Publications

Preprints

On Hagedorn wavepackets associated with different Gaussians

Zhan Tong Zhang, Jiří J. L. Vaníček

Ab initio simulation of single vibronic level fluorescence spectra of anthracene using Hagedorn wavepackets

Zhan Tong Zhang, Jiří J. L. Vaníček

Single vibronic level fluorescence spectra from Hagedorn wavepacket dynamics

Zhan Tong Zhang, Jiří J. L. Vaníček

Can increasing the size and flexibility of a molecule reduce decoherence?

Alan Scheidegger, Nikolay V. Golubev, Jiri J. L. Vanicek

2024

Journal Articles

High-order geometric integrators for the local cubic variational Gaussian wavepacket dynamics

R. Moghaddasi Fereidani; J. J. L. Vanicek 

Journal Of Chemical Physics. 2024. Vol. 160, num. 4, p. 044113. DOI : 10.1063/5.0180070.

Finite-temperature vibronic spectra from the split-operator coherence thermofield dynamics

Z. T. Zhang; J. Vanicek 

The Journal of Chemical Physics. 2024. Vol. 160, num. 8, p. 084103. DOI : 10.1063/5.0187823.

Theses

High-order geometric integrators for the variational Gaussian wavepacket dynamics and application to vibronic spectra at finite temperature

R. Moghaddasi Fereidani / J. Vanicek (Dir.)  

Lausanne, EPFL, 2024. 

Applications of the thawed Gaussian approximation to electronic spectroscopy

E. Kletnieks / J. Vanicek (Dir.)  

Lausanne, EPFL, 2024. 

Application of Hagedorn wavepackets to chemical dynamics and spectroscopy

Z. T. Zhang / J. Vanicek (Dir.)  

Lausanne, EPFL, 2024. 

2023

Journal Articles

Isotope Effects on the Electronic Spectra of Ammonia from Ab Initio Semiclassical Dynamics

E. Kletnieks; Y. Calvino Alonso; J. Vanicek 

The Journal of Physical Chemistry. 2023. DOI : 10.1021/acs.jpca.3c04607.

High-order geometric integrators for the variational Gaussian approximation

R. Moghaddasi Fereidani; J. Vanicek 

The Journal of Chemical Physics. 2023. Vol. 159, num. 9. DOI : 10.1063/5.0165489.

Family of Gaussian wavepacket dynamics methods from the perspective of a nonlinear Schrodinger equation

J. J. L. Vanicek 

Journal Of Chemical Physics. 2023. Vol. 159, num. 1, p. 014114. DOI : 10.1063/5.0146680.

How to Find Molecules with Long-lasting Charge Migration?

A. Scheidegger; N. V. Golubev; J. Vanicek 

Chimia. 2023. Vol. 77, num. 4, p. 201 – 205. DOI : 10.2533/chimia.2023.201.

Sampling strategies for the Herman-Kluk propagator of the wavefunction

F. Kroeninger; C. Lasser; J. J. L. Vanicek 

Frontiers In Physics. 2023. Vol. 11, p. 1106324. DOI : 10.3389/fphy.2023.1106324.

Conference Papers

NEMTO: Neural Environment Matting for Novel View and Relighting Synthesis of Transparent Objects

D. Wang; Z. T. Zhang; S. Süsstrunk 

2023. International Conference on Computer Vision 2023, Paris, France, Oct 2-6, 2023. DOI : 10.1109/ICCV51070.2023.00036.

2022

Journal Articles

Efficient Semiclassical Evaluation of Electronic Coherences in Polyatomic Molecules

N. V. Golubev; J. Vanicek 

Chimia. 2022. Vol. 76, num. 6, p. 575 – 581. DOI : 10.2533/chimia.2022.575.

Applicability of the Thawed Gaussian Wavepacket Dynamics to the Calculation of Vibronic Spectra of Molecules with Double-Well Potential Energy Surfaces br

T. Begusic; E. Tapavicza; J. Vanicek 

Journal Of Chemical Theory And Computation. 2022. Vol. 18, num. 5, p. 3065 – 3074. DOI : 10.1021/acs.jctc.2c00030.

Search for long-lasting electronic coherence using on-the-fly ab initio semiclassical dynamics

A. Scheidegger; J. Vanicek; N. V. Golubev 

Journal Of Chemical Physics. 2022. Vol. 156, num. 3, p. 034104. DOI : 10.1063/5.0076609.

Theses

High-order geometric integrators for nonadiabatic molecular quantum dynamics and their applications to explore conical intersections

S. Choi / J. Vanicek (Dir.)  

Lausanne, EPFL, 2022. 

Efficient geometric integrators for the linear and nonlinear time-dependent Schrödinger equation

J. Roulet / J. Vanicek (Dir.)  

Lausanne, EPFL, 2022. 

2021

Journal Articles

An implicit split-operator algorithm for the nonlinear time-dependent Schrödinger equation

J. Roulet; J. Vanicek 

The Journal of Chemical Physics. 2021. Vol. 155, num. 20, p. 204109. DOI : 10.1063/5.0071153.

High-order geometric integrators for representation-free Ehrenfest dynamics

S. Choi; J. Vanicek 

The Journal of Chemical Physics. 2021. Vol. 155, num. 12, p. 124104. DOI : 10.1063/5.0061878.

Core-Valence Attosecond Transient Absorption Spectroscopy of Polyatomic Molecules

N. V. Golubev; J. Vaníček; A. I. Kuleff 

Physical Review Letters. 2021. Vol. 127, num. 12, p. 123001. DOI : 10.1103/PhysRevLett.127.123001.

Time-reversible and norm-conserving high-order integrators for the nonlinear time-dependent Schrödinger equation: Application to local control theory

J. Roulet; J. Vaníček 

The Journal of Chemical Physics. 2021. Vol. 154, num. 15, p. 154106. DOI : 10.1063/5.0050071.

Efficient Semiclassical Dynamics for Vibronic Spectroscopy beyond Harmonic, Condon, and Zero-Temperature Approximations

T. Begušić; J. Vaníček 

CHIMIA International Journal for Chemistry. 2021. Vol. 75, num. 4, p. 261 – 266. DOI : 10.2533/chimia.2021.261.

How important are the residual nonadiabatic couplings for an accurate simulation of nonadiabatic quantum dynamics in a quasidiabatic representation?

S. Choi; J. Vaníček 

The Journal of Chemical Physics. 2021. Vol. 154, num. 12, p. 124119. DOI : 10.1063/5.0046067.

Finite-Temperature, Anharmonicity, and Duschinsky Effects on the Two-Dimensional Electronic Spectra from Ab Initio Thermo-Field Gaussian Wavepacket Dynamics

T. Begušić; J. Vaníček 

The Journal of Physical Chemistry Letters. 2021. Vol. 12, num. 11, p. 2997 – 3005. DOI : 10.1021/acs.jpclett.1c00123.

Tuning the Thermal Stability and Photoisomerization of Azoheteroarenes through Macrocycle Strain**

S. Vela; A. Scheidegger; R. Fabregat; C. Corminboeuf 

Chemistry-A European Journal. 2021. Vol. 27, num. 1, p. 419 – 426. DOI : 10.1002/chem.202003926.

Conference Papers

Decoherence and Revival of Attosecond Charge Migration Driven by Non-adiabatic Dynamics

D. T. Matselyukh; V. Despre; N. V. Golubev; A. Kuleff; H. J. Woerner 

2021. Conference on Lasers and Electro-Optics (CLEO), ELECTR NETWORK, May 09-14, 2021. DOI : 10.1364/CLEO_QELS.2021.FM1O.6.

Theses

Efficient ab initio semiclassical dynamics for linear and nonlinear electronic spectroscopy

T. Begusic / J. Vanicek (Dir.)  

Lausanne, EPFL, 2021. 

Book Chapters

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

J. Vanicek; T. Begusic 

Molecular Spectroscopy and Quantum Dynamics; Elsevier, 2021. p. 199 – 229.

2020

Journal Articles

Which form of the molecular Hamiltonian is the most suitable for simulating the nonadiabatic quantum dynamics at a conical intersection?

S. Choi; J. Vanicek 

The Journal of Chemical Physics. 2020. Vol. 153, num. 21, p. 211101. DOI : 10.1063/5.0033410.

On-the-fly ab initio semiclassical evaluation of third-order response functions for two-dimensional electronic spectroscopy

T. Begušić; J. Vaníček 

The Journal of Chemical Physics. 2020. Vol. 153, num. 18, p. 184110. DOI : 10.1063/5.0031216.

Effects of high pulse intensity and chirp in two-dimensional electronic spectroscopy of an atomic vapor

M. Binz; L. Bruder; L. Chen; M. F. Gelin; W. Domcke et al. 

Optics Express. 2020. Vol. 28, num. 18, p. 25806 – 25829. DOI : 10.1364/OE.396108.

Variational approach to time-dependent fluorescence of a driven qubit

Y. Yan; L. Chen; J. Luo; Y. Zhao 

Physical Review A. 2020. Vol. 102, num. 2, p. 023714. DOI : 10.1103/PhysRevA.102.023714.

On-the-Fly ab initio Semiclassical Evaluation of Electronic Coherences in Polyatomic Molecules Reveals a Simple Mechanism of Decoherence

N. V. Golubev; T. Begusic; J. Vanicek 

Physical Review Letters. 2020. Vol. 125, num. 8, p. 083001. DOI : 10.1103/PhysRevLett.125.083001.

On-the-fly ab initio semiclassical evaluation of vibronic spectra at finite temperature

T. Begušić; J. Vaníček 

The Journal of Chemical Physics. 2020. Vol. 153, num. 2, p. 024105. DOI : 10.1063/5.0013677.

Direct Observation of Aggregation-Induced Emission Mechanism

J. Guan; R. Wei; A. Prlj; J. Peng; K-H. Lin et al. 

Angewandte Chemie-International Edition. 2020. Vol. 59, num. 35, p. 14903 – 14909. DOI : 10.1002/anie.202004318.

Semiclassical Approach to Photophysics Beyond Kasha’s Rule and Vibronic Spectroscopy Beyond the Condon Approximation. The Case of Azulene

A. Prlj; T. Begušić; Z. T. Zhang; G. C. Fish; M. Wehrle et al. 

Journal of Chemical Theory and Computation. 2020. Vol. 16, num. 4, p. 2617 – 2626. DOI : 10.1021/acs.jctc.0c00079.

Instanton theory of ground-state tunneling splittings with general paths

M. Erakovic; C. L. Vaillant; M. T. Cvitas 

Journal Of Chemical Physics. 2020. Vol. 152, num. 8, p. 084111. DOI : 10.1063/1.5145278.

2019

Journal Articles

A time-reversible integrator for the time-dependent Schrödinger equation on an adaptive grid

S. Choi; J. Vaníček 

The Journal of Chemical Physics. 2019. Vol. 151, num. 23, p. 234102. DOI : 10.1063/1.5127856.

Tunneling Splittings in Water Clusters from Path Integral Molecular Dynamics

C. L. Vaillant; D. J. Wales; S. C. Althorpe 

Journal Of Physical Chemistry Letters. 2019. Vol. 10, num. 22, p. 7300 – 7304. DOI : 10.1021/acs.jpclett.9b02951.

Getting the Right Twist: Influence of Donor-Acceptor Dihedral Angle on Exciton Kinetics and Singlet-Triplet Gap in Deep Blue Thermally Activated Delayed Fluorescence Emitter

S. Weissenseel; N. A. Drigo; L. G. Kudriashova; M. Schmid; T. Morgenstern et al. 

Journal Of Physical Chemistry C. 2019. Vol. 123, num. 45, p. 27778 – 27784. DOI : 10.1021/acs.jpcc.9b08269.

Semiclassical analysis of the quantum instanton approximation (vol 151, 144111, 2019)

C. L. Vaillant; M. J. Thapa; J. Vanicek; J. O. Richardson 

Journal Of Chemical Physics. 2019. Vol. 151, num. 18, p. 189902. DOI : 10.1063/1.5133748.

A combined on-the-fly/interpolation procedure for evaluating energy values needed in molecular simulations

K. Karandashev; J. Vaníček 

The Journal of Chemical Physics. 2019. Vol. 151, num. 17, p. 174116. DOI : 10.1063/1.5124469.

Semiclassical analysis of the quantum instanton approximation

C. L. Vaillant; M. J. Thapa; J. Vaníček; J. O. Richardson 

The Journal of Chemical Physics. 2019. Vol. 151, num. 14, p. 144111. DOI : 10.1063/1.5123800.

Accelerating equilibrium isotope effect calculations. II. Stochastic implementation of direct estimators

K. Karandashev; J. Vaníček 

The Journal of Chemical Physics. 2019. Vol. 151, num. 13, p. 134116. DOI : 10.1063/1.5124995.

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

S. Choi; J. Vanicek 

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

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

J. Roulet; S. Choi; J. Vanicek 

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

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. 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. Vol. 150, num. 15, p. 154117. DOI : 10.1063/1.5090122.

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. 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. 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. 

2017

Journal Articles

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.

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.

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.

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. 

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.

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.

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.

Theses

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

M. Wehrle / J. Vanicek (Dir.)  

Lausanne, EPFL, 2015. 

2014

Journal Articles

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.

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.

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.

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.

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. DOI : 10.1051/medsci/20143001003.

Student Projects

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

J. Rohrbach 

2014.

2013

Journal Articles

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.

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.

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.

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.

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.

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.

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.

Conference Papers

Increasing the efficiency and accuracy of ultrafast time-resolved electronic spectra calculations with on-the-fly ab initio quantum dynamics methods

J. Vanicek 

2013. 

Accelerating the calculations of ultrafast time-resolved electronic spectra with on-the-fly ab initio quantum dynamics methods

J. Vanicek 

2013. 246th National Meeting of the American-Chemical-Society (ACS), Indianapolis, IN, SEP 08-12, 2013.

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

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.

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.

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.

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.

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. 

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

C. Mollica / J. Vanicek (Dir.)  

Lausanne, EPFL, 2012. 

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 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.

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.

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.

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.

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.

2010

Journal Articles

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.

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.

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.

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.

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.

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 equilibrium isotope effects (vol 131, 024111, 2009)

T. Zimmermann; J. Vanicek 

Journal Of Chemical Physics. 2009. Vol. 131, num. 4, p. 049903. DOI : 10.1063/1.3202533.

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.

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 the equilibrium isotope effect in [1,5] sigmatropic hydrogen shift reactions

T. Zimmermann; J. Vanicek 

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

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.

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.

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.

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.