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

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

High-order geometric integrators for the variational Gaussian approximation

R. Moghaddasi Fereidani; J. Vanicek 

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

J. J. L. Vanicek 

How to Find Molecules with Long-lasting Charge Migration?

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

Sampling strategies for the Herman-Kluk propagator of the wavefunction

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

Decoherence and revival in attosecond charge migration driven by non-adiabatic dynamics

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

Efficient Semiclassical Evaluation of Electronic Coherences in Polyatomic Molecules

N. V. Golubev; J. Vanicek 

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 

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

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

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

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

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

J. Roulet; J. Vanicek 

High-order geometric integrators for representation-free Ehrenfest dynamics

S. Choi; J. Vanicek 

Core-Valence Attosecond Transient Absorption Spectroscopy of Polyatomic Molecules

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

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

J. Roulet; J. Vaníček 

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

T. Begušić; J. Vaníček 

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

S. Choi; J. Vaníček 

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

T. Begušić; J. Vaníček 

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

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

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 

Efficient ab initio semiclassical dynamics for linear and nonlinear electronic spectroscopy

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

J. Vanicek; T. Begusic 

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

S. Choi; J. Vanicek 

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

T. Begušić; J. Vaníček 

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. 

Variational approach to time-dependent fluorescence of a driven qubit

Y. Yan; L. Chen; J. Luo; Y. Zhao 

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 

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

T. Begušić; J. Vaníček 

Direct Observation of Aggregation-Induced Emission Mechanism

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

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. 

Instanton theory of ground-state tunneling splittings with general paths

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

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

S. Choi; J. Vaníček 

Tunneling Splittings in Water Clusters from Path Integral Molecular Dynamics

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

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

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

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. 

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

K. Karandashev; J. Vaníček 

Semiclassical analysis of the quantum instanton approximation

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

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

K. Karandashev; J. Vaníček 

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

J. Roulet; S. Choi; J. Vanicek 

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

S. Choi; J. Vanicek 

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 

Single-Hessian thawed Gaussian approximation

T. Begušić; M. Cordova; J. Vaníček 

On-the-fly ab initio semiclassical evaluation of time-resolved electronic spectra

T. Begusic; J. Roulet; J. Vanicek 

On-the-fly ab initio three thawed Gaussians approximation: a semiclassical approach to Herzberg-Teller spectra

T. Begušić; A. Patoz; M. Šulc; J. Vaníček 

On-the-Fly Ab Initio Semiclassical Evaluation of Absorption Spectra of Polyatomic Molecules beyond the Condon Approximation

A. Patoz; T. Begušić; J. Vaníček 

Accelerating path integral evaluation of equilibrium and kinetic isotope effects

Nonadiabatic effects in electronic and nuclear dynamics

M. P. Bircher; E. Liberatore; N. J. Browning; S. Brickel; C. Hofmann et al. 

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. 

Kinetic isotope effects and how to describe them

K. Karandashev; Z-H. Xu; M. Meuwly; J. Vanicek; J. O. Richardson 

Several Semiclassical Approaches to Time-resolved Spectroscopy

J. Vanicek 

Accelerating equilibrium isotope effect calculations. I. Stochastic thermodynamic integration with respect to mass

K. Karandashev; J. Vanicek 

Geometric Integrators for Nonadiabatic Molecular Quantum Dynamics Induced by the Interaction with the Electromagnetic Field

Path integral approach to the quantum fidelity amplitude

J. Vanicek; D. Cohen 

Accelerating quantum instanton calculations of the kinetic isotope effects

K. Karandashev; J. Vanicek 

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

M. Wehrle; S. Oberli; J. Vanicek 

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

M. Šulc; R. M. Marín; H. S. Robins; J. Vaníček 

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

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 

Predicting the genes regulated by microRNAs via binding sites in the 3′ untranslated and coding regions

J. Vanicek 

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

M. Wehrle; M. Sulc; J. Vanicek 

Control of mitophagie by microRNAs – A key step of erythropoiesis

I. Barde; B. Rauwel; R. M. Marin-Florez; A. Corsinotti; E. Laurenti et al. 

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

C. M. O’Connor; J. Vanicek; E. A. Murphy 

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

J. Huang; M. Buchowiecki; T. Nagy; J. Vanicek; M. Meuwly 

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

J. Rohrbach 

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 

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

M. Buchowiecki; J. Vanicek 

Role of sampling in evaluating classical time autocorrelation functions

T. Zimmermann; J. Vanicek 

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

E. Zambrano; M. Sulc; J. Vanicek 

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 

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. 

Searching the coding region for microRNA targets

R. Marin; M. Sulc; J. Vanicek 

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 

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 

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 

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

M. Sulc; J. Vanicek 

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

T. Zimmermann; J. Vanicek 

Optimal use of conservation and accessibility filters in microRNA target prediction

R. Marin; J. Vanicek 

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. 

Highly Specific Methods for the Prediction of Genes Regulated by MicroRNAs

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

Quantum Instanton Evaluation of the Kinetic Isotope Effects and of the Temperature Dependence of the Rate Constant

J. Vanicek 

Efficient sampling avoids the exponential wall in classical simulations of fidelity

C. Mollica; T. Zimmermann; J. Vanicek 

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

C. Mollica; J. Vanicek 

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 

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

M. Wehrle; M. Sulc; J. Vanicek 

Efficient use of accessibility in microRNA target prediction

R. Marin; J. Vanicek 

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. 

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

T. Zimmermann; J. Vanicek 

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 

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

M. R. Buchowiecki; J. Vanicek 

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 

Amber 11

D. A. Case; T. A. Darden; T. E. Cheatham; C. L. Simmerling; J. Wang et al. 

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

T. Zimmermann; J. Vanicek 

Path integral evaluation of the equilibrium isotope effect in [1,5] sigmatropic hydrogen shift reactions

T. Zimmermann; J. Vanicek 

Efficient evaluation of accuracy of molecular quantum dynamics using dephasing representation

B. Li; C. Mollica; J. Vanicek 

Path integral evaluation of equilibrium isotope effects

T. Zimmermann; J. Vanicek 

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 

Amber 10

D. A. Case; T. A. Darden; T. E. Cheatham; C. L. Simmerling; J. Wang et al. 

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

J. Vanicek; W. H. Miller 

Dephasing representation of quantum fidelity for general pure and mixed states

J. Vanicek 

Quantum-instanton evaluation of the kinetic isotope effects

J. Vanicek; W. H. Miller; J. F. Castillo; F. Javier Aoiz 

Path integral evaluation of the kinetic isotope effects based on the quantum instanton approximation

J. Vanicek; W. H. Miller 

Dephasing representation: Unified semiclassical framework for fidelity decay

J. Vanicek 

Dephasing representation: Employing the shadowing theorem to calculate quantum correlation functions

J. Vanicek 

Survival probability and local density of states for one-dimensional Hamiltonian systems

J. Vanicek; D. Cohen 

Semiclassical evaluation of quantum fidelity

J. Vanicek; E. J. Heller 

Uniform semiclassical wave function for coherent two- dimensional electron flow

J. Vanicek; E. J. Heller 

Replacement manifolds: A method to uniformize semiclassical wave functions

J. Vanicek; E. J. Heller 

Atomic beam splitter based on multiple adiabatic passage in the optical interference pattern

M. Ol’shanii; J. Vanicek; M. Prentiss