Variational Thermal Quantum Simulation via Thermofield Double States

We present a variational approach for quantum simulators to realize finite temperature Gibbs states by preparing thermofield double (TFD) states. Our protocol is motivated by the quantum approximate optimization algorithm (QAOA) and involves alternating time evolution between the Hamiltonian of interest and interactions which entangle the system and its auxiliary counterpart. As a simple example, we demonstrate that thermal states of the 1d classical Ising model at any temperature can be prepared with perfect fidelity using L/2 iterations, where L is system size. We also show that a free fermion TFD can be prepared with nearly optimal efficiency. Given the simplicity and efficiency of the protocol, our approach enables near-term quantum platforms to access finite temperature phenomena via preparation of thermofield double states.Comment: 5 + 2 pages, 5 figure

Interrogation of alternative splicing events in duplicated genes during evolution

<p>Abstract</p> <p>Background</p> <p>Gene duplication provides resources for developing novel genes and new functions while retaining the original functions. In addition, alternative splicing could increase the complexity of expression at the transcriptome and proteome level without increasing the number of gene copy in the genome. Duplication and alternative splicing are thought to work together to provide the diverse functions or expression patterns for eukaryotes. Previously, it was believed that duplication and alternative splicing were negatively correlated and probably interchangeable.</p> <p>Results</p> <p>We look into the relationship between occurrence of alternative splicing and duplication at different time after duplication events. We found duplication and alternative splicing were indeed inversely correlated if only recently duplicated genes were considered, but they became positively correlated when we took those ancient duplications into account. Specifically, for slightly or moderately duplicated genes with gene families containing 2 - 7 paralogs, genes were more likely to evolve alternative splicing and had on average a greater number of alternative splicing isoforms after long-term evolution compared to singleton genes. On the other hand, those large gene families (contain at least 8 paralogs) had a lower proportion of alternative splicing, and fewer alternative splicing isoforms on average even when ancient duplicated genes were taken into consideration. We also found these duplicated genes having alternative splicing were under tighter evolutionary constraints compared to those having no alternative splicing, and had an enrichment of genes that participate in molecular transducer activities.</p> <p>Conclusions</p> <p>We studied the association between occurrences of alternative splicing and gene duplication. Our results implicate that there are key differences in functions and evolutionary constraints among singleton genes or duplicated genes with or without alternative splicing incidences. It implies that the gene duplication and alternative splicing may have different functional significance in the evolution of speciation diversity.</p

Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis

<p>Abstract</p> <p>Background</p> <p>sRNAs, which belong to the non-coding RNA family and range from approximately 50 to 400 nucleotides, serve various important gene regulatory roles. Most are believed to be <it>trans</it>-regulating and function by being complementary to their target mRNAs in order to inhibiting translation by ribosome occlusion. Despite this understanding of their functionality, the global properties associated with regulation by sRNAs are not yet understood. Here we use topological analysis of sRNA targets in terms of protein-protein interaction and transcription-regulatory networks in <it>Escherichia coli </it>to shed light on the global correlation between sRNA regulation and cellular control networks.</p> <p>Results</p> <p>The analysis of sRNA targets in terms of their networks showed that some specific network properties could be identified. In protein-protein interaction network, sRNA targets tend to occupy more central positions (higher closeness centrality, <it>p-val </it>= 0.022) and more cliquish (larger clustering coefficient, <it>p-val </it>= 0.037). The targets of the same sRNA tend to form a network module (shorter characteristic path length, <it>p-val </it>= 0.015; larger density, <it>p-val </it>= 0.019; higher in-degree ratio, <it>p-val </it>= 0.009). Using the transcription-regulatory network, sRNA targets tend to be under multiple regulation (higher indegree, <it>p-val </it>= 0.013) and the targets usually are important to the transfer of regulatory signals (higher betweenness, <it>p-val </it>= 0.012). As was found for the protein-protein interaction network, the targets that are regulated by the same sRNA also tend to be closely knit within the transcription-regulatory network (larger density, <it>p-val </it>= 0.036), and inward interactions between them are greater than the outward interactions (higher in-degree ratio, <it>p-val </it>= 0.023). However, after incorporating information on predicted sRNAs and down-stream targets, the results are not as clear-cut, but the overall network modularity is still evident.</p> <p>Conclusions</p> <p>Our results indicate that sRNA targeting tends to show a clustering pattern that is similar to the human microRNA regulation associated with protein-protein interaction network that was observed in a previous study. Namely, the sRNA targets show close interaction and forms a closely knit network module for both the protein-protein interaction and the transcription-regulatory networks. Thus, targets of the same sRNA work in a concerted way toward a specific goal. In addition, in the transcription-regulatory network, sRNA targets act as "multiplexor", accepting regulatory control from multiple sources and acting accordingly. Our results indicate that sRNA targeting shows different properties when compared to the proteins that form cellular networks.</p

Red Phosphorescence from Benzo[2,1,3]thiadiazoles at Room Temperature

We describe the red phosphorescence exhibited by a class of structurally simple benzo[2,1,3]thiadiazoles at room temperature. The photophysical properties of these molecules in deoxygenated cyclohexane, including their absorption spectra, steady-state photoluminescence and excitation spectra, and phosphorescence lifetimes, are presented. Time-dependent density functional theory calculations were carried out to better understand the electronic excited states of these benzo[2,1,3]thiadiazoles and why they are capable of phosphorescence.National Science Foundation (U.S.) (1122374)United States. Dept. of Energy. Office of Basic Energy Sciences (DE-FG02-07ER46474

On the Morphology and Chemical Composition of the HR 4796A Debris Disk

[abridged] We present resolved images of the HR 4796A debris disk using the Magellan adaptive optics system paired with Clio-2 and VisAO. We detect the disk at 0.77 \microns, 0.91 \microns, 0.99 \microns, 2.15 \microns, 3.1 \microns, 3.3 \microns, and 3.8 \microns. We find that the deprojected center of the ring is offset from the star by 4.76$\pm$1.6 AU and that the deprojected eccentricity is 0.06$\pm$0.02, in general agreement with previous studies. We find that the average width of the ring is 14$^{+3}_{-2}$, also comparable to previous measurements. Such a narrow ring precludes the existence of shepherding planets more massive than \about 4 \mj, comparable to hot-start planets we could have detected beyond \about 60 AU in projected separation. Combining our new scattered light data with archival HST/STIS and HST/NICMOS data at \about 0.5-2 \microns, along with previously unpublished Spitzer/MIPS thermal emission data and all other literature thermal data, we set out to constrain the chemical composition of the dust grains. After testing 19 individual root compositions and more than 8,400 unique mixtures of these compositions, we find that good fits to the scattered light alone and thermal emission alone are discrepant, suggesting that caution should be exercised if fitting to only one or the other. When we fit to both the scattered light and thermal emission simultaneously, we find mediocre fits (reduced chi-square \about 2). In general, however, we find that silicates and organics are the most favored, and that water ice is usually not favored. These results suggest that the common constituents of both interstellar dust and solar system comets also may reside around HR 4796A, though improved modeling is necessary to place better constraints on the exact chemical composition of the dust.Comment: Accepted to ApJ on October 27, 2014. 21 pages, 12 figures, 4 table

Hypocrea jecorina Cellobiohydrolase I Stabilizing Mutations Identified Using Noncontiguous Recombination

Noncontiguous recombination (NCR) is a method to identify pieces of structure that can be swapped among homologous proteins to create new, chimeric proteins. These “blocks” are encoded by elements of sequence that are not necessarily contiguous along the polypeptide chain. We used NCR to design a library in which blocks of structure from Hypocrea jecorina cellobiohydrolase I (Cel7A) and its two thermostable homologues from Talaromyces emersonii and Chaetomium thermophilum are shuffled to create 531,438 possible chimeric enzymes. We constructed a maximally informative subset of 35 chimeras to analyze this library and found that the blocks contribute additively to the stability of a chimera. Within two highly stabilizing blocks, we uncovered six single amino acid substitutions that each improve the stability of H. jecorina cellobiohydrolase I by 1−3 °C. The small number of measurements required to find these mutations demonstrates that noncontiguous recombination is an efficient strategy for identifying stabilizing mutations

Excreted/secreted Schistosoma mansoni venom allergen-like 9 (SmVAL9) modulates host extracellular matrix remodelling gene expression

AbstractThe Schistosoma mansoni venom allergen-like (SmVAL) protein family consists of 29 members, each possessing a conserved α-β-α sandwich tertiary feature called the Sperm-coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) domain. While the SmVALs have been found in both excretory/secretory (E/S) products and in intra/sub-tegumental (non-E/S) fractions, the role(s) of this family in host/parasite relationships or schistosome developmental processes remains poorly resolved. In order to begin quantifying SmVAL functional diversity or redundancy, dissecting the specific activity (ies) of individual family members is necessary. Towards this end, we present the characterisation of SmVAL9; a protein previously found enriched in both miracidia/sporocyst larval transformation proteins and in egg secretions. While our study confirms that SmVAL9 is indeed found in soluble egg products and miracidia/sporocyst larval transformation proteins, we find it to be maximally transcribed/translated in miracidia and subsequently down-regulated during in vitro sporocyst development. SmVAL9 localisation within sporocysts appears concentrated in parenchymal cells/vesicles as well as associated with larval germinal cells. Furthermore, we demonstrate that egg-derived SmVAL9 carries an N-linked glycan containing a schistosome-specific difucosyl element and is an immunogenic target during chronic murine schistosomiasis. Finally, we demonstrate that recombinant SmVAL9 affects the expression of extracellular matrix, remodelling matrix metalloproteinase (MMP) and tissue inhibitors of metalloproteinase (TIMP) gene products in both Biomphalaria glabrata embryonic cell (BgMMP1) and Mus musculus bone marrow-derived macrophage (MmMMP2, MmMMP9, MmMMP12, MmMMP13, MmMMP14, MmMMP28, TIMP1 and TIMP2) in vitro cultures. These findings importantly suggest that excreted/secreted SmVAL9 participates in tissue reorganisation/extracellular matrix remodelling during intra-mammalian egg translocation, miracidia infection and intra-molluscan sporocyst development/migration