Publications by Jiri Vanicek | EPFL Graph Search

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Accurate description of finite-temperature vibrational dynamics is indispensable in the computation of two-dimensional electronic spectra. Such simulations are often based on the density matrix evolution, statistical averaging of initial vibrational states ...

Hagedorn functions are carefully constructed generalizations of Hermite functions to the setting of many-dimensional squeezed and coupled harmonic systems. Wavepackets formed by superpositions of Hagedorn functions have been successfully used to solve the ...

The explicit split-operator algorithm is often used for solving the linear and nonlinear time-dependent Schrödinger equations. However, when applied to certain nonlinear time-dependent Schrödinger equations, this algorithm loses time reversibility and seco ...

Jiri Vanicek

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

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

Optimal use of conservation and accessibility filters in microRNA target prediction

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

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

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

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

Efficient use of accessibility in microRNA target prediction

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

Kinetic isotope effects and how to describe them

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

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

Searching the coding region for microRNA targets

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

Sampling strategies for the Herman-Kluk propagator of the wavefunction

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

High-order geometric integrators for the variational Gaussian approximation

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

On Hagedorn wavepackets associated with different Gaussians

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