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Jiri Vanicek

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Publications associées (76)

Several Semiclassical Approaches to Time-resolved Spectroscopy

Jiri Vanicek

Ultrafast spectroscopy allows molecular dynamics to be resolved on the femtosecond time scale. Whereas such short time scales obviously pose any experimental challenges, they provide an opportunity for semiclassica methods, which are naturally suited for s ...

Swiss Chemical Soc2017

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

Ursula Röthlisberger, Jiri Vanicek, Sergey Antipov, Swarnendu Bhattacharyya

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quant ...

2017

Kinetic isotope effects and how to describe them

Jiri Vanicek, Konstantin Karandashev

We review several methods for computing kinetic isotope effects in chemical reactions including semiclassical and quantum instanton theory. These methods describe both the quantization of vibrational modes as well as tunneling and are applied to the ⋅H + H ...

2017

Path integral approach to the quantum fidelity amplitude

Jiri Vanicek

The Loschmidt echo is a measure of quantum irreversibility and is determined by the fidelity amplitude of an imperfect time-reversal protocol. Fidelity amplitude plays an important role both in the foundations of quantum mechanics and its applications, suc ...

Royal Soc2016

Accelerating quantum instanton calculations of the kinetic isotope effects

Jiri Vanicek, Konstantin Karandashev

Path integral implementation of the quantum instanton approximation currently belongs among the most accurate methods for computing quantum rate constants and kinetic isotope effects, but its use has been limited due to the rather high computational cost. ...

American Institute of Physics2015

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

Marius Wehrle, Jiri Vanicek, Solène Oberli

We investigate the performance of on-the-fly ab initio (OTF-AI) semiclassical dynamics combined with the thawed Gaussian approximation (TGA) for computing vibrationally resolved absorption and photoelectron spectra. Ammonia is used as a prototype of floppy ...

American Chemical Society2015

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

Marius Wehrle, Jiri Vanicek, Miroslav Sulc

Vibrationally resolved spectra provide a stringent test of the accuracy of theoretical calculations. We combine the thawed Gaussian approximation (TGA) with an on-the-fly ab initio (OTF-AI) scheme to calculate the vibrationally resolved emission spectra of ...

American Institute of Physics2014

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

Jiri Vanicek

Reactivation of human cytomegalovirus (HCMV) is a significant cause of disease and death in immunocompromised patients underscoring the need to understand how latency is controlled. Here we demonstrate that HCMV has evolved to utilize cellular miRNAs in ce ...

American Society for Microbiology2014

Control of mitophagie by microRNAs - A key step of erythropoiesis

Didier Trono, Isabelle Barde, Sonia Verp, Andrea Corsinotti, Jiri Vanicek, Sandra Eloise Kjeldsen, Adamantia Kapopoulou, Ray Marcel Marin Florez, Benjamin Rauwel

Edp Sciences S A2014

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

Jiri Vanicek, Marcin Rafal Buchowiecki, Jing Huang

The primary H/D kinetic isotope effect on the intramolecular proton transfer in malonaldehyde is determined from quantum instanton path integral Monte Carlo simulations on a fully dimensional and validated potential energy surface for temperatures between ...

Royal Society of Chemistry2014

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

Jiri Vanicek, Marcin Rafal Buchowiecki

The Feynman path integral approach for computing equilibrium isotope effects and isotope fractionation corrects the approximations made in standard methods, although at significantly increased computational cost. We describe an accelerated path integral ap ...

Elsevier2013

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

Didier Trono, Isabelle Barde, Sonia Verp, Andrea Corsinotti, Jiri Vanicek, Sandra Eloise Kjeldsen, Adamantia Kapopoulou, Ray Marcel Marin Florez, Benjamin Rauwel

During hematopoiesis, lineage- and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. Here, we explored the role of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofa ...

American Association for the Advancement of Science2013

Role of sampling in evaluating classical time autocorrelation functions

Jiri Vanicek, Tomas Zimmermann

We analyze how the choice of the sampling weight affects efficiency of the Monte Carlo evaluation of classical time autocorrelation functions. Assuming uncorrelated sampling or sampling with constant correlation length, we propose a sampling weight for whi ...

American Institute of Physics2013

Searching the coding region for microRNA targets

Jiri Vanicek, Ray Marcel Marin Florez, Miroslav Sulc

Finding microRNA targets in the coding region is difficult due to the overwhelming signal encoding the amino acid sequence. Here, we introduce an algorithm (called PACCMIT-CDS) that finds potential microRNA targets within coding sequences by searching for ...

2013

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

Jiri Vanicek

Amer Chemical Soc2013

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

Jiri Vanicek, Miroslav Sulc, David Eduardo Zambrano Ramirez

Time-resolved electronic spectra can be obtained as the Fourier transform of a special type of time correlation function known as fidelity amplitude, which, in turn, can be evaluated approximately and efficiently with the dephasing representation. Here we ...

American Institute of Physics2013

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

Jiri Vanicek

American Chemical Society2013

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

Jiri Vanicek, Miroslav Sulc

We recently showed that the dephasing representation (DR) provides an efficient tool for computing ultrafast electronic spectra and that further acceleration is possible with cellularization [M. Šulc and J. Vaníček, Mol. Phys. 110, 945 (2012)]. Here, we fo ...

American Institute of Physics2013

Optimal use of conservation and accessibility filters in microRNA target prediction

Jiri Vanicek, Ray Marcel Marin Florez

It is generally accepted that filtering microRNA (miRNA) target predictions by conservation or by accessibility can reduce the false discovery rate. However, these two strategies are usually not exploited in a combined and flexible manner. Here, we introdu ...

Public Library of Science2012

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

Jiri Vanicek, Tomas Zimmermann

We propose to measure nonadiabaticity of molecular quantum dynamics rigorously with the quantum fidelity between the Born-Oppenheimer and fully nonadiabatic dynamics. It is shown that this measure of nonadiabaticity applies in situations where other criter ...

American Institute of Physics2012

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