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Winton Programme for the Physics of Sustainability

Department of Physics

Studying at Cambridge

 

Dr Rosana Collepardo-Guevara

Dr Rosana Collepardo-Guevara

Winton Advanced Research Fellow


Biography:

Rosana's research focuses on understanding DNA packaging insides cells, DNA structure, epigenetic phenomena, and the relationship between the structure of the genome and gene expression regulation. She received her undergraduate degree in Chemistry from the National Autonomous University of Mexico, and an MSc and DPhil in Theoretical Chemistry from the University of Oxford. She then did postdoctoral work with Tamar Schlick (NYU), Modesto Orozco (IRB Barcelona), Daan Frenkel (Cambridge), and David Wales (Cambridge). 
 

Research Interests

We develop and apply novel multi-scale computational models to investigate the structure of the genome at the nanoscale level, in conditions mimicking those inside cells. Our research aims to link epigenomes with the specific chromatin nanostructures they lead to, and also to elucidate the molecular-level mechanisms behind such link. Our multi-scale computational models are anchored in all-atom molecular dynamics simulations, coarse-graining techniques, theory, and experiments from collaborators. 

Key Publications

[19]     R. Collepardo-Guevara, G. Portella, D. Frenkel, M. Vendruscolo, T. Schlick, and M. Orozco, Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study, J Am Chem Soc, (2015) 137:10205

[18]     Gungor Ozer, R. Collepardo-Guevara and T. Schlick, Forced unravelling of chromatin fibers with nonuniform linker DNA lengths, J Phys: Cond Matt, (2015) 27:064113

[17]     R. Collepardo-Guevara and T. Schlick, Chromatin fiber polymorphism triggered by variations of DNA linker lengths, Proc Natl Acad Sci USA, (2014) 111:8061

[16]     D. Chakraborty, R. Collepardo-Guevara, D. J. Wales, Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins, J Am Chem Soc, (2014) 136:18052

[15]     A. Arcella, G. Portella, R. Collepardo-Guevara, D. Chakraborty, D. J. Wales, M. Orozco, Structure and Properties of DNA in Apolar Solvents, J Phys Chem B, (2014) 118:8540

[14]     A. Luque, R. Collepardo-Guevara, S. Grigoryev, and T. Schlick, Dynamic condensation of linker histone C-terminal domain regulates chromatin structure, Nucleic Acids Res, (2014) 42:7553

[13]     A. Hospital, I. Faustino, R. Collepardo-Guevara, C. González, J. Lluís Gelpí, M. Orozco, NAFlex: A web server for the study of nucleic acids flexibility, Nucleic Acids Res, (2013) 41:W47

[12]     R. Collepardo-Guevara and T. Schlick, Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments, Biochem Soc Trans, (2013) 41:494 

[11]     R. Collepardo-Guevara and T. Schlick, Crucial role of dynamic linker histone binding for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes, Nucleic Acids Res, (2012) 40:8803 

[10]   R. Collepardo-Guevara and T. Schlick, The effect of linker histone’s nucleosome binding affinity on chromatin unfolding mechanisms, Biophys J, (2011) 101:1670 

[9]   T. Schlick and R. Collepardo-Guevara, Biomolecular Modeling and Simulation: The Productive Trajectory of a Field, SIAM News, (2011) 44:6 

[8]   Y. Suleimanov, R. Collepardo-Guevara, and D. E. Manolopoulos, Bimolecular reaction rates from ring polymer molecular dynamics: application to H + CH4 → H2 + CH3, J Chem Phys, (2011) 134:044131 

[7]   T. Schlick, R. Collepardo-Guevara, L. A. Halvorsen, S. Jung, and X. Xiao, Biomolecular modelling and simulation: a field coming of age, Quart Rev Biophys, (2011) 43:1 

[6]   O. Perisic+, R. Collepardo-Guevara+, and T. Schlick, Modelling studies of chromatin fiber structure as a function of DNA linker length, J Mol Bio, (2010) 403:777 +co-first authors

[5]   R. Collepardo-Guevara, Y. Suleimanov, and D. E. Manolopoulos, Bimolecular chemical reaction rates from ring polymer rate theory, J Chem Phys, (2009) 130:174713 

[4]   R. Collepardo-Guevara, I. R. Craig, and D. E. Manolopoulos, Proton transfer in a polar solvent from ring polymer molecular dynamics reaction rate theory, J Chem Phys, (2008) 128:144502 

[3]   R. Collepardo-Guevara and E. Corvera Poiré, Controlling viscoelastic flow by tuning frequency during occlusions, Phys Review E, (2007) 76:026301 

[2]   R. Collepardo-Guevara and E. Corvera Poiré, Maximizing the dynamic permeability during occlusions, Eur. Phys. J. Special Topics, (2007) 143:95 

[1]   R. Collepardo-Guevara, D. Walter, and D. Neuhauser, and R. Baer, A Hückel study of the effect of a molecular resonance cavity on the quantum conductance of an alkene wire, Chem Phys Lett, (2004) 393:367