AG Knapp - Numata, Jorge

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Numata, Jorge

Freie Universität Berlin



Degree		MSc.
Organisation		DFG
Status		PhD-student
Telephone		+49-30-838-53484
Contact		numata(at)chemie.fu-berlin.de
Homepage

Funding	SFB765 Multivalency as chemical organization and action principle: New architectures, functions and applications. Support is gratefully acknowledged.
Current work	Techniques: Molecular dynamics simulation and statistical mechanical modeling Information theoretical approaches for biomolecular motion Development of a new method to calculate conformational entropy (for a copy of the program, contact me) Applications: Thermodynamics of protein folding and receptor-ligand binding Conformational entropy of beta-amyloid aggregation Dynamic modulation of photosynthetic pigment transition energies Cooperations: Michael Wan, Aspuru-Guzik Research group at Harvard University
Academic Degrees
1998	BSc. in Chemical Engineering - Tecnolgico de Monterrey (ITESM) Mexico Specialization in chemical process simulation
2005	MSc. in Bioinformatics - Freie UniversitÃ¤t Berlin - Germany Specialization in biological and biophysical modeling
Employment
1999-2001	Bayer de Mexico - MaterialScience Production leader for Polyurethanes: Production planning, chemical plant trouble-shooting, corporate culture correspondence with Bayer USA
Selected talks given
14.08.2008	MedILS Split, Croatia, Entropy in Biomolecular systems, "Conformational entropy from biomolecular simulation using information theory"
26.09.2007	Institut Franais du Petrol, Thermodynamics 2007, "Entropy in biomolecular simulation: Better methods through information theory"
01.08.2007	University of Tokyo, International Workshop on Bioinformatics and Systems Biology, "Protein thermodynamics from MD Simulation: Beyond the quasi-harmonic approximation"
20.07.2006	Harvard University, Chemistry and Chemical Biology, "Entropic contributions in macromolecules: the case of protein aggregation"

Publications

Influence of Spacer-Receptor Interactions on the Stability of Bivalent Ligand-Receptor Complexes
J. Phys. Chem. B, 116 (8), pp 2595 to 2604, 2012
Numata - Juneja - Diestler - Knapp

Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories
J. Chem. Theory Comput., http://dx.doi.org/10.1021/ct200910z, 2012
Numata - Knapp

Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol
J. Chem. Theory Comput., 6 (6), pp 1871-1883, 2010
Juneja - Numata - Nilsson - Knapp

Position dependent effects of fluorinated amino acids on hydrophobic core formation of a coiled coil heterodimer
Chem. Eur. J., 2009
Salwiczek - Samsonov - Vagt - Baldauf - Nyakatura - Fleige - Numata - Clfen - Pisabarro - Koksch

Entropy and thermodynamics in biomolecular simulation
Handbook of Res. on Sys. Biol. Applications in Medicine, 2008
Numata

Measuring correlations in metabolomic networks with mutual information
Genome Informatics Volume 20, 2008
Numata - Ebenhoeh - Knapp

Conformational entropy of biomolecules: Beyond the quasi-harmonic approximation
Genome Informatics Volume 18, 192-205, 2007
Numata - Wan - Knapp

The Application of Comparative Genomics and Structure Prediction in Dental Research
Handbook of Research on Informatics in Healthcare and Biomedicine, 2006
Numata