Ab Initio Construction of Interatomic Potentials for Uranium Dioxide Across all Interatomic Distances

We provide a methodology for generating interatomic potentials for use in classical molecular dynamics simulations of atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high energy collisions. A rigorous method to objectively determine the shape of an interatomic potential over all length scales is introduced by building upon a charged-ion generalization of the well-known Ziegler-Biersack-Littmark universal potential that provides the short- and long-range limiting behavior of the potential. At intermediate ranges the potential is smoothly adjusted by fitting to ab initio data. Our formalism provides a complete description of the interatomic potentials that can be used at any energy scale, and thus, eliminates the inherent ambiguity of splining different potentials generated to study different kinds of atomic materials behavior. We exemplify the method by developing rigid-ion potentials for uranium dioxide interactions under conditions ranging from thermodynamic equilibrium to very high atomic energy collisions relevant for fission events.Comment: Figure 4c correcte

Accurate Prediction of Core Properties for Chiral Molecules using Pseudo Potentials

Pseudo potentials (PPs) constitute perhaps the most common way to treat relativity, often in a formally non-relativistic framework, and reduce the electronic structure to the chemically relevant part. The drawback is that orbitals obtained in this picture (called pseudo orbitals (POs)) show a reduced nodal structure and altered amplitude in the vicinity of the nucleus, when compared to the corresponding molecular orbitals (MOs). Thus expectation values of operators localized in the spatial core region that are calculated with POs, deviate significantly from the same expectation values calculated with all-electron (AE) MOs. This study describes the reconstruction of AE MOs from POs, with a focus on POs generated by energy consistent pseudo Hamiltonians. The method reintroduces the nodal structure into the POs, thus providing an inexpensive and easily implementable method that allows to use nonrelativistic, efficiently calculated POs for good estimates of expectation values of core-like properties. The discussion of the method proceeds in two parts: Firstly, the reconstruction scheme is developed for atomic cases. Secondly, the scheme is discussed in the context of MO reconstruction and successfully applied to numerous numerical examples. Starting from the equations of the state-averaged multi-configuration self- consistent field method, used for the generation of energy consistent pseudo potentials, the electronic spectrum of the many-electron Hamiltonian is linked to the spectrum of the effective one-electron Fock operator by means of various models systems. This relation and the Topp–Hopfield–Kramers theorem, are used to show the shape-consistency of energy-consistent POs for atomic systems. Shape-consistency describes POs that follow distinct AOs exactly outside a core-radius r_core . In the cases presented here, shape-consistency holds to a high degree and it follows that in atomic systems every PO has one distinct partner in the set of AOs. The overlap integral between these two orbitals is close to one, as it is determined mainly by the spatial orbital parts outside r_core . Expanding, e.g., a 5s PO in occupied AOs, the 5s AOs will have the highest contribution. The POs itself contains contributions from high-energy unoccupied AOs as well (e.g. 15s), which damp the nodal structure of the POs near the nucleus. Consequently, neglecting contributions from unoccupied orbitals in a projection of the POs reintroduces the nodal structure. This approach is not directly suitable for the reconstruction of MOs, as they often need to be expanded in a full set of AOs at each atomic center, including all unoccupied orbitals, to properly account for the electron density distribution in the molecule. However, it is shown that the occupied MOs are well described by occupied and low-energy unoccupied AOs only and a mapping of the POs onto a basis containing only these orbitals reconstructs the nodal structure of the MO. The approach uses only standard integrals available in most quantum chemistry programs. The computational cost of these integrals scales with N^2 , where N is the number of basis functions. The most time consuming step is a Gram-Schmidt orthogonalization, which scales in this implementation with MN^2 , M being the number of reconstructed orbitals. The reconstruction method is subsequently tested: Valence orbitals of atomic, closed-shell systems were reconstructed numerically exactly. The influence of numerical parameters is investigated using the molecule BaF . It is shown that the method is basis set dependent: One has to ensure that the PO basis can be expanded exactly in the basis of AOs. Violating this rule of thumb may degrade the quality of reconstructed orbitals. Additionally, the representation of MOs by a linear combination of occupied and unoccupied AOs is investigated. For the exemplary systems, the shells included in the fitting procedure of the PP were sufficient. Reconstruction of the alkaline earth monofluorides showed that periodic trends can be reconstructed as well. Scaling of hyperfine structure parameters with increasing atomic number is discussed. For hydrogenic atoms, the scaling should be linear, whereas small deviations from the linear behavior were observed for molecules. The scaling laws computed from reconstructed and reference orbitals were almost identical. In this context, the failure of commonly used relativistic enhancement factors beyond atomic number 100 is discussed. Applicability of the method is also tested on parity violating properties for which the main contribution is generated by the valence orbitals near the nucleus. Symmetry-independence of the method is shown by successful reconstruction of orbitals of the tetrahedral PbCl_4 and chiral NWHClF. The reliable reconstruction of chemical trends is shown with the help of the NWHClF derivatives NWHBrF and NWHFI. The study of chiral compounds as, e.g., NWHClF and its group 17 derivatives, which have been proposed as paradigm for the detection of parity-violation in chiral molecules, remains of great importance. Especially the direct determination of absolute configuration of chiral centers is still non-trivial. The author contributed to this field with a self-written molecular dynamics (MD) program to simulate Coulomb explosions and thus to provide an insight especially into the early explosion stages directly after an instantaneous multi-ionization of the molecule CHBrClF, comparable to experiments using the Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS) technique. An algorithm for the determination of the investigated molecule’s absolute configuration from time-of-flight data and detection locations of molecular fragments is included in the program. The program was used to generate experiment-equivalent data which allowed for the first time the investigation of non-racemic mixtures by the analysis routines of the experiment. The MD program includes harmonic and anharmonic bond potentials. A charge-exchange model can model partial charges in early phases of the Coulomb explosion. Furthermore, Born–Oppenheimer MD simulations and statistical models are used to explain the relative abundance of products belonging to competing reaction channels, as obtained by photoion coincidence measurements. Additionally, qualitative statements about reaction branching ratios are made by comparing the partition functions of involved degrees of freedom. Analytic equations for partition functions of simple models are used to provide a simple formula allowing fast estimates of reaction branching ratios

Études de type structure fonction du couplage électromécanique et de la coopérativité sous-unitaire chez les canaux potassiques dépendants du voltage

Les canaux potassiques voltage-dépendants forment des tétramères dont chaque sous-unité comporte six segments transmembranaires (S1 à S6). Le pore, formé des segments S5-S6 de chaque sous-unité, est entouré de quatre domaines responsables de la sensibilité au potentiel membranaire, les senseurs de voltage (VS; S1-S4). Lors d’une dépolarisation membranaire, le mouvement des résidus chargés situés dans le VS entraine un mouvement de charges détectable en électrophysiologie, le courant de « gating ». L’activation du VS conduit à l'ouverture du pore, qui se traduit par un changement de conformation en C-terminal du segment S6. Pour élucider les principes qui sous-tendent le couplage électromécanique entre ces deux domaines, nous avons étudié deux régions présumées responsables du couplage chez les canaux de type Shaker K+, soit la région carboxy-terminale du segment S6 et le lien peptidique reliant les segments transmembranaire S4-S5 (S4-5L). Avec la technique du « cut-open voltage clamp fluorometry » (COVCF), nous avons pu déterminer que l’interaction inter-sous-unitaire RELY, formée par des acides aminés situés sur le lien S4-5L et S6 de deux sous-unités voisines, est impliquée dans le développement de la composante lente observée lors du retour des charges de « gating » vers leur état de repos, le « OFF-gating ». Nous avons observé que l’introduction de mutations dans la région RELY module la force de ces interactions moléculaires et élimine l’asymétrie observée dans les courants de « gating » de type sauvage. D’ailleurs, nous démontrons que ce couplage inter-sous-unitaire est responsable de la stabilisation du pore dans l’état ouvert. Nous avons également identifié une interaction intra-sous-unitaire entre les résidus I384 situé sur le lien S4-5L et F484 sur le segment S6 d’une même sous-unité. La déstabilisation de cette interaction hydrophobique découple complètement le mouvement des senseurs de voltage et l'ouverture du pore. Sans cette interaction, l’énergie nécessaire pour activer les VS est moindre en raison de l’absence du poids mécanique appliqué par le pore. De plus, l’abolition du couplage électromécanique élimine également le « mode shift », soit le déplacement de la dépendance au voltage des charges de transfert (QV) vers des potentiels hyperpolarisants. Ceci indique que le poids mécanique du pore imposé au VS entraine le « mode shift », en modulant la conformation intrinsèque du VS par un processus allostérique.Voltage-gated potassium channels are tetramers and each subunit is formed of six transmembrane segments (S1 to S6). The pore, formed by the S5-S6 segments of each subunit, is surrounded by four modules responsible for sensitivity to the membrane potential, the voltage sensors (VS, S1-S4). During membrane depolarization, the movement of charged residues located in the VS causes a detectable charge movement called the gating current. The activation of the VS led to the opening of the pore, resulting in a conformational change in the C-terminal segment of S6. To elucidate the principles underlying the electromechanical coupling between these two domains, we examined two regions presumed responsible for the coupling among channels of the Shaker K + family: the carboxy-terminal region of S6 and the peptide bond linking the transmembrane segments S4-S5 (S4-5L). Using the cut-open voltage clamp fluorometry (COVCF), we have determined that the RELY inter-subunit interaction, formed by amino acids located on the S4-5L linker and S6 of two neighboring subunits, is involved in the development of the slow component observed during the return of the gating charges (OFF-gating) to their resting state. The introduction of mutations in the RELY region modulates the strength of these molecular interactions and eliminates the asymmetry observed in the wild type gating currents. Moreover, we demonstrate that this inter-subunit coupling is responsible for stabilizing the pore in the open state. We have also identified an intra-subunit interaction between residues I384 located on the S4-5L linker and F484 on the S6 segment of the same subunit. The destabilization of this hydrophobic interaction uncouples completely the movement of voltage sensors from pore opening. Without this interaction, the energy required to activate the VS is diminished due to the absence of mechanical weight applied by the pore. Furthermore, this uncoupling also eliminates the "mode shift", defined as an amplified shift of the voltage dependence of gating charge (QV) to hyperpolarizing potentials during prolonged depolarization, thus indicating that the mechanical load of the pore influences the entry of the VS into this shifted mode by modulating the conformation of the VS threw an intrinsic allosteric process

Physics 516: Electromagnetic Phenomena (Spring 2020)

These course notes are made publicly available in the hope that they will be useful. All reports of errata will be gratefully received. I will also be glad to hear from anyone who reads them, whether or not you find errors: [email protected]

Study of dynamic processes at the electrochemical interface by in situ high speed STM: surface diffusion and adsorbate interactions

The knowledge about surface diffusion and adsorbate-adsorbate interactions is important for deep understanding of various processes on surfaces and interfaces, such as crystal growth, phase transitions, self-assembly or catalysis. Up to now, the direct microscopic measurements of adsorbate-adsorbate interactions were done in a number of selected systems under ultra-high vacuum condition, but no such studies were performed at solid-liquid interfaces. This work is a continuation of the recent in situ high-speed STM (scanning tunneling microscopy) study of tracer diffusion of sulphur adsorbates on Cu(100) in aqueous solution of 0.01 M HCl performed by T. Tansel [1]. It revealed a linear dependence of diffusion barriers on the electrode potential, which originates from electrostatic interaction of the adsorbate dipole moment with the electric field in the double layer. In the present work, development of software for image recognition and further quantitative analysis allowed the extraction of adsorbate-adsorbate interactions and diffusion barriers of adsorbates in the vicinity of neighboring adsorbates from experimental video sequences. For measurements of interactions between adsorbates, two different methods— dynamic and equilibrium analysis—were applied, providing consistent results, obtained for the first time at an electrochemical interface. The measured pairwise interatomic potential for Sad showed anisotropic behavior, with pronounced repulsion at nearest neighbor sites and attraction at next-nearest neighbor sites of the c(2 × 2) adlattice. The Sad diffusion barriers were considerably decreased in the vicinity of neighboring Sad, as compared to the tracer diffusion barrier of isolated Sad. In further STM measurements, the model system was modified by introducing species possessing a different (cationic) nature, such as Pb adsorbates. The results of tracer diffusion for Pbad revealed a similar potential dependence, as in the case of Sad. This behaviour was not expected because of different adsorbate dipole moments of these species, which are opposite in direction. The observed trend was rationalized by the dominant contribution of neighboring Clad forming the c(2 × 2) lattice to the total surface dipole moment during a single jump event. In addition, attractive pair interactions on the order of 20 meV were found between Pbad at nearest and next-nearest neighbor sites of the c(2 × 2) lattice. In the potential regime corresponding to Pb underpotential deposition on Cu(100), a Pb surface alloy phase nucleated at steps and continued by growing along the upper terraces. With our high temporal and spatial resolution STM we could study the fast dynamic processes associated with surface phase transitions during Pb alloying/dealloying. The formation of a novel transient (4×3) alloy phase with 0.25 ML Pb coverage and its continuous transformation into a c(4 × 4) Pb alloy phase with a coverage of 0.375 ML was observed. By changing the potential sweep in positive direction, Pb dissolution started, resulting in formation of a novel transient c(4 × 4) Pb alloy phase with lower coverage. Further Pb dissolution lead to the re-adsorption of Clad forming c(2 × 2) domains and development of closed-loop Pb ribbon structures. Based on analysis of high resolution STM images we have suggested a new model for this structure

Muon stopping sites in magnetic systems from density functional theory

This thesis concerns the use of density functional theory (DFT) to determine muon stopping sites in crystalline solids. New tools for carrying out these calculations are introduced and these techniques are demonstrated through the results of calculations on the skyrmion-hosting semiconductors GaV$_4$S$_8$ and GaV$_4$S$_8$ and the heavy-fermion metals URu$_2$Si$_2$ and CeRu$_2$Si$_2$. The results of three studies on significantly different magnetic systems are presented, where in each case the interpretation of the results of muon-spin spectroscopy ($\mu^+$SR) experiments is aided by knowledge of the muon site. The results of $\mu^+$SR measurements on the iron-pnictide compound FeCrAs are presented and indicate a magnetically ordered phase throughout the material below $T_\mathrm{N}$ =105(5) K. There are signs of fluctuating magnetism in a narrow range of temperatures above $T_\mathrm{N}$ involving low-energy excitations, while at temperatures well below $T_\mathrm{N}$ a characteristic freezing of dynamics is observed. Using DFT, a distinct muon stopping site is proposed for this system. The results of transverse-field (TF) $\mu^{+}$SR measurements on the molecular spin ladder compound (Hpip)$_{2}$CuBr$_4$, [Hpip=(C$_{5}$H$_{12}$N)] are reported. Characteristic behaviour in each of the regions of the phase diagram is identified in the TF $\mu^+$SR spectra. Analysis of the muon stopping sites, calculated using DFT, suggests that the muon plus its local distortion can lead to a local probe unit with good sensitivity to the magnetic state. Finally, the results of $\mu^+$SR measurements on the charge density wave system 1T-TaS$_2$ are presented, which show three distinct phases versus temperature. The critical exponents for each of these phases are compared with the predictions of quantum spin liquid models. Using DFT, a quantum delocalised state for the muon between the TaS$_2$ layers is proposed, which is used in conjunction with its associated hyperfine interactions to determine the coupling of the muon to the diffusing spinons

Model system approach to the study of UV induced DNA protein crosslink reactions

In this thesis the photoreaction leading from 5-benzyluracil (5BU) to the formation of a cyclized compound, the 5,6BU is studied using several ab initio molecular dynamics computational methods. The reaction is studied as model for the UV induced DNA protein crosslink reaction. The exploration of the reaction mechanism provides new insights in the construction of an efficient methodology to stabilize with UV puled lasers the transient interactions between DNA and close lying proteins in a biological environment

Atomistic modelling of charge trapping defects in silicon dioxide

This thesis focuses on the atomistic modelling of electron trapping sites in silicon dioxide (SiO2) and interactions of hydrogen with the SiO2 network and the resulting defects they produce. They are discussed in the context of electronic device reliability issues. The results presented here were calculated in both crystalline (c-) and amorphous (a-) SiO2. Due to its disordered nature, modelling a-SiO2 is challenging and required the use of a melt-and-quench technique using a classical interatomic potential. All models were evaluated against experimental data to ensure that they are indeed representative of a-SiO2. Using density functional theory (DFT) and the models described above, extra electrons were shown to trap in pure c- and a- SiO2 in deep band gap states for the first time. They can trap spontaneously on pre-existing structural precursors in a-SiO2. The optical absorption spectrum of the intrinsic electron traps was calculated using time-dependent DFT and shows a peak at 3.7 eV, which is in good agreement with a previously unidentified experimental absorption peak measured at low temperatures. Electronic device fabrication processes widely employ hydrogen due to its perceived ability to improve their reliability. The results in this thesis show that both atomic and molecular hydrogen are involved in defect generation processes. Atomic hydrogen was found to interact strongly with strained Si-O bonds to form a stable defect. The barriers to create and annihilate this defect as well as the distribution of its properties were calculated. Hydrogen molecules were found to generate Si-H bonds which can trap holes to form a similar defect and release a proton which can modulate the defect’s properties. These results provide insight into the atomistic nature of defects that can be involved in electronic device reliability issues and help guide the design of reliable fabrication processes