Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.

Empirical Studies on the Network of Social Groups: The Case of Tencent QQ

BACKGROUND

Participation in social groups are important but the collective behaviors of human as a group are difficult to analyze due to the difficulties to quantify ordinary social relation, group membership, and to collect a comprehensive dataset. Such difficulties can be circumvented by analyzing online social networks.

METHODOLOGY/PRINCIPAL FINDINGS

In this paper, we analyze a comprehensive dataset released from Tencent QQ, an instant messenger with the highest market share in China. Specifically, we analyze three derivative networks involving groups and their members-the hypergraph of groups, the network of groups and the user network-to reveal social interactions at microscopic and mesoscopic level.

CONCLUSIONS/SIGNIFICANCE

Our results uncover interesting behaviors on the growth of user groups, the interactions between groups, and their relationship with member age and gender. These findings lead to insights which are difficult to obtain in social networks based on personal contacts.

A Structural Model for a Self-Assembled Nanotube Provides Insight into Its Exciton Dynamics

The design and synthesis of functional self-assembled nanostructures is frequently an empirical process fraught with critical knowledge gaps about atomic-level structure in these noncovalent systems. Here, we report a structural model for a semiconductor nanotube formed via the self-assembly of naphthalenediimide-lysine (NDI-Lys) building blocks determined using experimental 13C-13C and 13C-15N distance restraints from solid-state nuclear magnetic resonance supplemented by electron microscopy and X-ray powder diffraction data. The structural model reveals a two-dimensional-crystal-like architecture of stacked monolayer rings each containing ∼50 NDI-Lys molecules, with significant π-stacking interactions occurring both within the confines of the ring and along the long axis of the tube. Excited-state delocalization and energy transfer are simulated for the nanotube based on time-dependent density functional theory and an incoherent hopping model. Remarkably, these calculations reveal efficient energy migration from the excitonic bright state, which is in agreement with the rapid energy transfer within NDI-Lys nanotubes observed previously using fluorescence spectroscopy.

Ab inito study on triplet excitation energy transfer in photosynthetic light-harvesting complexes

We have studied the triplet energy transfer (TET) for photosynthetic light-harvesting complexes, the bacterial light-harvesting complex II (LH2) of Rhodospirillum molischianum and Rhodopseudomonas acidophila, and the peridinin-chlorophyll a protein (PCP) from Amphidinium carterae. The electronic coupling factor was calculated with the recently developed fragment spin difference scheme (You and Hsu, J. Chem. Phys. 2010, 133, 074105), which is a general computational scheme that yields the overall coupling under the Hamiltonian employed. The TET rates were estimated based on the couplings obtained. For all light-harvesting complexes studied, there exist nanosecond triplet energy transfer from the chlorophylls to the carotenoids. This result supports a direct triplet quenching mechanism for the photoprotection function of carotenoids. The TET rates are similar for a broad range of carotenoid triplet state energy, which implies a general and robust TET quenching role for carotenoids in photosynthesis. This result is also consistent with the weak dependence of TET kinetics on the type or the number of π conjugation lengths in the carotenoids and their analogues reported in the literature. We have also explored the possibility of forming triplet excitons in these complexes. In B850 of LH2 or the peridinin cluster in PCP, it is unlikely to have triplet exciton since the energy differences of any two neighboring molecules are likely to be much larger than their TET couplings. Our results provide theoretical limits to the possible photophysics in the light-harvesting complexes.

Distribution and expression of recombinant plasmid encoding chicken interleukin-2

A plasmid DNA that encodes chicken interleukin-2 (pCI-ChIL-2-EGFP) was investigated for its distribution and expression after intramuscular (i.m.) injection in chickens. After the i.m. injection, serum distribution was detectable from 2 h post inoculation (p.i.), peaked at 8 h p.i., and disappeared at 7 days p.i. The plasmid DNA was also observed in several organs including heart, liver, lung, spleen, bursa and inoculated muscle at different time points, but at 19 days p.i. the plasmid DNA was not found in any organ except inoculated muscle. Fluorescence of enhanced green fluorescent protein (EGFP) was found in cytoplasm and nucleus of cultured Vero cells, chicken embryo fibroblasts and peripheral blood lymphocytes, which were transfected in vitro with the plasmid DNA or in vivo with Lipofectamine. The expression profile of the fusion gene (ChIL-2-EGFP) in vivo was measured by RT-PCR, ELISA and fluorescence microscopy. The EGFP expression was detected from 8 h p.i. to 14 days p.i. and peaked at 5 days p.i., when the number of EGFP-expression myocytes was about 5% in the injected site. These results demonstrate that intramuscular administration of plasmid DNA leads to widespread distribution and long-term expression in vivo.

Triplet-triplet energy-transfer coupling: Theory and calculation

Triplet-triplet (TT) energy transfer requires two molecular fragments to exchange electrons that carry different spin and energy. In this paper, we analyze and report values of the electronic coupling strengths for TT energy transfer. Two different methods were proposed and tested: (1) Directly calculating the off-diagonal Hamiltonian matrix element. This direct coupling scheme was generalized from the one used for electron transfer coupling, where two spin-localized unrestricted Hartree-Fock wave functions are used as the zero-order reactant and product states, and the off-diagonal Hamiltonian matrix elements are calculated directly. (2) From energy gaps derived from configuration-interaction-singles (CIS) scheme. Both methods yielded very similar results for the systems tested. For TT coupling between a pair of face-to-face ethylene molecules, the exponential attenuation factor is 2.59 A(-1)(CIS6-311+G(**)), which is about twice as large as typical values for electron transfer. With a series of fully stacked polyene pairs, we found that the TT coupling magnitudes and attenuation rates are very similar irrespective of their molecular size. If the polyenes were partially stacked, TT couplings were much reduced, and they decay more rapidly with distance than those of full-stacked systems. Our results showed that the TT coupling arises mainly from the region of close contact between the donor and acceptor frontier orbitals, and the exponential decay of the coupling with separation depends on the details of the molecular contacts. With our calculated results, nanosecond or picosecond time scales for TT energy-transfer rates are possible.

Charge transport properties of tris(8-hydroxyquinolinato)aluminum(III): why it is an electron transporter

The charge transport properties of mer-tris(8-hydroxyquinolinato)aluminum(III) (mer-Alq), which is the most widely used electron transport material in OLED, were investigated by quantum chemistry calculations within the framework of the charge hopping model and Marcus electron transfer theory. Internal reorganization energies of 0.276 and 0.242 eV were calculated by the DFT-B3LYP method employing a 6-31 G* basis set for the electrons lambdai(e) and holes lambdai(h), respectively. The relative distances and orientations of Alq molecules in amorphous film were simulated by those in the beta-phase. The intermolecular charge-transfer integrals, Hda(h) and Hda(e), along all 14 hopping pathways were then calculated by the Koopmans Theorem in conjunction with the Hartree-Fock method employing a 6-31 G* basis set as well as by the direct coupling method. The results showed that there were some Hda(e) that were 1 order of magnitude larger than any Hda(h), because hopping pathways with effective overlaps of LUMOs can occur and, thus, large Hda(e). On the other hand, effective overlap of HOMO was absent in all pathways, resulting in a relatively small Hda(h). This difference in the magnitudes of Hda(e) and Hda(h) would predict a 2 orders of magnitude difference in the electron-transfer rate constants and account for the observed 2 orders of magnitude difference in the mobilities of electrons and holes.

Hemorrhagic fever with renal syndrome. Separation of human peripheral blood T and B cells and detection of viral antigen

In this study, total blood lymphocytes were prepared from patients with hemorrhagic fever with renal syndrome (HFRS) by a density gradient on Ficoll-Hypaque. T and B cells were then purified by passing the total lymphocytes over a nylon wool column. The purities of total lymphocytes, T cells and B cells were 97.8 +/- 2.3%, 91.6 +/- 4.5% and 74.2 +/- 12.1%, respectively. Also, after modification of cell fixation and smear drying, the number of cells were increased and the time needed for slide preparation was shortened. Detection of viral antigen by immunofluorescence assay using monoclonal antibodies to Hantavirus (HTNV) showed that the total lymphocytes. T cells and B cells were infected by HTNV during the early stages of HFRS and no specific fluorescence was seen in the cells from the late diuretic phase to convalescent phase. The results suggest that virus replication in blood lymphocytes may partly contribute in the early stages to the impairment of cell immune response and in vivo spread of HTNV to its target sites.

Hemorrhagic fever with renal syndrome: separation of human peripheral blood T and B cells and detection of viral antigen

Total lymphocytes in peripheral blood were prepared from patients with hemorrhagic fever with renal syndrome by a density gradient on Ficoll-Hypaque, and then T and B cells purified by passing the lymphocytes over a nylon column with modifications. Also, after modification of cell fixation and use of a spinner for smear drying, the number of cells were increased and the duration for slide preparation was shortened, thus resulting in quality slides. Detection of viral antigen by immunofluorescence assay using monoclonal antibodies to Hantavirus (HTNV) showed that the total lymphocytes, T cells and B cells were infected with HTNV during the early stages of the illness and no specific fluorescence was seen in the cells from the late diuretic phase to convalescent phase.