Publications

Preprints

  • K. Karandashev, J. Vanicek; Accelerating equilibrium isotope effect calculations: II. Stochastic implementation of direct estimators; arXiv:1909.02910
  • K. Karandashev, J. Vanicek; A combined on-the-fly/interpolation procedure for evaluating energy values needed in molecular simulations; arXiv:1908.06960
  • C. L. Vaillant, M. J. Thapa, J. Vaníček, J. O. Richardson; Semiclassical analysis of the quantum instanton approximation; arXiv:1908.03419

2019

Journal Articles

Efficient geometric integrators for nonadiabatic quantum dynamics. II. The diabatic representation

J. Roulet; S. Choi; J. Vanicek 

The Journal of Chemical Physics. 2019-05-28. Vol. 150, num. 20, p. 204113. DOI : 10.1063/1.5094046.

Efficient geometric integrators for nonadiabatic quantum dynamics. I. The adiabatic representation

S. Choi; J. Vanicek 

The Journal of Chemical Physics. 2019-05-28. Vol. 150, num. 20, p. 204112. DOI : 10.1063/1.5092611.

Mechanisms of fluorescence quenching in prototypical aggregation-induced emission systems: excited state dynamics with TD-DFTB

T. Tran; A. Prlj; K-H. Lin; D. Hollas; C. Corminboeuf 

Physical Chemistry Chemical Physics. 2019-05-14. Vol. 21, num. 18, p. 9026-9035. DOI : 10.1039/c9cp00691e.

Single-Hessian thawed Gaussian approximation

T. Begušić; M. Cordova; J. Vaníček 

The Journal of Chemical Physics. 2019-04-19. Vol. 150, num. 15, p. 154117. DOI : 10.1063/1.5090122.

Book Chapters

Ab initio semiclassical evaluation of vibrationally resolved electronic spectra with thawed Gaussians

J. Vanicek; T. Begusic 

Molecular Spectroscopy and Quantum Dynamics; Elsevier, 2019-09-01.

2018

Journal Articles

On-the-fly ab initio semiclassical evaluation of time-resolved electronic spectra

T. Begusic; J. Roulet; J. Vanicek 

Journal Of Chemical Physics. 2018-12-28. Vol. 149, num. 24, p. 244115. DOI : 10.1063/1.5054586.

On-the-fly ab initio three thawed Gaussians approximation: a semiclassical approach to Herzberg-Teller spectra

T. Begušić; A. Patoz; M. Šulc; J. Vaníček 

Chemical Physics. 2018-08-03. Vol. 515, p. 152-163. DOI : 10.1016/j.chemphys.2018.08.003.

On-the-Fly Ab Initio Semiclassical Evaluation of Absorption Spectra of Polyatomic Molecules beyond the Condon Approximation

A. Patoz; T. Begušić; J. Vaníček 

The Journal of Physical Chemistry Letters. 2018. Vol. 9, p. 2367-2372. DOI : 10.1021/acs.jpclett.8b00827.

Theses

Accelerating path integral evaluation of equilibrium and kinetic isotope effects

K. Karandashev / J. Vanicek (Dir.)  

Lausanne: EPFL, 2018. DOI : 10.5075/epfl-thesis-8211.

2017

Journal Articles

Nonadiabatic effects in electronic and nuclear dynamics

M. P. Bircher; E. Liberatore; N. J. Browning; S. Brickel; C. Hofmann et al. 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061510. DOI : 10.1063/1.4996816.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

S. Antipov; S. Bhattacharyya; K. El Hage; Z-H. Xu; M. Meuwly et al. 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061509. DOI : 10.1063/1.4996559.

Kinetic isotope effects and how to describe them

K. Karandashev; Z-H. Xu; M. Meuwly; J. Vanicek; J. O. Richardson 

Structural Dynamics. 2017. Vol. 4, num. 6, p. 061501. DOI : 10.1063/1.4996339.

Several Semiclassical Approaches to Time-resolved Spectroscopy

J. Vanicek 

CHIMIA International Journal for Chemistry. 2017. Vol. 71, num. 5, p. 283-287. DOI : 10.2533/chimia.2017.283.

Accelerating equilibrium isotope effect calculations. I. Stochastic thermodynamic integration with respect to mass

K. Karandashev; J. Vanicek 

Journal of Chemical Physics. 2017. Vol. 146, num. 18, p. 184102. DOI : 10.1063/1.4981260.

Theses

Geometric Integrators for Nonadiabatic Molecular Quantum Dynamics Induced by the Interaction with the Electromagnetic Field

A. K. F. Patoz / J. Vanicek (Dir.)  

Lausanne: EPFL, 2017. DOI : 10.5075/epfl-thesis-8145.

2016

Journal Articles

Path integral approach to the quantum fidelity amplitude

J. Vanicek; D. Cohen 

Philosophical Transactions of the Royal Society A. 2016. Vol. 374, num. 2069, p. 20150164. DOI : 10.1098/rsta.2015.0164.

2015

Journal Articles

Accelerating quantum instanton calculations of the kinetic isotope effects

K. Karandashev; J. Vanicek 

Journal of Chemical Physics. 2015. Vol. 143, num. 19, p. 194104. DOI : 10.1063/1.4935701.

On-the-fly ab initio semiclassical dynamics of floppy molecules: Absorption and photoelectron spectra of ammonia

M. Wehrle; S. Oberli; J. Vanicek 

Journal of Physical Chemistry A. 2015. Vol. 119, num. 22, p. 5685-5690. DOI : 10.1021/acs.jpca.5b03907.

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

M. Šulc; R. M. Marín; H. S. Robins; J. Vaníček 

Nucleic Acids Research. 2015. Vol. 43, num. W1, p. W474-W479. DOI : 10.1093/nar/gkv457.

Theses

Evaluation and analysis of vibrationally resolved electronic spectra with ab initio semiclassical dynamics

M. Wehrle / J. Vanicek (Dir.)  

Lausanne: EPFL, 2015. DOI : 10.5075/epfl-thesis-6737.

2014

Journal Articles

Efficient on-the-fly ab initio semiclassical method for computing time-resolved nonadiabatic electronic spectra with surface hopping or Ehrenfest dynamics

T. Zimmermann; J. Vaníček 

Journal of Chemical Physics. 2014. Vol. 141, num. 13, p. 134102. DOI : 10.1063/1.4896735.

Predicting the genes regulated by microRNAs via binding sites in the 3' untranslated and coding regions

J. Vanicek 

CHIMIA International Journal for Chemistry. 2014. Vol. 68, num. 9, p. 629-632. DOI : 10.2533/chimia.2014.629.

On-the-fly ab initio semiclassical dynamics: Identifying degrees of freedom essential for emission spectra of oligothiophenes

M. Wehrle; M. Sulc; J. Vanicek 

Journal of Chemical Physics. 2014. Vol. 140, num. 24, p. 244114. DOI : 10.1063/1.4884718.

Control of mitophagie by microRNAs - A key step of erythropoiesis

I. Barde; B. Rauwel; R. M. Marin-Florez; A. Corsinotti; E. Laurenti et al. 

M S-Medecine Sciences. 2014. Vol. 30, num. 1, p. 12-15.

Host miRNA regulation of human cytomegalovirus immediate early protein translation promotes viral latency

C. M. O'Connor; J. Vanicek; E. A. Murphy 

Journal of Virology. 2014. Vol. 88, num. 10, p. 5524-5532. DOI : 10.1128/JVI.00481-14.

Kinetic isotope effect in malonaldehyde determined from path integral Monte Carlo simulations

J. Huang; M. Buchowiecki; T. Nagy; J. Vanicek; M. Meuwly 

Physical Chemistry Chemical Physics. 2014. Vol. 16, num. 1, p. 204-211. DOI : 10.1039/c3cp53698j.

Student Projects

Accelerating quantum dynamics calculations of time-resolved electronic spectra by optimizing Gaussian bases

J. Rohrbach 

2014.

2013

Journal Articles

Imaginary-time nonuniform mesh method for solving the multidimensional Schroedinger equation: Fermionization and melting of quantum Lennard-Jones crystals

A. Hernando de Castro; J. Vanicek 

Physical Review A. 2013. Vol. 88, p. 062107. DOI : 10.1103/PhysRevA.88.062107.

Monte Carlo evaluation of the equilibrium isotope effects using the Takahashi-Imada factorization of the Feynman path integral

M. Buchowiecki; J. Vanicek 

Chemical Physics Letters. 2013. Vol. 588, p. 11-16. DOI : 10.1016/j.cplett.2013.09.070.

Role of sampling in evaluating classical time autocorrelation functions

T. Zimmermann; J. Vanicek 

Journal of Chemical Physics. 2013. Vol. 139, num. 10, p. 104105. DOI : 10.1063/1.4820420.

Improving the accuracy and efficiency of time-resolved electronic spectra calculations: Cellular dephasing representation with a prefactor

E. Zambrano; M. Sulc; J. Vanicek 

Journal of Chemical Physics. 2013. Vol. 139, num. 5, p. 054109. DOI : 10.1063/1.4817005.

Relation of exact Gaussian basis methods to the dephasing representation: Theory and application to time-resolved electronic spectra

M. Sulc; H. Hernandez; T. Martinez; J. Vanicek 

Journal of Chemical Physics. 2013. Vol. 139, num. 3, p. 034112. DOI : 10.1063/1.4813124.

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

I. Barde; B. Rauwel; R. M. Marin-Flórez; A. Corsinotti; E. Laurenti et al. 

Science. 2013. Vol. 340, num. 6130, p. 350-353. DOI : 10.1126/science.1232398.

Searching the coding region for microRNA targets

R. Marin; M. Sulc; J. Vanicek 

RNA. 2013. Vol. 19, p. 467-474. DOI : 10.1261/rna.035634.112.

Student Projects

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

A. Patoz 

2013.

2012

Journal Articles

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

R. Marin; F. Voellmy; T. von Erlach; J. Vanicek 

RNA. 2012. Vol. 18, num. 10, p. 1760-1770. DOI : 10.1261/rna.033282.112.

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

T. Zimmermann; J. Vanicek 

Journal of Chemical Physics. 2012. Vol. 137, p. 22A516. DOI : 10.1063/1.4738878.

Accelerating the calculation of time-resolved electronic spectra with the cellular dephasing representation

M. Sulc; J. Vanicek 

Molecular Physics. 2012. Vol. 110, num. 9-10, p. 945-955. DOI : 10.1080/00268976.2012.668971.

Measuring nonadiabaticity of molecular quantum dynamics with quantum fidelity and with its efficient semiclassical approximation

T. Zimmermann; J. Vanicek 

Journal of Chemical Physics. 2012. Vol. 136, p. 094106. DOI : 10.1063/1.3690458.

Optimal use of conservation and accessibility filters in microRNA target prediction

R. Marin; J. Vanicek 

PLoS ONE. 2012. Vol. 7, num. 2, p. e32208. DOI : 10.1371/journal.pone.0032208.

Self-Assembled Molecular Rafts at Liquid|Liquid Interfaces for Four-Electron Oxygen Reduction

A. J. Olaya; D. H. Schaming; P-F. M. Brevet; H. Nagatani; T. Zimmermann et al. 

Journal of the American Chemical Society. 2012. Vol. 134, p. 498-506. DOI : 10.1021/ja2087322.

Theses

Highly Specific Methods for the Prediction of Genes Regulated by MicroRNAs

R. M. Marín Flórez / J. Vanicek (Dir.)  

Lausanne: EPFL, 2012. DOI : 10.5075/epfl-thesis-5443.

On the Efficiency of Semiclassical and Classical Approximations of Quantum Fidelity in Many-Dimensional Systems

C. Mollica / J. Vanicek (Dir.)  

Lausanne: EPFL, 2012. DOI : 10.5075/epfl-thesis-5383.

Book Chapters

Quantum Instanton Evaluation of the Kinetic Isotope Effects and of the Temperature Dependence of the Rate Constant

J. Vanicek 

Rate Constant Calculation for Thermal Reactions: Methods and Applications; Hoboken, New Jersey: Wiley, 2012. p. 67-92.

2011

Journal Articles

Efficient sampling avoids the exponential wall in classical simulations of fidelity

C. Mollica; T. Zimmermann; J. Vanicek 

Physical Review E. 2011. Vol. 84, p. 066205. DOI : 10.1103/PhysRevE.84.066205.

Beating the Efficiency of Both Quantum and Classical Simulations with a Semiclassical Method

C. Mollica; J. Vanicek 

Physical Review Letters. 2011. Vol. 107, p. 214101. DOI : 10.1103/PhysRevLett.107.214101.

Beyond Transition State Theory: Accurate Description of Nuclear Quantum Effects on the Rate and Equilibrium Constants of Chemical Reactions Using Feynman Path Integrals

J. Vanicek 

Chimia. 2011. Vol. 65, num. 9, p. 715-719. DOI : 10.2533/chimia.2011.715.

Accelerating Calculations of Ultrafast Time-Resolved Electronic Spectra with Efficient Quantum Dynamics Methods

M. Wehrle; M. Sulc; J. Vanicek 

Chimia. 2011. Vol. 65, num. 5, p. 334-338. DOI : 10.2533/chimia.2011.334.

Efficient use of accessibility in microRNA target prediction

R. Marin; J. Vanicek 

Nucleic Acids Research. 2011. Vol. 39, num. 1, p. 19-29. DOI : 10.1093/nar/gkq768.

2010

Journal Articles

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology

K. Wong; J. Sonnenberg; F. Paesani; T. Yamamoto; J. Vanicek et al. 

Journal of Chemical Theory and Computation. 2010. Vol. 6, num. 9, p. 2566-2580. DOI : 10.1021/ct900579k.

Communications: Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity

T. Zimmermann; J. Vanicek 

Journal of Chemical Physics. 2010. Vol. 132, num. 24, p. 241101/1-241101/4. DOI : 10.1063/1.3451266.

Efficient evaluation of the accuracy of molecular quantum dynamics on an approximate analytical or interpolated ab initio potential energy surface

T. Zimmermann; J. Ruppen; B. Li; J. Vanicek 

International Journal of Quantum Chemistry. 2010. Vol. 110, num. 13, p. 2426-2435. DOI : 10.1002/qua.22730.

Direct evaluation of the temperature dependence of the rate constant based on the quantum instanton approximation

M. R. Buchowiecki; J. Vanicek 

Journal of Chemical Physics. 2010. Vol. 132, p. 194106/1-194106/10. DOI : 10.1063/1.3425617.

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

T. Zimmermann; J. Vanicek 

Journal of Molecular Modeling. 2010. Vol. 16, num. 11, p. 1779-1787. DOI : 10.1007/s00894-010-0711-y.

Books

Amber 11

D. A. Case; T. A. Darden; T. E. Cheatham; C. L. Simmerling; J. Wang et al. 

San Francisco: University of California, 2010.

2009

Journal Articles

Path integral evaluation of the equilibrium isotope effect in [1,5] sigmatropic hydrogen shift reactions

T. Zimmermann; J. Vanicek 

Flash informatique. 2009. num. 8, p. 37-40.

Efficient evaluation of accuracy of molecular quantum dynamics using dephasing representation

B. Li; C. Mollica; J. Vanicek 

Journal of Chemical Physics. 2009. Vol. 131, num. 4, p. 041101/1-041101/4. DOI : 10.1063/1.3187240.

Path integral evaluation of equilibrium isotope effects

T. Zimmermann; J. Vanicek 

Journal of Chemical Physics. 2009. Vol. 131, num. 2, p. 024111/1-024111/13. DOI : 10.1063/1.3167353.

2008

Journal Articles

Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: Implications for latency

E. Murphy; J. Vanicek; H. Robins; T. Shenk; A. J. Levine 

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.

Books

Amber 10

D. A. Case; T. A. Darden; T. E. Cheatham; C. L. Simmerling; J. Wang et al. 

San Francisco: University of California, 2008.

2007

Journal Articles

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

J. Vanicek; W. H. Miller 

Journal of Chemical Physics. 2007. Vol. 127, num. 11, p. 114309/1-114309/9. DOI : 10.1063/1.2768930.

2006

Journal Articles

Dephasing representation of quantum fidelity for general pure and mixed states

J. Vanicek 

Physical Review E. 2006. Vol. 73, num. 4-2, p. 046204/1-046204/12. DOI : 10.1103/PhysRevE.73.046204.

2005

Journal Articles

Quantum-instanton evaluation of the kinetic isotope effects

J. Vanicek; W. H. Miller; J. F. Castillo; F. Javier Aoiz 

Journal of Chemical Physics. 2005. Vol. 123, num. 5, p. 054108/1-054108/14. DOI : 10.1063/1.1946740.

Conference Papers

Path integral evaluation of the kinetic isotope effects based on the quantum instanton approximation

J. Vanicek; W. H. Miller 

2005. The 8th International Conference: Path Integrals from Quantum Information to Cosmology, Prague, Czech Republic, June 6-10, 2005. p. 1-11.

2004

Journal Articles

Dephasing representation: Unified semiclassical framework for fidelity decay

J. Vanicek 

Los Alamos National Laboratory, Preprint Archive, Quantum Physics. 2004. num. arXiv:quant-ph/0410205v1, p. 1-4.

Dephasing representation: Employing the shadowing theorem to calculate quantum correlation functions

J. Vanicek 

Physical Review E. 2004. Vol. 70, num. 5-2, p. 055201/1-055201/4. DOI : 10.1103/PhysRevE.70.055201.

2003

Journal Articles

Survival probability and local density of states for one-dimensional Hamiltonian systems

J. Vanicek; D. Cohen 

Journal of Physics A: Mathematical and General. 2003. Vol. 36, p. 9591-9608. DOI : 10.1088/0305-4470/36/36/310.

Semiclassical evaluation of quantum fidelity

J. Vanicek; E. J. Heller 

Physical Review E. 2003. Vol. 68, num. 5-2, p. 056208/1-056208/5. DOI : 10.1103/PhysRevE.68.056208.

Uniform semiclassical wave function for coherent two- dimensional electron flow

J. Vanicek; E. J. Heller 

Physical Review E. 2003. Vol. 67, num. 1-2, p. 016211/1-016211/8. DOI : 10.1103/PhysRevE.67.016211.

2001

Journal Articles

Replacement manifolds: A method to uniformize semiclassical wave functions

J. Vanicek; E. J. Heller 

Physical Review E. 2001. Vol. 64, num. 2-2, p. 026215/1-026215/11. DOI : 10.1103/PhysRevE.64.026215.

1996

Journal Articles

Atomic beam splitter based on multiple adiabatic passage in the optical interference pattern

M. Ol'shanii; J. Vanicek; M. Prentiss 

Quantum and Semiclassical Optics. 1996. Vol. 8, num. 3, p. 655-663. DOI : 10.1088/1355-5111/8/3/025.