Towards High-Quality Black-Box Chemical Reaction Rates with System-Specific Potential Energy Surfaces

The calculation of highly-accurate reaction rate constants (k(T)) is one of the central topics in theoretical chemical kinetics. Two approaches for doing this are dominant in literature: application of heuristic corrections of the transition state theory (TST) and wave packet propagation with the aim to represent exact quantum mechanical dynamics. While the first approach is easy to handle but suffers from intrinsic approximations and limited accuracy, the second approach enables convergence towards the exact result, but at the expense of a complex handling and massive costs. This limits its application to a small circle of highly-specialized theoreticians. A new method that might be able to bridge the gap between easy application and convergence towards the exact result is the ring polymer molecular dynamics (RPMD) method. It is based on the isomorphism between quantum statistical mechanics and classical statistical mechanics of a fictitious ring polymer. With this, configurational state sums and free energy surfaces can be obtained from probabilistic samplings of the system's accessible phase space with classical MD of ring polymers. Based on these free energy surfaces reaction rate constants can be obtained that converge towards the results of wave packet propagations, if the size of the ring polymer is adequate. In order to conduct RPMD calculations, a sufficiently accurate representation of the thermally accessible potential energy surface (PES) of the system on which the ring polymers are propagated is needed. In principle, this surface could be represented by ad hoc calculations of energies and gradients based on quantum chemical methods like density functional theory (DFT) or second order Moller-Plesset perturbation theory (MP2). However, since many millions of single gradient calculations are needed to converge a free energy surface and the associated k(T) value, this approach is impractical. Instead, analytical representations of PESs that are fitted to DFT or MP2 results are commonly used. The parametrization of these representations is quite demanding, though, thus being a task for experts. The present thesis deals with new methods for the automated parametrization of analytical PES representations of reactive systems and the successive k(T) calculations based on RPMD. These representations are built on a combination of the quantum mechanical derived force field (QMDFF) method by \Grimme and the empirical valence bond method (EVB) by Warshel, being plugged together recently by Hartke and Grimme (EVB-QMDFF). In line with this thesis a crucial improvement of this combination of methods was done, complementing it with newly developed EVB concepts. For practical usage a new program package was developed, which enables the automated generation of an EVB-QMDFF-PES representation and calculations of RPMD-free-energy surfaces, recrossing corrections as well as k(T) values and Arrhenius parameters for comparison with experimental data, based on the preoptimized reaction path of an arbitrary thermal ground state system. The abilities of the new methods and the associated implementation were thoroughly benchmarked in different kinds of applications. These are calculations of k(T) values and Arrhenius parameters of arbitrary systems from a reaction data base and their comparison to literature values, theoretical molecular force experiments with quantitative investigations of force-dependent reactivities for different systems, a thorough study of urethane synthesis being part of our cooperation with Covestro AG and finally a combination of calculated rate constants of several elementary reactions for describing the dynamics of larger systems based on the kinetic Monte Carlo (KMC) method

Computation of elementary modes: a unifying framework and the new binary approach

BACKGROUND: Metabolic pathway analysis has been recognized as a central approach to the structural analysis of metabolic networks. The concept of elementary (flux) modes provides a rigorous formalism to describe and assess pathways and has proven to be valuable for many applications. However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods. RESULTS: We show that computing the set of elementary modes is equivalent to computing the set of extreme rays of a convex cone. This standard mathematical representation provides a unified framework that encompasses the most prominent algorithmic methods that compute elementary modes and allows a clear comparison between them. Taking lessons from this benchmark, we here introduce a new method, the binary approach, which computes the elementary modes as binary patterns of participating reactions from which the respective stoichiometric coefficients can be computed in a post-processing step. We implemented the binary approach in FluxAnalyzer 5.1, a software that is free for academics. The binary approach decreases the memory demand up to 96% without loss of speed giving the most efficient method available for computing elementary modes to date. CONCLUSIONS: The equivalence between elementary modes and extreme ray computations offers opportunities for employing tools from polyhedral computation for metabolic pathway analysis. The new binary approach introduced herein was derived from this general theoretical framework and facilitates the computation of elementary modes in considerably larger networks

Nuclear Magnetic Resonance in High Magnetic Field: Application to Condensed Matter Physics

In this review, we describe the potentialities offered by the nuclear magnetic resonance (NMR) technique to explore at a microscopic level new quantum states of condensed matter induced by high magnetic fields. We focus on experiments realised in resistive (up to 34~T) or hybrid (up to 45~T) magnets, which open a large access to these quantum phase transitions. After an introduction on NMR observable, we consider several topics: quantum spin systems (spin-Peierls transition, spin ladders, spin nematic phases, magnetisation plateaus and Bose-Einstein condensation of triplet excitations), the field-induced charge density wave (CDW) in high $T_c$~superconductors, and exotic superconductivity including the Fulde-Ferrel-Larkin-Ovchinnikov superconducting state and the field-induced superconductivity due to the Jaccarino-Peter mechanism.Comment: 19 pages, 6 figure

Clinical parameters and biomarkers predicting spontaneous operational tolerance after liver transplantation: a scoping review protocol

Objective:; This scoping review aims at systematically mapping reported prognostic factors for spontaneous immunosuppression (IS) free allograft tolerance (operational tolerance, OT) in non-viral hepatitis and non-autoimmune disease liver transplant (LT) recipients who are undergoing immunosuppression withdrawal (ISW). The results may inform the subsequent conduct of a systematic review with a more specific review question.; Background:; LT is currently the most effective treatment for end-stage liver diseases. Whereas the short-term outcomes after LT have dramatically improved over the last decades, the long-term outcomes remain unsatisfactory, mainly because of side effects of lifelong IS, such as infections, cardiovascular diseases, malignancies, and nephrotoxicity. ISW studies have shown that OT can be achieved by a subset of LT recipients and recent research has identified biomarkers of OT in these patients. However, an evidence-based selection algorithm for patients that can predictably benefit from ISW is not available to date. The planned review will, therefore, map existing knowledge on prognostic clinical parameters and biomarkers for OT.; Inclusion criteria:; We will consider studies that record any clinical parameter or biomarker before the initiation of ISW in paediatric or adult non-viral hepatitis and non-autoimmune disease LT recipients and analyse their possible association with ISW outcomes (OT or non-tolerance). Studies addressing the effectiveness of OT-inducing treatments will be excluded.; Methods:; Embase, MEDLINE, and Cochrane Library will be searched for relevant articles or conference abstracts. Full-texts of selected abstracts will be independently screened for inclusion by two reviewers. References and citing articles of included records will be screened for additional relevant records. Clinical trial registries will be searched for ongoing studies, and their investigators contacted for the sharing of unpublished data. Data from included records will be independently extracted by two reviewers using a prespecified data extraction table and presented in both tabular and narrative form

Lie symmetries applied to guaranteed integration: application to mobile robotics localisation

[no abstract available

A constraint programming approach for polytopic simulation of ordinary differential equations - a collision detection application

[no abstract available

A Generic Framework for Representing and Analysing Model Concurrency

International audienceRecent results in language engineering simplify the development of tool-supported executable domain-specific modelling languages (xDSMLs), including editing (e.g., completion and error checking) and execution analysis tools (e.g., debugging, monitoring and live modelling). However, such frameworks are currently limited to sequential execution traces, and cannot handle execution traces resulting from an execution semantics with a concurrency model supporting parallelism or interleaving. This prevents the development of concurrency analysis tools, like debuggers supporting the exploration of model executions resulting from different interleavings. In this paper, we present a generic framework to integrate execution semantics with either implicit or explicit concurrency models, to explore the possible execution traces of conforming models, and to define strategies for helping in the exploration of the possible executions. This framework is complemented with a protocol to interact with the resulting executions and hence to build advanced concurrency analysis tools. The approach has been implemented within the GEMOC Studio. We demonstrate how to integrate two representative concurrent meta-programming approaches (MoCCML/Java and Henshin), which use different paradigms and underlying foundations to define an xDSML's concurrency model. We also demonstrate the ability to define an advanced concurrent omniscient debugger with the proposed protocol. The paper, thus, contributes key abstractions and an associated protocol for integrating concurrent meta-pro\-gram\-ming approaches in a language workbench, and dynamically exploring the possible executions of a model in the modelling workbench

Locally commensurate charge-density wave with three-unit-cell periodicity in YBCO

In order to identify the mechanism responsible for the formation of charge-density waves (CDW) in cuprate superconductors, it is important to understand which aspects of the CDW's microscopic structure are generic and which are material-dependent. Here, we show that, at the local scale probed by NMR, long-range CDW order in YBa2Cu3Oy is unidirectional with a commensurate period of three unit cells (lambda = 3b), implying that the incommensurability found in X-ray scattering is ensured by phase slips (discommensurations). Furthermore, NMR spectra reveal a predominant oxygen character of the CDW with an out-of-phase relationship between certain lattice sites but no specific signature of a secondary CDW with lambda = 6b associated with a putative pair-density wave. These results shed light on universal aspects of the cuprate CDW. In particular, its spatial profile appears to generically result from the interplay between an incommensurate tendency at long length scales, possibly related to properties of the Fermi surface, and local commensuration effects, due to electron-electron interactions or lock-in to the lattice.Comment: Original submission (revised version available upon request

Unraveling the Effect of Rh Isolation on Shallow d States of Gallium–Rhodium Alloys

In this study, we report the electronic and chemical structure of supported GaRh alloys as model systems for the active phase in supported catalytically active liquid metal solutions (SCALMS). We prepared a series of gallium–rhodium samples with different Rh contents and tracked the evolution of the sample topography and surface electronic structure via photoemission spectroscopy in combination with ab initio calculations and electron microscopy. Our results reveal a characteristic shift of the Rh 3d core levels and narrowing and shifting of the Rh 4d derived band with decreasing Rh content. Calculations show that these spectroscopic observations can be explained by the coexistence of isolated Rh atoms in random GaRh alloys and GaRh intermetallic compounds (IMCs). These results contribute to an enhancement of the fundamental understanding of the electronic surface structure of GaRh alloys, which is crucially required for apprehending and thus further exploiting the improved catalytic activity of GaRh SCALMS

Bromination of 2D materials

The adsorption, reaction and thermal stability of bromine on Rh(111)-supported hexagonal boron nitride (h-BN) and graphene were investigated. Synchrotron radiation-based high-resolution x-ray photoelectron spectroscopy (XPS) and temperature-programmed XPS allowed us to follow the adsorption process and the thermal evolution in situ on the molecular scale. On h-BN/Rh(111), bromine adsorbs exclusively in the pores of the nanomesh while we observe no such selectivity for graphene/Rh(111). Upon heating, bromine undergoes an on-surface reaction on h-BN to form polybromides (170–240 K), which subsequently decompose to bromide (240–640 K). The high thermal stability of Br/h-BN/Rh(111) suggests strong/covalent bonding. Bromine on graphene/Rh(111), on the other hand, reveals no distinct reactivity except for intercalation of small amounts of bromine underneath the 2D layer at high temperatures. In both cases, adsorption is reversible upon heating. Our experiments are supported by a comprehensive theoretical study. DFT calculations were used to describe the nature of the h-BN nanomesh and the graphene moiré in detail and to study the adsorption energetics and substrate interaction of bromine. In addition, the adsorption of bromine on h-BN/Rh(111) was simulated by molecular dynamics using a machine-learning force field