Improved algorithm for the direct dynamics variational multi-configurational Gaussian method.

The Direct Dynamics variational Multi-Configurational Gaussian (DD-vMCG) method provides a fully quantum mechanical solution to the time-dependent Schrödinger equation for the time evolution of nuclei with potential surfaces calculated on-the-fly using a quantum chemistry program. Initial studies have shown its potential for flexible and accurate simulations of non-adiabatic excited-state molecular dynamics. In this paper, we present developments to the DD-vMCG algorithm that improve both its accuracy and efficiency. First, a new, efficient parallel algorithm to control the DD-vMCG database of quantum chemistry points is presented along with improvements to the Shepard interpolation scheme. Second, the use of symmetry in describing the potential surfaces is introduced along with a new phase convention in the propagation diabatization. Benchmark calculations on the allene radical cation including all degrees of freedom then show that the new scheme is able to produce a consistent non-adiabatic coupling vector field. This new DD-vMCG version thus opens the route for effectively and accurately treating complex chemical systems using quantum dynamics simulations

Complex symplectic lie algebras with large abelian subalgebras

We present two constructions of complex symplectic structures on Lie algebras with large Abelian ideals. In particular, we completely classify complex symplectic structures on almost Abelian Lie algebras. By considering compact quotients of their corresponding connected, simply connected Lie groups we obtain many examples of complex symplectic manifolds which do not carry (hyper)kähler metrics. We also produce examples of compact complex symplectic manifolds endowed with a fibration whose fibers are Lagrangian tori

Prediction Through Quantum Dynamics Simulations: Photo-excited Cyclobutanone

Quantum dynamics simulations are becoming a standard tool for simulating photo-excited molecular systems involving a manifold of coupled states, known as non-adiabatic dynamics. While these simulations have had many successes in explaining experiments and giving details of non-adiabatic transitions, the question remains as to their predictive power. In this work, we present a set of quantum dynamics simulations on cyclobutanone, using both grid-based multi-configuration time-dependent Hartree (MCTDH) and direct dynamics variational multi-configuration Gaussian (DD-vMCG) methods. The former used a parameterised vibronic coupling model Hamiltonian and the latter generated the potential energy surfaces on-the-fly. The results give a picture of the non-adiabatic behaviour of this molecule and were used to calculate the signal from a gas-phase ultrafast electron diffraction (GUED) experiment. Corresponding experimental results will be obtained and presented at a later stage for comparison to test the predictive power of the methods. The results show that over the first 500 fs after photo-excitation to the S$_2$ state, cyclobutanone relaxes quickly to the S$_1$ state, but only a small population relaxes further to the S$_0$ state. No significant transfer of population to the triplet manifold is found. It is predicted that the GUED experiments over this time scale will see s signal related mostly to the C-O stretch motion and elongation of the molecular ring along the C-C-O axis.Comment: 31 pages, 7 figure

Closed forms and multi-moment maps

We extend the notion of multi-moment map to geometries defined by closed forms of arbitrary degree. We give fundamental existence and uniqueness results and discuss a number of essential examples, including geometries related to special holonomy. For forms of degree four, multi-moment maps are guaranteed to exist and are unique when the symmetry group is (3,4)-trivial, meaning that the group is connected and the third and fourth Lie algebra Betti numbers vanish. We give a structural description of some classes of (3,4)-trivial algebras and provide a number of examples.Comment: 36 page

Isochronal annealing effects on local structure, crystalline fraction, and undamaged region size of radiation damage in Ga-stabilized δ\delta-Pu

The effects on the local structure due to self-irradiation damage of Ga stabilized $\delta$-Pu stored at cryogenic temperatures have been examined using extended x-ray absorption fine structure (EXAFS) experiments. Extensive damage, seen as a loss of local order, was evident after 72 days of storage below 15 K. The effect was observed from both the Pu and Ga sites, although less pronounced around Ga. Isochronal annealing was performed on this sample to study the annealing processes that occur between cryogenic and room temperature storage conditions, where damage is mostly reversed. Damage fractions at various points along the annealing curve have been determined using an amplitude-ratio method, standard EXAFS fitting, and a spherical crystallite model, and provide information complementary to previous electrical resistivity- and susceptibility-based isochronal annealing studies. The use of a spherical crystallite model accounts for the changes in EXAFS spectra using just two parameters, namely, the crystalline fraction and the particle radius. Together, these results are discussed in terms of changes to the local structure around Ga and Pu throughout the annealing process and highlight the unusual role of Ga in the behavior of the lowest temperature anneals.Comment: 13 pages, 10 figure

Thermodynamics and electrodynamics of unusual narrow-gap semiconductors

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL) that has led to a fully funded DOE program to continue this work. The project was directed toward exploring the Ettingshausen effect, which is the direct extension of the familiar Peltier-effect refrigerator (the process used in popular coolers that run off automotive electrical power) in which a magnetic field is used to enhance refrigeration effects at temperatures well below room temperature. Such refrigeration processes are all-solid-state and are of potentially great commercial importance, but essentially no work has been done since the early 1970s. Using modern experimental and theoretical techniques, the authors have advanced the state-of-the-art significantly, laying the groundwork for commercial cryogenic solid-state refrigeration

Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC

Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO2, but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions is the electron-bifurcating [FeFe]-hydrogenase HydABC that reduces low-potential ferredoxins (Fd) by oxidizing hydrogen gas (H2). By combining single-particle cryo-electron microscopy (cryoEM) under catalytic turnover conditions with site-directed mutagenesis experiments, functional studies, infrared spectroscopy, and molecular simulations, we show that HydABC from the acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui employ a single flavin mononucleotide (FMN) cofactor to establish electron transfer pathways to the NAD(P)+ and Fd reduction sites by a mechanism that is fundamentally different from classical flavin-based electron bifurcation enzymes. By modulation of the NAD(P)+ binding affinity via reduction of a nearby iron–sulfur cluster, HydABC switches between the exergonic NAD(P)+ reduction and endergonic Fd reduction modes. Our combined findings suggest that the conformational dynamics establish a redox-driven kinetic gate that prevents the backflow of the electrons from the Fd reduction branch toward the FMN site, providing a basis for understanding general mechanistic principles of electron-bifurcating hydrogenases

UV photochemistry of the L-cystine disulfide bridge in aqueous solution investigated by femtosecond X-ray absorption spectroscopy

The photolysis of disulfide bonds is implicated in denaturation of proteins exposed to ultraviolet light. Despite this biological relevance in stabilizing the structure of many proteins, the mechanisms of disulfide photolysis are still contested after decades of research. Herein, we report new insight into the photochemistry of L-cystine in aqueous solution by femtosecond X-ray absorption spectroscopy at the sulfur K-edge. We observe homolytic bond cleavage upon ultraviolet irradiation and the formation of thiyl radicals as the single primary photoproduct. Ultrafast thiyl decay due to geminate recombination proceeds at a quantum yield of >80 % within 20 ps. These dynamics coincide with the emergence of a secondary product, attributed to the generation of perthiyl radicals. From these findings, we suggest a mechanism of perthiyl radical generation from a vibrationally excited parent molecule that asymmetrically fragments along a carbon-sulfur bond. Our results point toward a dynamic photostability of the disulfide bridge in condensed-phase