Biomolecular Dynamics @ Uni Freiburg

Publications

- Titles are linked with the Journal's URL of the article
- pdfs are available for personal use only and are subject to the following copyrights
* Copyright by the American Institute of Physics
** Copyright by the American Chemical Society
*** Copyright by the American Physical Society
**** Copyright by Taylor & Francis



2009

Free energy landscape of an RNA hairpin constructed via dihedral angle principal component analysis,
L. Riccardi, P. H. Nguyen, and G. Stock, J. Phys. Chem. B 113, 16660 (2009) pdf** 107

Nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides:
theory meets experiment,

P. H. Nguyen, Peter Hamm, and G. Stock,
in: Proteins: Energy, Heat and Signal Flow, eds. D. Leitner and J. Straub, CRC Press, 151 (2009) 106

Energy transport in peptide helices around the glass transition,
E. Backus, P. H. Nguyen, V. Botan, R. Pfister, A. Moretto, M. Crisma, C. Toniolo, G. Stock, P. Hamm,
in: Ultrafast Phenoma, Vol (XVI) Corkum, S. de Silvestri , K. A. Nelson, E. Riedle, R. W. Schoenlein, (Springer Verlag, Heidelberg), 532 (2009) 105

Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent,
S. M. Park, P. H. Nguyen, and G. Stock, J. Chem. Phys. 131, 184503 (2009) pdf* 104

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of guanine sensing riboswitch,
A. Villa, J. Wöhnert, and G. Stock, Nucl. Acids Res. 37, 4774 (2009) pdf 103

Energy flow and long-range correlation in guanine-binding riboswitch: A nonequilibrium molecular dynamics study,
P. H. Nguyen, P. Derreumaux, and G. Stock, J. Phys. Chem. B 113, 9340 (2009) pdf** 102

Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces,
H. Fujisaki, K. Yagi, J. E. Straub, and G. Stock, Int. J. Quant. Chem. 109, 2047 (2009) pdf 101

Classical simulation of quantum energy flow in biomolecules,
G. Stock, Phys. Rev. Lett. 102, 118301 (2009) pdf 100

Molecular orientation studied by PELDOR experiments,
A. Marko, D. Markgraf, H.Yu, Y. Mu, G. Stock, and T. Prisner, J. Chem. Phys. 130, 064102 (2009) pdf* 99

Multidimensional Langevin modeling of biomolecular dynamics,
R. Hegger and G. Stock, J. Chem. Phys. 130, 034106 (2009) pdf* 98


2008

Influence of Nitroxide Spin Labels on RNA Structure: A Molecular Dynamics Simulation Study,
H. Yu, Y. Mu, L. Nodenskiold, and G. Stock, J. Chem. Theo. Comp. 4, 1781 (2008) pdf 97

Dynamic treatment of vibrational energy relaxation in heterogeneous and fluctuating environment,
H. Fujisaki and G. Stock, J. Chem. Phys. 129, 134110 (2008) pdf* 96

Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties,
E. Backus, P.H. Nguyen, V. Botan, R. Pfister, A. Moretto, M. Crisma, C. Toniolo, O. Zerbe, G.Stock, and P. Hamm, J. Phys. Chem. B 112, 15487-15492 (2008) pdf** 95

Glass transition regulates heat transport through a helical polypeptide,
E. Backus, P. H. Nguyen, V. Botan, R. Pfister, A. Moretto, M. Crisma, C. Toniolo, G. Stock, and P. Hamm,
Ultrafast Phenomena (Springer, Heidelberg) (2008) 94

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis,
A. Altis, M. Otten, P.H. Nguyen, R. Hegger, and G. Stock, J. Chem. Phys. 128, 245102 (2008) pdf * 93

Special Issue on Ultrafast photoinduced processes in polyatomic molecules:
Electronic structure, dynamics and spectroscopy (in honour of Wolfgang Domcke),

M. Thoss, G. Stock, and T. Martinez, Chem. Phys. 347, 1 (2008) pdf 92

Maximum Caliber: A variational approach applied to two-state dynamics,
G. Stock, K. Ghosch, and K. A. Dill, J. Chem. Phys. 128, 194102 (2008) pdf * 91

Energy Transport in Peptide Helices: A Comparison between UV and IR pumping,
E. Backus, P.H. Nguyen, V. Botan, R. Pfister,B A. Moretto, M. Crisma, C. Toniolo, G. Stock, and P. Hamm,
J. Phys. Chem. B 112, 9091-9099 (2008) pdf** 90

Nonadiabatic vibrational dynamics and spectroscopy of peptides: A quantum-classical description,
M. Kobus, R. D. Gorbunov, P.H. Nguyen, and G. Stock, Chem. Phys. 347, 208 (2008) pdf 89

NMR and MD Studies of the Temperature-Dependent Dynamics of RNAYMNG Tetraloops,
J. Ferner, A. Villa, E. Durchardt, E. Widjajakusuma, G. Stock, and H. Schwalbe,
Nucl. Acids. Res. 36, 1928-1940 (2008) pdf 88

Molecular dynamics simulation of the structure, dynamics and thermostability of the RNA hairpins uCACGg and cUUCGg,
A. Villa, E. Widjajakusuma, and G. Stock, J. Phys. Chem. B 112, 134 (2008) pdf** 87


2007

Energy Transport in Peptide Helices,
V. Botan, E. Backus, R. Pfister, A. Moretto, M. Crisma, C. Toniolo, P. H. Nguyen, G. Stock, and P. Hamm,
Proc. Nat. Acad. Sci.104, 12749-12754 (2007) pdf 86

Dihedral angle principal component analysis of molecular dynamics simulations,
A. Altis, P. H. Nguyen, R. Hegger, and G. Stock, J. Chem. Phys. 126, 244111 (2007) pdf* 85

Base-specific spinlabeling of RNA for structure determination,
N. Piton, O. Schiemann, Y. Mu, G. Stock, T. F. Prisner, J. Engels, Nucl. Acids Res. 35, 3128 (2007) pdf 84

Ab initio based building block model of amide I vibrations in peptides,
R. D. Gorbunov and G. Stock, Chem. Phys. Lett. 437, 272 (2007) pdf 83

Quantum-classical description of the amide I spectrum of trialanine,
R. D. Gorbunov, P. H. Nguyen, M. Kobus, and G. Stock, J. Chem. Phys. 126, 054509 (2007) pdf* 82

How Complex is the Dynamics of Peptide Folding?
R. Hegger, A. Altis, P. H. Nguyen, and G. Stock, Phys. Rev. Lett. 98, 028102, (2007) pdf 81

Structure and dynamics of the homologues series of alanine peptides: A joint molecular-dynamics/NMR study,
J. Graf, P. H. Nguyen, G. Stock, and H. Schwalbe, J. Am. Chem. Soc. 129, 1179 (2007) pdf 80

Monomer adds to preformed structured oligomers of Ab-peptides by a two-stage dock-lock mechanism,
P. H. Nguyen, M. S. Li, G. Stock, J. E. Straub, and D. Thirumalai, Proc. Nat. Acad. Sci. (USA) 104, 111 (2007) pdf 79


2006

Classical calculation of transient absorption spectra monitoring ultrafast electron transfer processes,
I. Uspenskiy, B. Balzer, and G. Stock, J. Chem. Theo. Comp. 2, 1605 (2006) pdf 78

What NMR relaxation can tell us about the internal motion of an RNA hairpin: A molecular dynamics simulation study,
A. Villa and G. Stock, J. Chem. Theo. Comp. 2, 1228 (2006) pdf 77

Photoinduced conformational dynamics of a photoswitchable peptide:
A nonequilibrium molecular dynamics simulation study,

P. H. Nguyen, R. D. Gorbunov, and G. Stock, Biophys. J. 91, 1224 (2006) pdf 76

Classical description of the dynamics and time-resolved spectroscopy of nonadiabatic cis-trans photoisomerization,
I. Uspenskiy, B. Balzer, and G. Stock, Chem. Phys. 329, 109 (2006) pdf 75

Reply to the Comment on "Energy Landscape of a Small Peptide Revealed by Dihedral Angle Principal Component Analysis,
Y. Mu, P. H. Nguyen, and G. Stock, Proteins 64, 798 (2006) pdf 74

Improved Wang-Landau sampling through the use of smoothed potential energy surfaces,
P. H. Nguyen, E. Mittag, A. E. Torda, and G. Stock J. Chem. Phys. 124, 154107 (2006) pdf* 73

Quantum modeling of transient infrared spectra reflecting photoinduced electron-transfer dynamics,
B. Balzer und G. Stock, J. Chem. Phys. 124, 114105 (2006) pdf* 72

Conformational dynamics in RNA-peptide binding: A molecular dynamics simulation study,
Y. Mu and G. Stock, Biophys. J. 90, 391 (2006) pdf 71

Nonequilibrium molecular dynamics simulation of a photoswitchable peptide,
P. H. Nguyen and G. Stock, Chem. Phys. 323, 36 (2006) pdf 70

Special Issue on "Nonequilibrium Dynamics in Biomolecules",
G. Stock, J. Wachtveitl, and H. Grubmüllermüller, Chem. Phys. 323, 1 (2006) pdf 69


2005

Energy Landscape and Folding Mechanism of a b-Hairpin: A Replica Exchange Molecular Dynamics Study,
P. H. Nguyen, G. Stock, E. Mittag, C.-K. Hu, and M. S. Li, Proteins 61, 796 (2005) pdf 68

Structure and dynamics of an RNA tetraloop: A joint moleculardynamics/ NMR study,
J. Koplin, Y. Mu, C. Richter, H. Schwalbe, and G. Stock, Structure 13, 1255-1267 (2005) pdf 67

"Structure and Dynamics of a photoswitchable peptide: A Replica Exchange Molecular Dynamics Simulations
P. H. Nguyen, Y. Mu, and G. Stock, Proteins 60, 485 (2005) pdf 66

Synthesis of spin labeled RNA's for long range distance measurements by PELDOR,
N. Piton, O. Schiemann, Y. Mu, G. Stock, T. F. Prisner, J. Engels, Nucleotides 24, 771-775 (2005) pdf 65

Ab initio-based exciton model of amide I vibrations in peptides:
Definition, conformational dependence, and transferability,

R. D. Gorbunov, D. S. Kosov, and G. Stock, J. Chem. Phys. 122, 224904 (2005) pdf* 64

Trendbericht: Quantendynamik komplexer Systeme,
G. Stock, Nachrichten aus der Chemie 53, 288 (2005) pdf 63

Classical Description of Nonadiabatic Quantum Dynamics,
G. Stock and M. Thoss, Adv. Chem. Phys. 131, 243 (2005) 62

Energy Landscape of a Small Peptide Revealed by Dihedral Angle Principal Component Analysis,
Y. Mu, P. H. Nguyen, and G. Stock, Proteins 58, 45 (2005) pdf 61

Modeling of decoherence and dissipation in nonadiabatic photoreactions by an effective-scaling nonsecular Redfield algorithm,
B. Balzer and G. Stock, Chem. Phys. 310, 33 (2005) pdf 60


2004

Transient spectral features of a cis-trans photoreaction in the condensed phase: A model study,
B. Balzer and G. Stock, J. Phys. Chem. A 108, 6464, (2004) pdf** 59

A PELDOR Based Nanometer Distance Ruler for Oligonucleotides,
O. Schiemann, N. Piton, Y. Mu, G. Stock, J. Engels, T. F. Prisner, J. Chem. Soc. Am. 126, 5722 (2004 )pdf 58


2003

Nonequilibrium molecular-dynamics study of the vibrational energy relaxation of peptides in water,
P. H. Nguyen and G. Stock, J. Chem. Phys. 119, 11350 (2003) pdf* 57

Mechanism of a photochemical funnel: A dissipative wave-packet dynamics study,
B. Balzer, S. Hahn, and G. Stock, Chem. Phys. Lett 379, 351 (2003) pdf 56

Quasiclassical and semiclassical wave-packet dynamics in periodic potentials,
B. Balzer, S. Dilthey, G. Stock, and M. Thoss, J. Chem. Phys. 119, 5795 (2003) pdf* 55

Quasiperiodic orbit analysis of nonadiabatic cis-trans photoisomerization dynamics,
B. Balzer, S. Dilthey, S. Hahn, M. Thoss, and G. Stock, J. Chem. Phys. 119, 4204 (2003) pdf* 54

Conformational Dynamics of Trialanine in Water II: Comparison of AMBER, CHARMM, GROMOS,
and OPLS Force Fields to NMR and Infrared Experiment
s,
Y. Mu, D. Kosov, and G. Stock, J. Phys. Chem. B 107, 5064 (2003) pdf** 53

Femtosecond time-resolved spectroscopy of the dynamics at conical intersections,
G. Stock and W. Domcke,
In: Conical Intersections, eds. W. Domcke, D. R. Yarkony and H. Köppel,(World Scientific Singapore, 2003) 52

Mixed quantum-classical description of the dynamics at conical intersections,
G. Stock and M. Thoss, in: Conical Intersections, eds. W. Domcke, D. R. Yarkony and H. Köppel, (World Scientific Singapore, 2003) 51


2002

Classical description of the level density and the relaxation behavior of multi-dimensional molecular curve-crossing systems,
S. Dilthey and G. Stock, Israel J. Chem. 42, 203 (2002) 50

Peptide conformational heterogeneity revealed from nonlinear vibrational spectroscopy and molecular dynamics simulation,
S. Woutersen, R. Pfister, P. Hamm, Y. Mu, D. Kosov, and G. Stock, J. Chem. Phys. 117, 6833 (2002) pdf * 49

Periodic-orbit analysis of coherent electron-transfer femtosecond experiments,
S. Dilthey and G. Stock, J. Phys. Chem. A 106, 8483 (2002) pdf** 48

Conformational dynamics of trialanine in water: A molecular dynamics study,
Y. Mu and G. Stock, J. Phys. Chem. B 106, 5294 (2002) pdf**47

Ultrafast cis-trans photoswitching: A model study,
S. Hahn and G. Stock, J. Chem. Phys. 116, 1085 (2002) pdf* 46

Classical phase-space analysis of vibronically coupled systems,
S. Dilthey, B. Mehlig, and G. Stock, J. Chem. Phys. 116, 69 (2002) pdf * 45


2001

Periodic Orbit Description of Nonadiabatic Quantum Dynamics,
S. Dilthey and G. Stock,
Phys. Rev. Lett. 87, 140404 (2001) pdf 44

Efficient calculation of femtosecond ionization spectra,
S. Hahn and G. Stock,
Phys. Chem. Phys. 3, 2331 (2001) 43

Subpicosecond Conformational Dynamics of Small Peptides Probed by Two-dimensional Vibrational Spectroscopy,
S. Woutersen, Y. Mu, G. Stock, and P. Hamm,
Proc. Natl. Acad. Sci. USA. 98, 11254 (2001)pdf 42

Hydrogen-Bond Lifetime Measured by Time Dependent 2D-IR Spectroscopy: N-Methylacetamide in Methanol,
S. Woutersen, Y. Mu, G. Stock, and P. Hamm,
Chem. Phys. 266, 137 (2001) pdf 41


2000

Theoretical description of secondary-emission spectra reflecting ultrafast nonadiabatic isomerization,
S. Hahn and G. Stock,
J. Phys. Chem. A, 105, 2626 (2000) pdf** 40

Quantum-classical Liouville description of multidimensional nonadiabatic molecular dynamics,
M. Santer, U. Manthe, and G. Stock,
J. Chem. Phys. 114, 2001 (2000) pdf* 39

Femtosecond secondary emission arising from the nonadiabatic photoisomerization in rhodopsin,
S. Hahn and G. Stock,
Chem. Phys. 259, 297 (2000) pdf 38

Semiclassical description of nonadiabatic quantum dynamics: Application to the S1-S2 conical intersection in pyrazine,
M. Thoss, W. H. Miller, and G. Stock,
J. Chem Phys. 112, 10282 (2000) pdf* 37

Approximate calculation of femtosecond pump-probe spectra monitoring nonadiabatic excited-state dynamics,
S. Dilthey, S. Hahn, and G. Stock,
J. Chem. Phys. 112, 4910 (2000) pdf*

Quantum-mechanical modeling of the femtosecond isomerization in rhodopsin,
S. Hahn and G. Stock,
J. Phys. Chem. B 104, 1146 (2000) pdf**35


1999

Flow of zero-point energy and exploration of phase space in classical simulationsof quantum relaxation dynamics II. Application to nonadiabatic processes,
U. Müller and G. Stock,
J. Chem. Phys. 111, 77 (1999) pdf * 34

Flow of zero-point energy and exploration of phase space in classical simulations of quantum relaxation dynamics,
G. Stock and U. Müller,
J. Chem. Phys. 111, 65 (1999) pdf * 33

Mapping approach to the semiclassical description of nonadiabatic quantum dynamics,
B. M. Thoss and G. Stock,
Phys. Rev. A 59, 64 (1999) pdf 32


1998

Modulation of Ultrafast Electron Transfer Dynamics by Wavepacket Motion in Oxazine 1,
S. Engleitner, M. Seel, B. Wolfseder, G. Stock, W. Domcke, and W. Zinth,
in: Ultrafast Phenomena XI, eds. T. ElsC$sser, J. G. Fujimoto, D. A. Wiersma, W. Zinth, (Springer, Heidelberg, 1998), p 630 31

Conical Intersections and Femtosecond Dynamics,
W. Domcke, L. Seidner, and G. Stock,
in: Ultrafast Phenomena XI, eds. T. Elsässer, J. G. Fujimoto, D. A. Wiersma, W. Zinth, (Springer, Heidelberg, 1998), p 491 30

Efficient calculation of time- and frequency-resolved spectra: A mixed nonperturbative/perturbative approach,
S. Hahn and G.Stock,
Chem. Phys. Lett. 296, 137 (1998) pdf 29

Vibrational coherence in ultrafast electron-transfer dynamics of oxazine 1 in N,N-dimethylaniline:
Simulation of a femtosecond pump-probe experiment
,
B. Wolfseder, L. Seidner, W. Domcke, G. Stock, M. Seel, S. Engleitner and W. Zinth,
Chem. Phys. 233, 323 (1998) pdf 28

Consistent treatment of quantum-mechanical and classical degrees of freedom in mixed quantum-classical simulations, U. Müller and G. Stock, J. Chem. Phys. 108, 7516 (1998) pdf * 27


1997

Surface-hopping modeling of photoinduced relaxation dynamics on coupled potential-energy surfaces,
U. Müller and G. Stock, J. Chem. Phys. 107, 6230 (1997) pdf * 26

Femtosecond pump-probe spectroscopy of electron-transfer systems: A nonperturbative approach,
B. Wolfseder, L.Seidner, G. Stock, and W. Domcke, Chem. Phys. 217, 275 (1997)pdf 25

Theory of ultrafast nonadiabatic excited-state processes and their spectroscopic detection in real time,
W. Domcke and G. Stock, Adv. Chem. Phys. 100, 1 (Wiley, New York, 1997) 24

Semiclassical Description of Nonadiabatic Quantum Dynamics,
G. Stock and M. Thoss, Phys. Rev. Lett. 78, 578 (1997) pdf 23


1996

Ultrafast non-Born Oppenheimer dynamics detected by resonance Raman spectroscopy:
A case study on pyrazine,

G. Stock, C. Woywod, and W. Domcke, in: XVth International Conference on Raman Spectroscopy, eds. S. A. Asher and P. B. Stein (Wiley, New York, 1996), S. 58 22

Classical approach to femtosecond spectroscopy of nonadiabatic photo-isomerization processes
in the condensed phase,

G. Stock, in: Femto-chemistry, ed. M. Chergui (World Scientific, Singapore, 1996), p 596 21


1995

Classical description of nonadiabatic photoisomerization processes and their real-time detection via femtosecond spectroscopy,
G. Stock, J. Chem. Phys. 103, 10015 (1995) pdf * 20

Resonance Raman spectroscopy of the S1 and S2 states of pyrazine: Experiment and first principles calculation of spectra,
G. Stock, C. Woywod, W. Domcke, T. Swinney, and B. S. Hudson, J. Chem. Phys. 103, 6851 (1995) pdf * 19

Nonperturbative approach to femtosecond spectroscopy:
General theory and application to multidimensional nonadiabatic photoisomerization processes,

L. Seidner, G. Stock, and W. Domcke, J. Chem. Phys. 103, 3998 (1995) pdf * 18

A nonperturbative generalized master equation for the spin-boson problem,
G. Stock, Phys. Rev. E 51, 3038 (1995) pdf 17

A semiclassical self-consistent-field approach to dissipative dynamics: II. Internal conversion processes,
G. Stock, J. Chem. Phys. 103, 2888 (1995) pdf * 16

A semiclassical self-consistent-field approach to dissipative dynamics: The spin-boson problem,
G. Stock, J. Chem. Phys. 103, 1561 (1995) pdf * 15


1994

Model studies on femtosecond spectroscopy of multidimensional photo-isomerization and internal-conversion dynamics: A nonperturbative approach,
L. Seidner, G. Stock, and W. Domcke,
Chem. Phys. Lett. 228, 665 (1994) pdf 14

Femtosecond spectroscopy of nonadiabatic photoisomerization processes: Semiclassical modelling,
G. Stock, L. Seidner, and W. Domcke,
in: Ultrafast Phenomena IX, eds. P. F. Barbara, W. H.  Knox, G. A. Mourou, and A. H. Zewail, (Springer, Heidelberg, 1994), p 512 13

Photoinduced large amplitude dynamics as mechanism for pure electronic dephasing and its manifestation in cw and time-resolved spectroscopy,
G. Stock, J. Chem. Phys. 101, 246 (1994) pdf *

Classical description of ultrafast internal conversion processes. The benzene cation,
G. Stock, Chem. Phys. Lett. 224, 131 (1994) pdf 11


1993

Femtosecond spectroscopy of ultrafast nonadiabatic excited-state dynamics on the basis of ab initio potential-energy surfaces: the S2 state of pyrazine,
G. Stock and W. Domcke, J. Phys. Chem. 97,12466 (1993) pdf**10

Classical formulation of the spectroscopy of nonadiabatic excited-state dynamics,
G. Stock and W. H.Miller, J. Chem. Phys. 99, 1545 (1993) pdf * 9


1992

Model study on the real-time detection of ultrafast nonadiabatic dynamics associated with the Wulf-Cappuis bands of ozone,
G. Stock, C. Woywod, and W. Domcke,
Chem. Phys. Lett. 200, 163 (1992) pdf 8

A classical model for time- and frequency-resolved spectroscopy of nonadiabatic excited-state dynamics,
G. Stock and W. H. Miller, Chem. Phys. Lett. 197, 396 (1992) pdf 7

Ab initio characterization of the S1-S2 conical intersection in pyrazine and calculation of spectra,
L. Seidner, G. Stock, A.L. Sobolewski, and W. Domcke, J. Chem. Phys. 96, 5298 (1992) pdf * 6

Detection of ultrafast molecular excited-state dynamics with time- and frequency-resolved pump-probe spectroscopy,
G. Stock and W. Domcke,
Phys. Rev. A 45, 3032 (1992) pdf 5


1990

Theory of resonance Raman scattering and fluorescence from strongly vibronically coupled excited-states of polyatomic molecules,
G. Stock and W. Domcke, J. Chem. Phys. 93, 5496 (1990) pdf * 4

Theory of femtosecond pump-probe spectroscopy of ultrafast internal conversion processes in polyatomic molecules,
G. Stock and W. Domcke, J. Opt. Soc. Am. B, 7, 1970 (1990 pdf 3


1989

Theoretical studies on the femtosecond real-time measurement of ultrafast electronic decay in polyatomic molecules,
G. Stock, R. Schneider, and W. Domcke,
J. Chem. Phys. 90, 7184 (1989) pdf * 2


1988

Model studies on the time-resolved measurement of excited-state vibrational dynamics and vibronic coupling,
G. Stock and W. Domcke,
Chem. Phys. 124, 227 (1988) pdf 1