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Jiri Vanicek

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Related publications (71)

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Efficient Semiclassical Evaluation of Electronic Coherences in Polyatomic Molecules

Jiri Vanicek, Nikolay Golubev

Exposing a molecule to an intense light pulse can create a nonstationary quantum state, thus launching correlated dynamics of electrons and nuclei. Although much had been achieved in the understanding of fundamental physics behind the electron-nuclear inte ...

SWISS CHEMICAL SOC2022

Semiclassical analysis of the quantum instanton approximation

Jiri Vanicek, Christophe Louis Joseph Jean-Luc Vaillant

We explore the relation between the quantum and semiclassical instanton approximations for the reaction rate constant. From the quantum instanton expression, we analyze the contributions to the rate constant in terms of minimum-action paths and find that t ...

2019

Efficient evaluation of accuracy of molecular quantum dynamics using dephasing representation

Jiri Vanicek, Cesare Mollica

Ab initio methods for the electronic structure of molecules have reached a satisfactory accuracy for calculations of static properties but remain too expensive for quantum dynamics calculations. We propose an efficient semiclassical method for evaluating t ...

American Institute of Physics2009

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

Jiri Vanicek, Seonghoon Choi

One of the most accurate methods for solving the time-dependent Schrödinger equation uses a combination of the dynamic Fourier method with the split-operator algorithm on a tensor-product grid. To reduce the number of required grid points, we let the grid ...

2019

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

Jiri Vanicek, Yannick Calvino Alonso, Eriks Kletnieks

Despite its simplicity, the single-trajectory thawed Gaussian approximation has proven useful for calculating the vibrationally resolved electronic spectra of molecules with weakly anharmonic potential energy surfaces. Here, we show that the thawed Gaussia ...

2023

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

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

Jiri Vanicek, Miroslav Sulc, Marius Wehrle

We explore three specific approaches for speeding up the calculation of quantum time correlation functions needed for time-resolved electronic spectra. The first relies on finding a minimum set of sufficiently accurate electronic surfaces. The second incre ...

2011

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

Jiri Vanicek

A quantitative algorithm was developed and applied to predict target genes of microRNAs encoded by herpesviruses. Although there is almost no conservation among microRNAs of different herpesvirus subfamilies, a common pattern of regulation emerged. The alg ...

National Academy of Sciences2008

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

Jiri Vanicek, Alan Scheidegger

Coherent superposition of electronic states, created by ionizing a molecule, can initiate ultrafast dynamics of the electron density. Correlation between nuclear and electron motions, however, typically dissipates the electronic coherence in only a few fem ...

NAS2025

Efficient use of accessibility in microRNA target prediction

Jiri Vanicek, Ray Marcel Marin Florez

Considering accessibility of the 3'UTR is believed to increase the precision of microRNA target predictions. We show that, contrary to common belief, ranking by the hybridization energy or by the sum of the opening and hybridization energies, used in curre ...

Oxford University Press2011

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

Jiri Vanicek, Nikolay Golubev, Alan Scheidegger

Using a combination of high-level ab initio electronic structure methods with efficient on-the-fly semiclassical evaluation of nuclear dynamics, we performed a massive scan of small polyatomic molecules searching for a long-lasting oscillatory dynamics of ...

AIP Publishing2022

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

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

David Eduardo Zambrano Ramirez, Jiri Vanicek, Miroslav Sulc

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

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

Jiri Vanicek, Miroslav Sulc, Marius Wehrle

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

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

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

Jiri Vanicek, Tomislav Begusic

To compute and analyze vibrationally resolved electronic spectra at zero temperature, we have recently implemented the on-the-fly ab initio extended thawed Gaussian approximation [A. Patoz et al., J. Phys. Chem. Lett. 9, 2367 (2018)], which accounts for an ...

2020

Sampling strategies for the Herman-Kluk propagator of the wavefunction

Fabian Kröninger, Jiri Vanicek

When the semiclassical Herman-Kluk propagator is used for evaluating quantum-mechanical observables or time-correlation functions, the initial conditions for the guiding trajectories are typically sampled from the Husimi density. Here, we employ this propa ...

2023

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

High-order geometric integrators for the variational Gaussian approximation

Jiri Vanicek, Roya Moghaddasi Fereidani

Among the single-trajectory Gaussian-based methods for solving the time-dependent Schrödinger equation, the variational Gaussian approximation is the most accurate one. In contrast to Heller’s original thawed Gaussian approximation, it is symplectic, conse ...

2023