Industrial and Applied Math (SIAM). (2007 - 2007)

     Other, Reviewer for Physical Review E. (2002 - 2002)

     Other, Reviewer for the Proceedings of the National Academy of Sciences. (2002 - 2002)

     Other, Reviewer for the Journal of Chemical Physics. (2002 - 2002)

     Other, Reviewer for the Biophysical Journal. (2002 - 2002)

     Other, Reviewer for RECOMB '03. (2002 - 2002)

     Other, Reviewer for Binational Science Foundation. (2002 - 2002)

    Supervised Theses & Dissertations
     Amarda Shehua, Master Degree in Computer Science Sampling Biomolecular Conformations with Spatial and Energetic Constraints. (2004) (Thesis Committee Member)

     Piyush Srivastava, Master Degree in Chemical Engineering Properties of self-assembled monolayer (SAM) on metal surfaces. (2004) (Thesis Committee Member)

     Silvina Matysiak, PhD in Chemistry A multiscale approach for Macromolecular Systems. (2007) (Thesis Director)

     Hernan Francisco Stamati, Master in Computer Science Analysis of Molecular Motion using Non-Linear Dimensionality Reduction. (2007) (Thesis Committee Member)

     Payel Das, PhD in Chemistry Understanding protein landscapes at multiple resolutions. (2007) (Thesis Director)

     Amarda Shehu, Ph.D. Molecules in Motion: Computing Structural Flexibility. (2008) (Thesis Co-Director)

     Silvina Matysiak, Ph.D. A Multi-scale Approach for Macromolecular Systems. (2008) (Thesis Director)

     Wenwei Zheng, PhD Multiscale Analylsis of Macromolecular Systems. (Thesis Director)

    Awards, Prizes, & Fellowships
     Outstanding Faculty Associate, Lovett College (May, 2012)

     Norman Hackerman Award in Chemical Research, Welch Foundation (2009)

     Hamill Innovation Award, Institute for Biosciences and Bioengineering (July 2007)

     NSF CAREER AWARD, National Science Foundation (2004-2009)

     Norman Hackerman - Welch Young Investigator, The Welch Foundation (2001-2003)

     La Jolla Interfaces in Science (LJIS) fellowship, Burroughs Wellcome Fund (1998-2001)

    Residencies & Summer Festivals
     Residency
     Program Organizer. Organizer of the UCLA/IPAM program "Bridging Time and Length Scales in Materials Science and Bio-Physics" held on September 12-December 16, 2005 (http://www.ipam.ucla.edu/programs/ma2005/) Chair of the organizing committee for "Workshop I: Multiscale Modeling in Soft Matter and Biophysics" (http://www.ipam.ucla.edu/programs/maws1/) held on September 26 - 30, 2005 within the IPAM program. , IPAM/UCLA, Los Angeles, CA. (9/2005 - 12/2005)
    Juries
     Master Class
     External opponent in PhD thesis defense. Invited, as expert in the field of protein modeling and simulations, to serve as external opponent in the PhD thesis defense of Stefan Wallin, department of Theoretical Physics, University of Lund, Sweden. Title of the thesis was: "Physical Models for Protein Folding". , University of Lund, Lund, Sweden. (June 2003)
    Positions Held
     Chair of Biophysical Subdivision of the American Chemical Society, ACS. (2007 - 2007)

     vice-chair of biophysical subdivision, American Chemical Society. (2005 - 2005)