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Jiri Vanicek

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Related publications (76)

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

Franziska Voellmy, Thibaud Edouard Alistair von Erlach, Jiri Vanicek, Ray Marcel Marin Florez

To find out whether the AGO-miRNA complex is more sensitive to the accessibility of a particular region inside the seed match, we analyze in detail the accessibility of a wide set of miRNA binding sites validated by PAR-CLIP and HITS-CLIP experiments. Our ...

Cold Spring Harbor Lab Press, Publications Dept2012

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

Jiri Vanicek, Tomas Zimmermann

We propose to measure the importance of spin-orbit couplings (SOCs) in the nonadiabatic molecular quantum dynamics rigorously with quantum ﬁdelity. To make the criterion practical, quantum ﬁdelity is estimated efﬁciently with the multiple-surface dephasing ...

American Institute of Physics2012

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

Jiri Vanicek, Miroslav Sulc

Dephasing representation of fidelity, also known as the phase averaging method, can be considered as a special case of Miller's linearized semiclassical initial value representation and belongs among the most efficient approximate semiclassical approaches ...

Taylor & Francis2012

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

Jiri Vanicek, Cesare Mollica

While rigorous quantum dynamical simulations of many-body systems are extremely difficult (or impossible) due to exponential scaling with dimensionality, the corresponding classical simulations ignore quantum effects. Semiclassical methods are generally mo ...

American Physical Society2011

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

Efficient sampling avoids the exponential wall in classical simulations of fidelity

Jiri Vanicek, Cesare Mollica, Tomas Zimmermann

We analyze the efficiency of available algorithms for the simulation of classical fidelity and show that their computational costs increase exponentially with the number of degrees of freedom. Then we present an algorithm for which the number of trajectori ...

American Physical Society2011

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

Marius Wehrle, Jiri Vanicek, Miroslav Sulc

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

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

Jiri Vanicek, Tomas Zimmermann

Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibr ...

Springer Verlag2010

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

Jiri Vanicek, Tomas Zimmermann

We propose an approximate method for evaluating the importance of non-Born–Oppenheimer effects on the quantum dynamics of nuclei. The method uses a generalization of the dephasing representation (DR) of quantum fidelity to several diabatic potential energy ...

American Institute of Physics2010

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

Jiri Vanicek, Marcin Rafal Buchowiecki

A general method for the direct evaluation of the temperature dependence of the quantum-mechanical reaction rate constant in many-dimensional systems is described. The method is based on the quantum instanton approximation for the rate constant, thermodyna ...

American Institute of Physics2010

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

Julien Ruppen, Jiri Vanicek, Tomas Zimmermann

Ab initio electronic structure methods have reached a satisfactory accuracy for the calculation of static properties, but remain too expensive for quantum dynamical calculations. Recently, an efficient semiclassical method was proposed to evaluate the accu ...

Wiley-Blackwell2010

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

Path integral evaluation of equilibrium isotope effects (vol 131, 024111, 2009)

Jiri Vanicek, Tomas Zimmermann

2009

Path integral evaluation of equilibrium isotope effects

Jiri Vanicek, Tomas Zimmermann

A general and rigorous methodology to compute the quantum equilibrium isotope effect is described. Unlike standard approaches, ours does not assume separability of rotational and vibrational motions and does not make the harmonic approximation for vibratio ...

2009

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects

Jiri Vanicek

2008

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

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