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

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. In addition, we present the full-dimensional simulations of the electronic coherences coupled to nuclear motion in several molecules which were studied previously only in the fixed nuclei approximation.& nbsp;(c) 2022 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

Tools to study molecules in high electric fields

Denis Bucher

This thesis describes the application of the quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello methodology to two systems of high biological interest: (a) The potassium channel KcsA from Streptomyces lividans and (b) The DNA repair enzyme EndoIV of E.Coli. bacteria. The two studies provide new insights into key biological mechanisms such as the ion selectivity of cell membranes and the DNA repair system. Special emphasize was put on the importance of polarization effects in these systems. Most classical simulations performed today are based on non-polarizable force fields which only include electronic polarization implicitly. This thesis work shows that non-polarizable potential functions do not describe accurately the permeation in ion channels in all cases. Indeed, most current biomolecular packages were developed for the study of globular proteins and have only recently been applied to the study of ion channels. The importance of ion/protein induced polarization effects in the KcsA channel was demonstrated using different computational approaches: first, the fluctuations in the electronic density were studied (Chapter 3). Second, the quantum mechanical electrostatic potential inside the channel was compared to the corresponding result of popular MM force fields (Chapter 4). Third, the coordination geometry of the K+ and Na+ ions inside the channel was investigated (Chapter 5). It was found that the binding geometry of Na+ observed in classical simulations differs significantly from the results of ab initio simulations. In Chapter 6, the protonation state of the Glu71 and Asp80 residues is investigated. While errors due to a neglect of induced polarization effects amount to typically ∼0.1e/per atom, errors in the attribution of a protonation state cause an error of 1e. Thus a correct description of protonation states of the Glu71 and Asp80 residues is crucial. These residues located in the vicinity of the conductive pore in the KcsA K+ channel were found to share dynamically a proton, which may directly influence ion conduction. The proton exchange was found to be faster (sub-picosecond) than the ion translocation (nanosecond). It is important to stress that this mechanism could not have been seen by a classical study. The influence of Glu-71 on the ionic conduction was subsequently confirmed by structural and electrophysiological experiments (Cordero-Morales, Cuello et al. 2006; Cordero-Morales, Cuello et al. 2006), which indicate that Glu71 acts as a voltage sensor regulating the gating of the channel. Chapter 7 deals with an investigation of the catalytic efficiency of the DNA repair enzyme Endonuclease IV. The enzyme catalyses the hydrolysis of DNA at the phosphodiester bond of apurinic/apyrimidinic (AP) sites. The computer model highlighted the importance of electrostatic interactions in the stabilization of the phosphorane transition state. A revised catalytic mechanism is proposed for the phosphohydrolysis which involves a proton transfer. Our results also suggest that the reaction rate is not controlled by the chemical step, which is in agreement with experimental results.

EPFL2006

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

Seonghoon Choi

Accurate simulations of molecular quantum dynamics are crucial for understanding numerous natural processes and experimental results. Yet, such high-accuracy simulations are challenging even for relatively simple systems where the Born-Oppenheimer approximation is valid. Worse still, due to the ubiquity of conical intersections in molecules, it is often necessary to go beyond this celebrated approximation and employ even more sophisticated methods that can describe nonadiabatic processes involving multiple coupled electronic states.Geometric integrators provide a way to simulate nonadiabatic quantum dynamics with high accuracy while exactly conserving geometric properties, such as norm, energy, symplecticity, and time reversibility. However, the exact conservation of these properties typically leads to a higher computational cost when compared with non-geometric integrators of the same order of accuracy. We remedy this lack of efficiency by employing various composition methods to obtain high-order geometric integrators, competitive in efficiency even with some non-geometric integrators.To overcome the limited applicability of the popular split-operator algorithms, we present geometric integrators that can solve the time-dependent Schroedinger equation efficiently regardless of the form of the Hamiltonian. Employing these integrators, we systematically compare the different representations of the molecular Hamiltonian for their suitability for simulating nonadiabatic dynamics at a conical intersection and find that the rarely used exact quasidiabatic Hamiltonian, which includes the often-neglected residual nonadiabatic couplings, yields the most accurate results. Accordingly, we present a method for quantifying the validity of ignoring these residual couplings and show that depending on the system, initial state, and employed quasidiabatization scheme, neglecting the residual couplings can indeed result in inaccurate dynamics.The computational cost of exact quantum simulations quickly becomes prohibitively high as the system size increases. For high-dimensional simulations, one can either optimize the available basis set, e.g., by employing adaptive phase space grids or, alternatively, employ a more approximate approach, such as mixed quantum-classical Ehrenfest dynamics, that provides a useful qualitative picture. Although Ehrenfest dynamics and exact quantum dynamics simulated on an adaptive grid may appear unrelated, we show that, surprisingly, the high-order geometric integrators for these two problems can, in fact, be obtained by using the same splitting and composition methods.

EPFL2022

Electron Cyclotron Heating and Suprathermal Electron Dynamics in the TCV Tokamak

Silvano Gnesin

This thesis is concerned with the physics of suprathermal electrons in thermonuclear, magnetically confined plasmas. Under a variety of conditions, in laboratory as well as space plasmas, the electron velocity distribution function is not in thermodynamic equilibrium owing to internal or external drives. Accordingly, the distribution function departs from the equilibrium Maxwellian, and in particular generally develops a high-energy tail. In tokamak plasmas, this occurs especially as a result of injection of high-power electromagnetic waves, used for heating and current drive, as well as a result of internal magnetohydrodynamic (MHD) instabilities. The physics of these phenomena is intimately tied to the properties and dynamics of this suprathermal electron population. This motivates the development of instrumental apparatus to measure its properties as well as of numerical codes to simulate their dynamics. Both aspects are reflected in this thesis work, which features advanced instrumental development and experimental measurements as well as numerical modeling. The instrumental development consisted of the complete design of a spectroscopic and tomographic system of four multi-detector hard X-ray (HXR) cameras for the TCV tokamak. The goal is to measure bremsstrahlung emission from suprathermal electrons with energies in the 10-300 keV range, with the ultimate aim of providing the first full tomographic reconstruction at these energies in a noncircular plasma. In particular, suprathermal electrons are generated in TCV by a high-power electron cyclotron heating (ECH) system and are also observed in the presence of MHD events, such as sawtooth oscillations and disruptive instabilities. This diagnostic employs state-of-the-art solid-state detectors and is optimized for the tight space requirements of the TCV ports. It features a novel collimator concept that combines compactness and flexibility as well as full digital acquisition of the photon pulses, greatly enhancing its potential for full spectral analysis in high-fluency scenarios. Additional flexibility is afforded by the possibility to rotate the orientation of two of the cameras, permitting the crucial comparison of radiation emitted perpendicular and parallel to the primary magnetic field. The design of the HXR system was optimized through an extensive iterative simulation process with the aid of tomographic reconstruction codes as well as quasilinear Fokker-Planck modeling of ECH-driven TCV plasmas. In parallel, the selection of the detectors for this system was performed through comprehensive laboratory testing of several candidate detectors available on the market. While the design was completed in the course of the thesis work, commissioning of the system has only commenced recently with one of the four cameras installed on TCV. The first preliminary results, discussed in the last part of this thesis, include basic parameter scans of ECH wave-plasma interaction and the investigation of the dynamic response of suprathermal electrons to modulated ECH. In addition, the cameras possess the novel ability to discriminate against very high-energy γ-ray radiation that cannot be collimated and must thus be excluded from spatial distribution analysis. A basic study of the conditions for γ-ray suppression was conducted in preparation for future experiments. The Fokker-Planck modeling tool used in this diagnostic development was acquired through a collaboration with CEA-Cadarache, initially with the primary motivation of studying the simultaneous plasma heating by 2nd and 3rd harmonic electron cyclotron waves that is uniquely possible on TCV. This motivated a dedicated study, both theoretical and experimental, of one particular instance of this combined heating, which became a second primary subject of this thesis work. The particular scenario studied here is one in which a single ECH frequency is resonant at both harmonics in the same plasma. The primary objective of this study was to determine whether a synergy effect existed, permitting an enhancement of the intrinsically weak 3rd harmonic absorption by the suprathermal electrons generated at the 2nd harmonic resonance. An associated question was whether this effect, if it existed, was experimentally measurable or was in fact observed in TCV. The simulations performed in the course of this study indeed predict the existence of such a synergy, although the answer to the second question was ultimately negative, at least within the current technical limitations. This study has proven nevertheless highly valuable in providing new insight into the complex velocity-space dynamics that govern ECH wave-particle interaction and suprathermal electron dynamics.

EPFL2011