Molecular dynamics of conformational substates for a simplified protein model.

Extended molecular dynamics simulations covering a total of 0.232 μs have been carried out on a simplified protein model. Despite its simplified structure, that model exhibits properties similar to those of more realistic protein models. In particular, the model was found to undergo transitions between conformational substates at a time scale of several hundred picoseconds. The computed trajectories turned out to be sufficiently long as to permit a statistical analysis of that conformational dynamics. To check whether effective descriptions neglecting memory effects can reproduce the observed conformational dynamics, two stochastic models were studied. A one‐dimensional Langevin effective potential model derived by elimination of subpicosecond dynamical processes could not describe the observed conformational transition rates. In contrast, a simple Markov model describing the transitions between but neglecting dynamical processes within conformational substates reproduced the observed distribution of first passage times. These findings suggest, that protein dynamics generally does not exhibit memory effects at time scales above a few hundred picoseconds, but confirms the existence of memory effects at a picosecond time scale

Robust Parafoil Terminal Guidance Using Massively Parallel Processing

Terminal guidance of autonomous parafoils is a difficult problem in which wind uncertainty and system underactuation are major challenges. Existing strategies almost exclusively use impact error as the criterion for optimality. Practical airdrop systems, however, must also include other criteria that maybe even more important than impact error for some missions, such as ground speed at impact or constraints imposed by drop zones with restrictions on flight patterns. Furthermore, existing guidance schemes determine terminal trajectories using deterministic wind information and may result in a solution that works in ideal wind but may be sensitive to variations. The work described here develops a guidance strategy that uses massively parallel Monte Carlo simulation performed on a graphics processing unit to rank candidate trajectories in terms of robustness to wind uncertainty. The result is robust guidance, as opposed to optimal guidance. Through simulation results, the proposed path planning scheme proves more robust in realistic dynamic wind environments compared with previous optimal trajectory planners that assume perfect knowledge of a constant wind

Triterpenic and phenolic acids production changed in Salvia officinalis via in vitro and in vivo polyploidization: A consequence of altered genes expression

The induction of polyploidy is an efficient technique for creating a diversity of genetic, phenotypic, and phytochemical novelties in plant taxa. Sage (Salvia officinalis L.) is a well-known medicinal plant rich of valuable bioactive molecules such as triterpenic and phenolic acids. In the present study, the effect of in vitro and in vivo polyploidization on morphological characteristics, anatomical structures, phytochemical traits, and expression level of the genes involved in the biosynthesis of major triterpenic acids (ursolic, betulinic, and oleanolic acids) of the plant was studied. The sterile seeds treated with different concentrations (0, 0.05, 0.1, and 0.2%) of colchicine for 24 and 48 h were considered for polyploidy induction. Flow cytometry and chromosome counting were used to confirm the ploidy level of diploid (2n = 2x = 14, 2C DNA = 1.10 pg) and tetraploid (2n = 4x = 28, 2C DNA = 2.12 pg) plants after seven months. The highest polyploidy induction was obtained by applying 0.1% (w/v) colchicine for 48 h with an efficiency of 19.05% in vitro tetraploidy. Polyploids showed differences in leaf shape and color, leaf and stem thickness, trichrome density, root length, plant height, and number of leaves compared to diploid plants. There was also a significant decrease in rosmarinic acid content in polyploid (plants) as compared to diploid plants. Although a significant decrease in ursolic acid content was observed in polyploids, betulinic acid content associated with the expression levels of genes encoding enzymes being active in triterpene biosynthesis such as squalene epoxidase (SQE) and lupeol synthase (LUS). The expression of SQE and LUS was significantly increased in in vitro tertaploids (2.9-fold) and in vivo mixoploids (2.4-fold). The results confirm the idea that induced polyploidy can randomly alter breeding traits of plants as well as the content of bioactive compounds

Induced polyploidy and broad variation in phytochemical traits and altered gene expression in Salvia multicaulis

Induced polyploidy is nowadays an important strategy in plant breeding and for the development of new crops. Salvia multicaulis Vahl is a valuable medicinal plant that produce precious bioactive metabolites including triterpenic acids (TAs) and phenolic compounds. Hence, at first, for selecting elite lines, both HPLC and GC-MC analyses were performed on fourteen S. multicaulis lines. Then, seeds of selected lines of S. multicaulis were exposed to different concentrations (0.00, 0.05, 0.1, and 0.2 %) of colchicine for 24 or 48 h. The flow cytometric analysis and chromosome counting were used to confirm ploidy level of tetraploid control (2n = 4x = 28, 2C DNA = 1.36 pg) and hexaploid (2n = 6x = 42, 2C DNA = 1.97 pg) plants after seven-month. For the first time, the effects of in vitro polyploidization on morphological characteristics, TAs and phenolic acid contents as well as on the expression of six TAs biosynthesis related genes were investigated. The highest efficiency of hexaploidy (12.76 %) was achieved 48 h after exposure to 0.1 % colchicine concentration. The hexaploid plants showed different growth traits compared with those of tetraploid control plant; indeed, hexaploid plants had leaves with a darker green color, a lower trichome density, and lower plant height and root length. Moreover, there was a significant increase in rosmarinic acid and caffeic acid content in hexaploid plants compared with tetraploid control plants. Also, the increase of oleanolic acid (1.33 fold) content in hexaploids was associated with a significant increased expression of squalene synthase (SQS) and β-amyrin synthase (BAS) genes in hexaploid plants. Nevertheless, a significant decreased expression of squalene epoxidase (SQE), mixed-function amyrin synthase (MFAS), and lupeol synthase (LUS) was observed in hexaploid plants, that led to a reduced content of ursolic acid and betulinic acid compared with tetraploid control plants. These results confirmed that polyploidization is a breeding method with stochastic results in secondary metabolites production and gene expression related to biosynthetic pathways

Phenolics diversity among wild populations of Salvia multicaulis: as a precious source for antimicrobial and antioxidant applications

The genus Salvia L. belongs to the Lamiaceae family including several known species rich in natural compounds that are extensively used in pharmaceutical, food, and cosmetic industries. Salvia multicaulis populations contain a broad diversity of flavonoids and phenolic acids. The present study aimed to explore biological and pharmacological effects including antimicrobial and antioxidant activities of nineteen S. multicaulis populations (SMPs) grown in Iran for the first time. High content of rosmarinic acid (RA) in SMP12 (Gazan) (5.65 ± 0.33 mg/g DW) caused high antimicrobial activity against two bacteria (Staphylococcus aureus, Escherichia coli) and the fungus Candida albicans, while methanolic extract of SMP1 (Taleghan) showed high antioxidant activity due to high content of salvianolic acid A (SAA) and quercetin (0.53 ± 0.04 and 0.49 ± 0.12 mg/g DW, respectively). Altogether these results can be considered for further commercial exploitations to meet the demands of the food and pharmaceutical industries

Correlated theory of triplet photoinduced absorption in phenylene-vinylene chains

In this paper we present results of large-scale correlated calculations of triplet photoinduced absorption (PA) spectrum of oligomers of poly-(para)phenylenevinylene (PPV) containing up to five phenyl rings. In particular, the high-energy features in the triplet PA spectrum of oligo-PPVs are the focus of this study, which, so far, have not been investigated theoretically, or experimentally. The calculations were performed using the Pariser-Parr-Pople (PPP) model Hamiltonian, and many-body effects were taken into account by means of multi-reference singles-doubles configuration interaction procedure (MRSDCI), without neglecting any molecular orbitals. The computed triplet PA spectrum of oligo-PPVs exhibits rich structure consisting of alternating peaks of high and low intensities. The predicted higher energy features of the triplet spectrum can be tested in future experiments. Additionally, theoretical estimates of exciton binding energy are also presented.Comment: To appear in Phys. Rev.

Prediction of infrared light emission from pi-conjugated polymers: a diagrammatic exciton basis valence bond theory

There is currently a great need for solid state lasers that emit in the infrared, as this is the operating wavelength regime for applications in telecommunications. Existing $\pi$--conjugated polymers all emit in the visible or ultraviolet, and whether or not $\pi$--conjugated polymers that emit in the infrared can be designed is an interesting challenge. On the one hand, the excited state ordering in trans-polyacetylene, the $\pi$--conjugated polymer with relatively small optical gap, is not conducive to light emission because of electron-electron interaction effects. On the other hand, excited state ordering opposite to that in trans-polyacetylene is usually obtained by chemical modification that increases the effective bond-alternation, which in turn increases the optical gap. We develop a theory of electron correlation effects in a model $\pi$-conjugated polymer that is obtained by replacing the hydrogen atoms of trans-polyacetylene with transverse conjugated groups, and show that the effective on-site correlation in this system is smaller than the bare correlation in the unsubstituted system. An optical gap in the infrared as well as excited state ordering conducive to light emission is thereby predicted upon similar structural modifications.Comment: 15 pages, 15 figures, 1 tabl

The Capillary Flow Experiments Aboard the International Space Station: Increments 9-15

This report provides a summary of the experimental, analytical, and numerical results of the Capillary Flow Experiment (CFE) performed aboard the International Space Station (ISS). The experiments were conducted in space beginning with Increment 9 through Increment 16, beginning August 2004 and ending December 2007. Both primary and extra science experiments were conducted during 19 operations performed by 7 astronauts including: M. Fincke, W. McArthur, J. Williams, S. Williams, M. Lopez-Alegria, C. Anderson, and P. Whitson. CFE consists of 6 approximately 1 to 2 kg handheld experiment units designed to investigate a selection of capillary phenomena of fundamental and applied importance, such as large length scale contact line dynamics (CFE-Contact Line), critical wetting in discontinuous structures (CFE-Vane Gap), and capillary flows and passive phase separations in complex containers (CFE-Interior Corner Flow). Highly quantitative video from the simply performed flight experiments provide data helpful in benchmarking numerical methods, confirming theoretical models, and guiding new model development. In an extensive executive summary, a brief history of the experiment is reviewed before introducing the science investigated. A selection of experimental results and comparisons with both analytic and numerical predictions is given. The subsequent chapters provide additional details of the experimental and analytical methods developed and employed. These include current presentations of the state of the data reduction which we anticipate will continue throughout the year and culminate in several more publications. An extensive appendix is used to provide support material such as an experiment history, dissemination items to date (CFE publication, etc.), detailed design drawings, and crew procedures. Despite the simple nature of the experiments and procedures, many of the experimental results may be practically employed to enhance the design of spacecraft engineering systems involving capillary interface dynamics

Accounting for both electron--lattice and electron--electron coupling in conjugated polymers: minimum total energy calculations on the Hubbard--Peierls hamiltonian

Minimum total energy calculations, which account for both electron--lattice and electron--electron interactions in conjugated polymers are performed for chains with up to eight carbon atoms. These calculations are motivated in part by recent experimental results on the spectroscopy of polyenes and conjugated polymers and shed light on the longstanding question of the relative importance of electron--lattice vs. electron--electron interactions in determining the properties of these systems.Comment: 6 pages, Plain TeX, FRL-PSD-93GR