Publications

Preprints

  • J. Roulet; S. Choi; J. Vaníček : Efficient geometric integrators for nonadiabatic quantum dynamics in the diabatic basisarXiv:1903.04946
  • S. Choi; J. Vaníček : Efficient geometric integrators for nonadiabatic quantum dynamics in the adiabatic basisarXiv:1902.04661

Journal Articles

2019

S. Choi; J. Vanicek : Efficient geometric integrators for nonadiabatic quantum dynamics in the adiabatic basis. 2019-02-14.

2018

T. Begusic; J. Roulet; J. Vanicek : On-the-fly ab initio semiclassical evaluation of time-resolved electronic spectra; Journal Of Chemical Physics. 2018-12-28. Vol. 149, num. 24, p. 244115. DOI : 10.1063/1.5054586.
T. Begušić; A. Patoz; M. Šulc; J. Vaníček : On-the-fly ab initio three thawed Gaussians approximation: a semiclassical approach to Herzberg-Teller spectra; Chemical Physics. 2018-08-03. Vol. 515, p. 152-163. DOI : 10.1016/j.chemphys.2018.08.003.
A. Patoz; T. Begušić; J. Vaníček : On-the-Fly Ab Initio Semiclassical Evaluation of Absorption Spectra of Polyatomic Molecules beyond the Condon Approximation; The Journal of Physical Chemistry Letters. 2018. Vol. 9, p. 2367-2372. DOI : 10.1021/acs.jpclett.8b00827.

2017

M. P. Bircher; E. Liberatore; N. J. Browning; S. Brickel; C. Hofmann et al. : Nonadiabatic effects in electronic and nuclear dynamics; Structural Dynamics. 2017. Vol. 4, num. 6, p. 061510. DOI : 10.1063/1.4996816.
S. Antipov; S. Bhattacharyya; K. El Hage; Z.-H. Xu; M. Meuwly et al. : Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches; Structural Dynamics. 2017. Vol. 4, num. 6, p. 061509. DOI : 10.1063/1.4996559.
K. Karandashev; Z.-H. Xu; M. Meuwly; J. Vanicek; J. O. Richardson : Kinetic isotope effects and how to describe them; Structural Dynamics. 2017. Vol. 4, num. 6, p. 061501. DOI : 10.1063/1.4996339.
J. Vanicek : Several Semiclassical Approaches to Time-resolved Spectroscopy; CHIMIA International Journal for Chemistry. 2017. Vol. 71, num. 5, p. 283-287. DOI : 10.2533/chimia.2017.283.
K. Karandashev; J. Vanicek : Accelerating equilibrium isotope effect calculations. I. Stochastic thermodynamic integration with respect to mass; Journal of Chemical Physics. 2017. Vol. 146, num. 18, p. 184102. DOI : 10.1063/1.4981260.

2016

J. Vanicek; D. Cohen : Path integral approach to the quantum fidelity amplitude; Philosophical Transactions of the Royal Society A. 2016. Vol. 374, num. 2069, p. 20150164. DOI : 10.1098/rsta.2015.0164.

2015

K. Karandashev; J. Vanicek : Accelerating quantum instanton calculations of the kinetic isotope effects; Journal of Chemical Physics. 2015. Vol. 143, num. 19, p. 194104. DOI : 10.1063/1.4935701.
M. Wehrle; S. Oberli; J. Vanicek : On-the-fly ab initio semiclassical dynamics of floppy molecules: Absorption and photoelectron spectra of ammonia; Journal of Physical Chemistry A. 2015. Vol. 119, num. 22, p. 5685–5690. DOI : 10.1021/acs.jpca.5b03907.
M. Šulc; R. M. Marín; H. S. Robins; J. Vaníček : PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences; Nucleic Acids Research. 2015. Vol. 43, num. W1, p. W474-W479. DOI : 10.1093/nar/gkv457.

2014

T. Zimmermann; J. Vaníček : Efficient on-the-fly ab initio semiclassical method for computing time-resolved nonadiabatic electronic spectra with surface hopping or Ehrenfest dynamics; Journal of Chemical Physics. 2014. Vol. 141, num. 13, p. 134102. DOI : 10.1063/1.4896735.
J. Vanicek : Predicting the genes regulated by microRNAs via binding sites in the 3' untranslated and coding regions; CHIMIA International Journal for Chemistry. 2014. Vol. 68, num. 9, p. 629-632. DOI : 10.2533/chimia.2014.629.
M. Wehrle; M. Sulc; J. Vanicek : On-the-fly ab initio semiclassical dynamics: Identifying degrees of freedom essential for emission spectra of oligothiophenes; Journal of Chemical Physics. 2014. Vol. 140, num. 24, p. 244114. DOI : 10.1063/1.4884718.
I. Barde; B. Rauwel; R. M. Marin-Florez; A. Corsinotti; E. Laurenti et al. : Control of mitophagie by microRNAs - A key step of erythropoiesis; M S-Medecine Sciences. 2014. Vol. 30, num. 1, p. 12-15.
C. M. O'Connor; J. Vanicek; E. A. Murphy : Host miRNA regulation of human cytomegalovirus immediate early protein translation promotes viral latency; Journal of Virology. 2014. Vol. 88, num. 10, p. 5524-5532. DOI : 10.1128/JVI.00481-14.
J. Huang; M. Buchowiecki; T. Nagy; J. Vanicek; M. Meuwly : Kinetic isotope effect in malonaldehyde determined from path integral Monte Carlo simulations; Physical Chemistry Chemical Physics. 2014. Vol. 16, num. 1, p. 204-211. DOI : 10.1039/c3cp53698j.

2013

A. Hernando de Castro; J. Vanicek : Imaginary-time nonuniform mesh method for solving the multidimensional Schroedinger equation: Fermionization and melting of quantum Lennard-Jones crystals; Physical Review A. 2013. Vol. 88, p. 062107. DOI : 10.1103/PhysRevA.88.062107.
M. Buchowiecki; J. Vanicek : Monte Carlo evaluation of the equilibrium isotope effects using the Takahashi-Imada factorization of the Feynman path integral; Chemical Physics Letters. 2013. Vol. 588, p. 11-16. DOI : 10.1016/j.cplett.2013.09.070.
T. Zimmermann; J. Vanicek : Role of sampling in evaluating classical time autocorrelation functions; Journal of Chemical Physics. 2013. Vol. 139, num. 10, p. 104105. DOI : 10.1063/1.4820420.
E. Zambrano; M. Sulc; J. Vanicek : Improving the accuracy and efficiency of time-resolved electronic spectra calculations: Cellular dephasing representation with a prefactor; Journal of Chemical Physics. 2013. Vol. 139, num. 5, p. 054109. DOI : 10.1063/1.4817005.
M. Sulc; H. Hernandez; T. Martinez; J. Vanicek : Relation of exact Gaussian basis methods to the dephasing representation: Theory and application to time-resolved electronic spectra; Journal of Chemical Physics. 2013. Vol. 139, num. 3, p. 034112. DOI : 10.1063/1.4813124.
I. Barde; B. Rauwel; R. M. Marin-Flórez; A. Corsinotti; E. Laurenti et al. : A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy; Science. 2013. Vol. 340, num. 6130, p. 350-353. DOI : 10.1126/science.1232398.
R. Marin; M. Sulc; J. Vanicek : Searching the coding region for microRNA targets; RNA. 2013. Vol. 19, p. 467-474. DOI : 10.1261/rna.035634.112.

2012

R. Marin; F. Voellmy; T. von Erlach; J. Vanicek : Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3'-end of the seed match; RNA. 2012. Vol. 18, num. 10, p. 1760-1770. DOI : 10.1261/rna.033282.112.
T. Zimmermann; J. Vanicek : Evaluation of the importance of spin-orbit couplings in the nonadiabatic quantum dynamics with quantum fidelity and with its efficient “on-the-fly” ab initio semiclassical approximation; Journal of Chemical Physics. 2012. Vol. 137, p. 22A516. DOI : 10.1063/1.4738878.
M. Sulc; J. Vanicek : Accelerating the calculation of time-resolved electronic spectra with the cellular dephasing representation; Molecular Physics. 2012. Vol. 110, num. 9-10, p. 945-955. DOI : 10.1080/00268976.2012.668971.
T. Zimmermann; J. Vanicek : Measuring nonadiabaticity of molecular quantum dynamics with quantum fidelity and with its efficient semiclassical approximation; Journal of Chemical Physics. 2012. Vol. 136, p. 094106. DOI : 10.1063/1.3690458.
R. Marin; J. Vanicek : Optimal use of conservation and accessibility filters in microRNA target prediction; PLoS ONE. 2012. Vol. 7, num. 2, p. e32208. DOI : 10.1371/journal.pone.0032208.
A. J. Olaya; D. H. Schaming; P.-F. M. Brevet; H. Nagatani; T. Zimmermann et al. : Self-Assembled Molecular Rafts at Liquid|Liquid Interfaces for Four-Electron Oxygen Reduction; Journal of the American Chemical Society. 2012. Vol. 134, p. 498-506. DOI : 10.1021/ja2087322.

2011

C. Mollica; T. Zimmermann; J. Vanicek : Efficient sampling avoids the exponential wall in classical simulations of fidelity; Physical Review E. 2011. Vol. 84, p. 066205. DOI : 10.1103/PhysRevE.84.066205.
C. Mollica; J. Vanicek : Beating the Efficiency of Both Quantum and Classical Simulations with a Semiclassical Method; Physical Review Letters. 2011. Vol. 107, p. 214101. DOI : 10.1103/PhysRevLett.107.214101.
J. Vanicek : Beyond Transition State Theory: Accurate Description of Nuclear Quantum Effects on the Rate and Equilibrium Constants of Chemical Reactions Using Feynman Path Integrals; Chimia -Zurich-. 2011. Vol. 65, num. 9, p. 715-719. DOI : 10.2533/chimia.2011.715.
M. Wehrle; M. Sulc; J. Vanicek : Accelerating Calculations of Ultrafast Time-Resolved Electronic Spectra with Efficient Quantum Dynamics Methods; Chimia. 2011. Vol. 65, num. 5, p. 334-338. DOI : 10.2533/chimia.2011.334.
R. Marin; J. Vanicek : Efficient use of accessibility in microRNA target prediction; Nucleic Acids Research. 2011. Vol. 39, num. 1, p. 19-29. DOI : 10.1093/nar/gkq768.

2010

K. Wong; J. Sonnenberg; F. Paesani; T. Yamamoto; J. Vanicek et al. : Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology; Journal of Chemical Theory and Computation. 2010. Vol. 6, num. 9, p. 2566–2580. DOI : 10.1021/ct900579k.
T. Zimmermann; J. Vanicek : Communications: Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity; Journal of Chemical Physics. 2010. Vol. 132, num. 24, p. 241101/1-241101/4. DOI : 10.1063/1.3451266.
T. Zimmermann; J. Ruppen; B. Li; J. Vanicek : Efficient evaluation of the accuracy of molecular quantum dynamics on an approximate analytical or interpolated ab initio potential energy surface; International Journal of Quantum Chemistry. 2010. Vol. 110, num. 13, p. 2426–2435. DOI : 10.1002/qua.22730.
M. R. Buchowiecki; J. Vanicek : Direct evaluation of the temperature dependence of the rate constant based on the quantum instanton approximation; Journal of Chemical Physics. 2010. Vol. 132, p. 194106/1-194106/10. DOI : 10.1063/1.3425617.
T. Zimmermann; J. Vanicek : Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene; Journal of Molecular Modeling. 2010. Vol. 16, num. 11, p. 1779-1787. DOI : 10.1007/s00894-010-0711-y.

2009

T. Zimmermann; J. Vanicek : Path integral evaluation of the equilibrium isotope effect in [1,5] sigmatropic hydrogen shift reactions; Flash informatique. 2009. num. 8, p. 37-40.
B. Li; C. Mollica; J. Vanicek : Efficient evaluation of accuracy of molecular quantum dynamics using dephasing representation; Journal of Chemical Physics. 2009. Vol. 131, num. 4, p. 041101/1-041101/4. DOI : 10.1063/1.3187240.
T. Zimmermann; J. Vanicek : Path integral evaluation of equilibrium isotope effects; Journal of Chemical Physics. 2009. Vol. 131, num. 2, p. 024111/1-024111/13. DOI : 10.1063/1.3167353.

2008

E. Murphy; J. Vanicek; H. Robins; T. Shenk; A. J. Levine : Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: Implications for latency; Proceedings of the National Academy of Sciences of the United States of America. 2008. Vol. 105, num. 14, p. 5453-5458. DOI : 10.1073/pnas.0711910105.

2007

J. Vanicek; W. H. Miller : Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene; Journal of Chemical Physics. 2007. Vol. 127, num. 11, p. 114309/1-114309/9. DOI : 10.1063/1.2768930.

2006

J. Vanicek : Dephasing representation of quantum fidelity for general pure and mixed states; Physical Review E. 2006. Vol. 73, num. 4-2, p. 046204/1-046204/12. DOI : 10.1103/PhysRevE.73.046204.

2005

J. Vanicek; W. H. Miller; J. F. Castillo; F. Javier Aoiz : Quantum-instanton evaluation of the kinetic isotope effects; Journal of Chemical Physics. 2005. Vol. 123, num. 5, p. 054108/1-054108/14. DOI : 10.1063/1.1946740.

2004

J. Vanicek : Dephasing representation: Unified semiclassical framework for fidelity decay; Los Alamos National Laboratory, Preprint Archive, Quantum Physics. 2004. num. arXiv:quant-ph/0410205v1, p. 1-4.
J. Vanicek : Dephasing representation: Employing the shadowing theorem to calculate quantum correlation functions; Physical Review E. 2004. Vol. 70, num. 5-2, p. 055201/1-055201/4. DOI : 10.1103/PhysRevE.70.055201.

2003

J. Vanicek; D. Cohen : Survival probability and local density of states for one-dimensional Hamiltonian systems; Journal of Physics A: Mathematical and General. 2003. Vol. 36, p. 9591-9608. DOI : 10.1088/0305-4470/36/36/310.
J. Vanicek; E. J. Heller : Semiclassical evaluation of quantum fidelity; Physical Review E. 2003. Vol. 68, num. 5-2, p. 056208/1-056208/5. DOI : 10.1103/PhysRevE.68.056208.
J. Vanicek; E. J. Heller : Uniform semiclassical wave function for coherent two- dimensional electron flow; Physical Review E. 2003. Vol. 67, num. 1-2, p. 016211/1-016211/8. DOI : 10.1103/PhysRevE.67.016211.

2001

J. Vanicek; E. J. Heller : Replacement manifolds: A method to uniformize semiclassical wave functions; Physical Review E. 2001. Vol. 64, num. 2-2, p. 026215/1-026215/11. DOI : 10.1103/PhysRevE.64.026215.

1996

M. Ol'shanii; J. Vanicek; M. Prentiss : Atomic beam splitter based on multiple adiabatic passage in the optical interference pattern; Quantum and Semiclassical Optics. 1996. Vol. 8, num. 3, p. 655-663. DOI : 10.1088/1355-5111/8/3/025.

Conference Papers

2005

J. Vanicek; W. H. Miller : Path integral evaluation of the kinetic isotope effects based on the quantum instanton approximation. 2005. The 8th International Conference: Path Integrals from Quantum Information to Cosmology, Prague, Czech Republic, June 6-10, 2005. p. 1-11.

Books

2010

D. A. Case; T. A. Darden; T. E. Cheatham; C. L. Simmerling; J. Wang et al. : Amber 11 ; San Francisco: University of California.

2008

D. A. Case; T. A. Darden; T. E. Cheatham; C. L. Simmerling; J. Wang et al. : Amber 10 ; San Francisco: University of California.

Theses

2018

K. Karandashev : Accelerating path integral evaluation of equilibrium and kinetic isotope effects. Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8211.

2017

A. K. F. Patoz : Geometric Integrators for Nonadiabatic Molecular Quantum Dynamics Induced by the Interaction with the Electromagnetic Field. Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-8145.

2015

M. Wehrle : Evaluation and analysis of vibrationally resolved electronic spectra with ab initio semiclassical dynamics. Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6737.

2012

R. M. Marín Flórez : Highly Specific Methods for the Prediction of Genes Regulated by MicroRNAs. Lausanne, EPFL, 2012. DOI : 10.5075/epfl-thesis-5443.
C. Mollica : On the Efficiency of Semiclassical and Classical Approximations of Quantum Fidelity in Many-Dimensional Systems. Lausanne, EPFL, 2012. DOI : 10.5075/epfl-thesis-5383.

Book Chapters

2012

J. Vanicek : Quantum Instanton Evaluation of the Kinetic Isotope Effects and of the Temperature Dependence of the Rate Constant; Rate Constant Calculation for Thermal Reactions: Methods and Applications; Hoboken, New Jersey: Wiley, 2012. p. 67-92.

Student Projects

2014

J. Rohrbach : Accelerating quantum dynamics calculations of time-resolved electronic spectra by optimizing Gaussian bases ; 2014.

2013

A. Patoz : Implementation of exact and approximate methods for nonadiabatic quantum molecular dynamics induced by the interaction with the electromagnetic field and their applications to local quantum control ; 2013.