Publications by authors named "Jiri Vanicek"

MRI is becoming increasingly available and more common. However, it is a long examination, within a limited space, and making strong demands on the patient for proper co-operation. Using survey data collected by prospective questionnaire, this work examines the influence of patient preparation and type of MRI device on patients' subjective perception of the examination.

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In single vibronic level (SVL) fluorescence experiments, the electronically excited initial state is also excited in one or several vibrational modes. Because computing such spectra by evaluating all contributing Franck-Condon factors becomes impractical (and unnecessary) in large systems, here we propose a time-dependent approach based on Hagedorn wavepacket dynamics. We use Hagedorn functions-products of a Gaussian and carefully generated polynomials-to represent SVL initial states because in systems whose potential is at most quadratic, Hagedorn functions are exact solutions to the time-dependent Schrödinger equation and can be propagated with the same equations of motion as a simple Gaussian wavepacket.

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Background And Objective: Subpleural located pulmonary nodules are perioperatively invisible to the surgeon. Their precise identification is conventionally possible by palpation, but often at the cost of performing a thoracotomy. The aim of the study was to evaluate the success rate and feasibility of the pre-operative CT-guided marking subpleural localized nodule using a mixture of Patent Blue V and an iodine contrast agent prior to the extra-anatomical video-assisted thoracoscopic surgery (VATS) resection in patients for whom the primary anatomical resection in terms of segmentectomy or lobectomy was not indicated.

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Background: Changes in the hippocampus after brain metastases radiotherapy can significantly impact neurocognitive functions. Numerous studies document hippocampal atrophy correlating with the radiation dose. This study aims to elucidate volumetric changes in patients undergoing whole-brain radiotherapy (WBRT) or targeted stereotactic radiotherapy (SRT) and to explore volumetric changes in the individual subregions of the hippocampus.

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We present a numerically exact approach for evaluating vibrationally resolved electronic spectra at finite temperatures using the coherence thermofield dynamics. In this method, which avoids implementing an algorithm for solving the von Neumann equation for coherence, the thermal vibrational ensemble is first mapped to a pure-state wavepacket in an augmented space, and this wavepacket is then propagated by solving the standard, zero-temperature Schrödinger equation with the split-operator Fourier method. We show that the finite-temperature spectra obtained with the coherence thermofield dynamics in a Morse potential agree exactly with those computed by Boltzmann-averaging the spectra of individual vibrational levels.

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Gaussian wavepacket dynamics has proven to be a useful semiclassical approximation for quantum simulations of high-dimensional systems with low anharmonicity. Compared to Heller's original local harmonic method, the variational Gaussian wavepacket dynamics is more accurate, but much more difficult to apply in practice because it requires evaluating the expectation values of the potential energy, gradient, and Hessian. If the variational approach is applied to the local cubic approximation of the potential, these expectation values can be evaluated analytically, but they still require the costly third derivative of the potential.

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Under certain conditions, the ionization of a molecule may create a superposition of electronic states, leading to ultrafast electron dynamics. If controlled, this motion could be used in attochemistry applications, but it has been shown that the decoherence induced by the nuclear motion typically happens in just a few femtoseconds. We recently developed an efficient algorithm for finding molecules exhibiting long-lasting electronic coherence and charge migration across the molecular structure after valence ionization.

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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 Gaussian approximation can capture surprisingly well even more subtle observables, such as the isotope effects in the absorption spectra, and we demonstrate it on the four isotopologues of ammonia (NH, NDH, NDH, and ND). The differences in their computed spectra are due to the differences in the semiclassical trajectories followed by the four isotopologues, and the isotope effects─narrowing of the transition band and reduction of the peak spacing─are accurately described by this semiclassical method.

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Background: Identifying relevant perforators is crucial in planning a deep inferior epigastric perforator (DIEP) flap. Color Doppler ultrasonography (CDU) has gained popularity for localizing perforators; however, current evidence on its efficiency is still inconclusive. This study aimed to compare the efficiency of CDU with that of computed tomography angiography (CTA) in localizing and selecting the relevant perforators.

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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, conserves energy exactly, and may partially account for tunneling. However, the variational method is also much more expensive.

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Purpose: To investigate the safety and efficacy of baseline antiplatelet treatment in patients with acute ischemic stroke (AIS) undergoing mechanical thrombectomy (MT).

Materials And Methods: Baseline use of antiplatelet medication before MT for (AIS) may provide benefit on reperfusion and clinical outcome but could also carry an increased risk of intracranial hemorrhage (ICH). All consecutive patients with AIS and treated with MT with and without intravenous thrombolysis (IVT) between January 2012 and December 2019 in all centers performing MT nationwide were reviewed.

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Objectives: The study aims to analyze our first experience with direct percutaneous embolization of carotid body tumors (CBTs) using ethylene-vinyl alcohol copolymer (Onyx) along with balloon test occlusion (BTO).

Methods: A retrospective preliminary single-center study was conducted at the Otorhinolaryngology and Head and Neck Surgery Department and the Medical Imaging Department of the University Teaching Hospital. A consecutive series of three patients with CBTs was treated at the local institution between October 2018 and June 2019.

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Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of fundamental physics behind the electron-nuclear interactions and dynamics, accurate numerical simulations of light-induced processes taking place in polyatomic molecules remain a formidable challenge. Here, we review a recently developed theoretical approach for evaluating electronic coherences in molecules, in which the ultrafast electronic dynamics is coupled to nuclear motion.

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Simulating vibrationally resolved electronic spectra of anharmonic systems, especially those involving double-well potential energy surfaces, often requires expensive quantum dynamics methods. Here, we explore the applicability and limitations of the recently proposed single-Hessian thawed Gaussian approximation for the simulation of spectra of systems with double-well potentials, including 1,2,4,5-tetrafluorobenzene, ammonia, phosphine, and arsine. This semiclassical wavepacket approach is shown to be more robust and to provide more accurate spectra than the conventional harmonic approximation.

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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 the electron density triggered by the outer-valence ionization. We observed that in most of the studied molecules, either the sudden removal of an electron from the system does not lead to the appearance of the electronic coherence or the created coherences become damped by the nuclear rearrangement on a time scale of a few femtoseconds. However, we report several so far unexplored molecules with the electronic coherences lasting up to 10 fs, which can be good candidates for experimental studies.

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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 second-order accuracy, which makes it very inefficient. Here, we propose to overcome the limitations of the explicit split-operator algorithm by abandoning its explicit nature.

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Ehrenfest dynamics is a useful approximation for ab initio mixed quantum-classical molecular dynamics that can treat electronically nonadiabatic effects. Although a severe approximation to the exact solution of the molecular time-dependent Schrödinger equation, Ehrenfest dynamics is symplectic, is time-reversible, and conserves exactly the total molecular energy as well as the norm of the electronic wavefunction. Here, we surpass apparent complications due to the coupling of classical nuclear and quantum electronic motions and present efficient geometric integrators for "representation-free" Ehrenfest dynamics, which do not rely on a diabatic or adiabatic representation of electronic states and are of arbitrary even orders of accuracy in the time step.

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Tracing ultrafast processes induced by interaction of light with matter is often very challenging. In molecular systems, the initially created electronic coherence becomes damped by the slow nuclear rearrangement on a femtosecond timescale which makes real-time observations of electron dynamics in molecules particularly difficult. In this work, we report an extension of the theory underlying the attosecond transient absorption spectroscopy (ATAS) for the case of molecules, including a full account for the coupled electron-nuclear dynamics in the initially created wave packet, and apply it to probe the oscillations of the positive charge created after outer-valence ionization of the propiolic acid molecule.

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Understanding light-induced processes in biological and human-made molecular systems is one of the main goals of physical chemistry. It has been known for years that the photoinduced dynamics of atomic nuclei can be studied by looking at the vibrational substructure of electronic absorption and emission spectra. However, theoretical simulation is needed to understand how dynamics translates into the spectral features.

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The explicit split-operator algorithm has been extensively used for solving not only linear but also nonlinear time-dependent Schrödinger equations. When applied to the nonlinear Gross-Pitaevskii equation, the method remains time-reversible, norm-conserving, and retains its second-order accuracy in the time step. However, this algorithm is not suitable for all types of nonlinear Schrödinger equations.

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Diabatization of the molecular Hamiltonian is a standard approach to remove the singularities of nonadiabatic couplings at conical intersections of adiabatic potential energy surfaces. In general, it is impossible to eliminate the nonadiabatic couplings entirely-the resulting "quasidiabatic" states are still coupled by smaller but nonvanishing residual nonadiabatic couplings, which are typically neglected. Here, we propose a general method for assessing the validity of this potentially drastic approximation by comparing quantum dynamics simulated either with or without the residual couplings.

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Remyelination is a naturally occurring response to demyelination and has a central role in the pathophysiology of multiple sclerosis and traumatic brain injury. Recently we demonstrated that a novel MRI technique entitled Relaxation Along a Fictitious Field (RAFF) in the rotating frame of rank n (RAFFn) achieved exceptional sensitivity in detecting the demyelination processes induced by lysophosphatidylcholine (LPC) in rat brain. In the present work, our aim was to test whether RAFF4, along with magnetization transfer (MT) and diffusion tensor imaging (DTI), would be capable of detecting the changes in the myelin content and microstructure caused by modifications of myelin sheets around axons or by gliosis during the remyelination phase after LPC-induced demyelination in the corpus callosum of rats.

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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, or approximate classical or semiclassical limits. While many practical approaches exist, they are often of limited accuracy and difficult to interpret.

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Choosing an appropriate representation of the molecular Hamiltonian is one of the challenges faced by simulations of the nonadiabatic quantum dynamics around a conical intersection. The adiabatic, exact quasidiabatic, and strictly diabatic representations are exact and unitary transforms of each other, whereas the approximate quasidiabatic Hamiltonian ignores the residual nonadiabatic couplings in the exact quasidiabatic Hamiltonian. A rigorous numerical comparison of the four different representations is difficult because of the exceptional nature of systems where the four representations can be defined exactly and the necessity of an exceedingly accurate numerical algorithm that avoids mixing numerical errors with errors due to the different forms of the Hamiltonian.

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