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We investigate two well-known approaches for extending the fewest switches surface hopping (FSSH) algorithm to periodic time-dependent couplings. The first formalism acts as if the instantaneous adiabatic electronic states were standard adiabatic states, which just happen to evolve in time. The second formalism replaces the role of the usual adiabatic states by the timeindependent adiabatic Floquet states. For a set of modified Tully model problems, the Floquet FSSH (F-FSSH) formalism gives a better estimate for both transmission and reflection probabilities than the instantaneous adiabatic FSSH (IA-FSSH) formalism, especially for slow nuclear velocities. More importantly, only F-FSSH predicts the correct final scattering momentum. Finally, in order to use Floquet theory accurately, we find that it is crucial to account for the interference between wavepackets on different Floquet states. Our results should be of interest to all those interested in laser-induced molecular dynamics.

We examine the many open questions that arise for nonadiabatic dynamics in the presence of degenerate electronic states, e.g., for singlet-to-triplet intersystem crossing where a minimal Hamiltonian must include four states (two of which are always degenerate). In such circumstances, the standard surface hopping approach is not sufficient as the algorithm does not include Berry force. Yet, we hypothesize that such a Berry force may be crucial as far as creating chiral induced spin separation, which is now a burgeoning field of study. Thus, this Perspective highlights the fact that if one can generate a robust and accurate semiclassical approach for the case of degenerate states, one will take a big step forward toward merging chemical physics with spintronics.

We investigate a simple and robust scheme for choosing the phases of adiabatic electronic states smoothly (as a function of geometry) so as to maximize the performance of ab initio non-adiabatic dynamics methods. Our approach is based upon consideration of the overlap matrix (U) between basis functions at successive points in time and selecting the phases so as to minimize the matrix norm of log(U). In so doing, one can extend the concept of parallel transport to cases with sharp curve crossings. We demonstrate that this algorithm performs well under extreme situations where dozens of states cross each other either through trivial crossings (where there is zero effective diabatic coupling), or through nontrivial crossings (when there is a nonzero diabatic coupling), or through a combination of both. In all cases, we compute the time-derivative coupling matrix elements (or equivalently non-adiabatic derivative coupling matrix elements) that are as smooth as possible.Our results should be of interest to all who are interested in either non-adiabatic dynamics, or more generally, parallel transport in large systems.

Two luminescent metal-organic-frameworks (LMOFs) constructed by a molecular chromophore [tri(4-pyridylphenyl)amine] (tppa) were synthesized by solvothermal reactions and characterized by single crystal and powder X-ray diffraction, thermogravimetric analysis, optical diffuse reflection, photoluminescence spectroscopy, and internal quantum yield measurements. Both compound 1 [Zn(tppa)(ndc)·(DMF)] and compound 2 [Zn(tppa)(sdc)(NO)·(DMF)·(ACN)] (ndc = 2,6-naphthalenedicarboxylic acid, sdc = (E)-4,4'-(ethene-1,2-diyl)dibenzoic acid, DMF = dimethylformamide, ACN = acetonitrile) exhibit intense yellow emission under blue light (455 nm) excitation. The Commission International de I'Eclairage (CIE) coordinates of 1 (0.42, 0.53) and 2 (0.42, 0.54) are close to that of YAG:Ce (0.41, 0.55) (λ = 455 nm). The two phosphor materials show promise for use in phosphor-converted white LEDs (PC-WLEDs).

BackgroundReed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy grass of the temperate regions of the world. Despite its economic importance, it is lacking in public genomic data. We explore comparative exomics of the grass cultivars in the context of response to salt exposure. The limited data set poses challenges to the computational pipeline.MethodsAs a prerequisite for the comparative study, we generate the Phalaris reference transcriptome sequence, one of the first steps in addressing the issue of paucity of processed genomic data in this species. In addition, the differential expression (DE) and active-but-stable genes for salt stress conditions were analyzed by a novel method that was experimentally verified on human RNA-seq data. For the comparative exomics, we focus on the DE and stable genic regions, with respect to salt stress, of the genome.Results and conclusionsIn our comparative study, we find that phylogeny of the DE and stable genic regions of the Phalaris cultivars are distinct. At the same time we find the phylogeny of the entire expressed reference transcriptome matches the phylogeny of only the stable genes. Thus the behavior of the different cultivars is distinguished by the salt stress response. This is also reflected in the genomic distinctions in the DE genic regions. These observations have important implications in the choice of cultivars, and their breeding, for bio-energy fuels. Further, we identified genes that are representative of DE under salt stress and could provide vital clues in our understanding of the stress handling mechanisms in general.

Genome-wide association studies (GWAS) are a common approach for systematic discovery of single nucleotide polymorphisms (SNPs) which are associated with a given disease. Univariate analysis approaches commonly employed may miss important SNP associations that only appear through multivariate analysis in complex diseases. However, multivariate SNP analysis is currently limited by its inherent computational complexity. In this work, we present a computational framework that harnesses supercomputers. Based on our results, we estimate a three-way interaction analysis on 1.1 million SNP GWAS data requiring over 5.8 years on the full "Avoca" IBM Blue Gene/Q installation at the Victorian Life Sciences Computation Initiative. This is hundreds of times faster than estimates for other CPU based methods and four times faster than runtimes estimated for GPU methods, indicating how the improvement in the level of hardware applied to interaction analysis may alter the types of analysis that can be performed. Furthermore, the same analysis would take under 3 months on the currently largest IBM Blue Gene/Q supercomputer "Sequoia" at the Lawrence Livermore National Laboratory assuming linear scaling is maintained as our results suggest. Given that the implementation used in this study can be further optimised, this runtime means it is becoming feasible to carry out exhaustive analysis of higher order interaction studies on large modern GWAS.

Three new LMOFs, complexes 1–3, have been solvothermally synthesized. 1 and 2 are 2-D structures, whiles 3 is a 3-D structure. And 1 exhibits in detecting Fe3+ and Cr3+. All of them have potential applications in chemical sensing.