Publications: Biophysics


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These papers are ordered by article relevance.

Photo-excitation of a light-harvesting supra-molecular triad: a Time-Dependent DFT 
N. Spallanzani, C. A. Rozzi, D. Varsano, T. Baruah, M. R. Pederson, F. Manghi, A. Rubio
Journal Of Physical Chemistry B 113, 5345 - 5349 (2009)
Fingerprints of bonding motifs in DNA duplexes of adenine and thymine revealed from circular dichroism: synchrotron radiation experiments and TDDFT calculations
L. Nielsen, A. Holm, D. Varsano, U. Kadhana, S. Hoffmann, R. Di Felice, A. Rubio, S. Nielsen
Journal Of Physical Chemistry B 113, 9614 - 9619 (2009)
Ab initio electronic and optical spectra of free-base porphyrins: the role of electronic correlation
M. Palummo, C. Hogan, P. Bagalá, F. Sottile, A. Rubio
Journal of Chemical Physics 131, 84101 (2009)
Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base
T. Keal, M. Wanko, W. Thiel
Theoretical Chemistry Accounts 123, 145 - 156 (2009)
Effect of Polarization on the Opsin Shift in Rhodopsins. 1. A Combined QM/QM/MM Model for Bacteriorhodopsin and Pharaonis Sensory Rhodopsin II
M. Wanko, M. Hoffmann, Th. Frauenheim, M. Elstner
Journal Of Physical Chemistry B 112, 11462 - 11467 (2008)
Effect of polarization on the opsin shift in rhodopsins. 2. empirical polarization models for proteins
M. Wanko, M. Hoffmann, J. Frähmcke, Th. Frauenheim, M. Elstner
Journal Of Physical Chemistry B 112, 11468 - 11478 (2008)
Pseudo-Jahn-Teller origin of the low barrier hydrogen bond in N2H7+
P. García-Fernández, L. García-Canales, J. M. García-Lastra, J. Junquera, M. Moreno, J. A. Aramburu
Journal of Chemical Physics 129, 124313 (2008)
Analytical excited state forces for the time-dependent density-functional tight-binding method
D. Heringer, T. A. Niehaus, M. Wanko, Th. Frauenheim
Journal Of Computational Chemistry 28, 2589 - 2601 (2007)
Color Tuning in Rhodopsins: The Mechanism for the Spectral Shift between Bacteriorhodopsin and Sensory Rhodopsin II
M. Hoffmann, M. Wanko, P. Strodel, P. H. König, T. Frauenheim, K. Schulten, W. Thiel, E. Tajkhorshid, M. Elstner
Journal Of The American Chemical Society 128, 10808 - 10818 (2006)
A TDDFT study of the excited states of DNA bases and their assemblies
D. Varsano, R. Di Felice, M.A.L. Marques, A. Rubio
Journal Of Physical Chemistry B 110, 7129 - 7138 (2006)
Computational Photochemistry of Retinal Proteins
M. Wanko, M. Hoffmannand T. Frauenheim, M. Elstner
Journal Of Computer-Aided Molecular Design 20, 511 - 518 (2006)
Optical Absorption in the Blue Fluorescent Protein: a First Principles Study
X. López, M.A.L. Marques, A. Castro, A. Rubio
Journal Of The American Chemical Society 127, 12329 - 12337 (2005)
Calculating Absorption Shifts for Retinal Proteins: Computational Challenges
M. Wanko, M. Hoffmann, P. Strodel, A. Koslowski, W. Thiel, F. Neese, T. Frauenheim, M. Elstner
Journal Of Physical Chemistry B 109, 3606 - 3615 (2005)
A global investigation of excited state surfaces within time-dependent density-functional response theory
M. Wanko, M. Garavelli, F. Bernardi, T. A. Niehaus, Th. Frauenheim,, M. Elstner
Journal of Chemical Physics 120, 1674 - 1692 (2004)
Time-dependent Density-functional approach for biological photoreceptors: the case of the Green Fluorescent Protein
M.A.L. Marques, X. López, D. Varsano, A. Castro, A. Rubio
Physical Review Letters 90, 258101 - 4 (2003)