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1.
David Dubbeldam Sofía Calero Donald E. Ellis Randall Q. Snurr 《Molecular simulation》2016,42(2):81-101
A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License. 相似文献
2.
Faster running is not performed with proportional increase in all joint torque/work exertions. Although previous studies have investigated lumbopelvic kinetics for a single velocity, it is unclear whether each lumbopelvic torque should increase for faster running. We examined the relationship between running velocity and lumbopelvic kinetics. We calculated the three-dimensional lumbosacral kinetics of 10 male sprinters during steady-state running on a temporary indoor running track at five target velocities: 3.0 (3.20 ± 0.16), 4.5 (4.38 ± 0.18), 6.0 (5.69 ± 0.47), 7.5 (7.30 ± 0.41), and maximal sprinting (9.27 ± 0.36 m/s). The lumbosacral axial rotation torque increased more markedly (from 0.37 ± 0.06 to 1.99 ± 0.46 Nm/kg) than the extension and lateral flexion torques. The increase in the axial rotation torque was larger above 7.30 m/s. Conversely, the extension and lateral flexion torques plateaued when running velocity increased above 7.30 m/s. Similar results were observed for mechanical work. The results indicate that faster running required larger lumbosacral axial rotation torque. Conversely, the extension and lateral flexion torques were relatively invariant to running velocity above 7 m/s, implying that faster running below 7 m/s might increase the biomechanical loads causing excessive pelvic posterior tilt and excessive pelvic drop which has the potential to cause pain/injury related to lumbopelvic extensors and lateral flexors, whereas these biomechanical loads might not relate with running velocity above 7 m/s. 相似文献
3.
Mykola Isaiev Sergii Burian Leonid Bulavin Michel Gradeck Fabrice Lemoine Konstantinos Termentzidis 《Molecular simulation》2016,42(11):910-915
Spherical and cylindrical water droplets on silicon surface are studied to tune the silicon–oxygen interaction. We use molecular dynamics simulations to estimate the contact angle of two different shaped droplets. We found that the cylindrical droplets are independent of the line tension as their three phases curvature is equal zero. Additionally, we compare an analytical model, taking into account or not the Tolman length and we show that for spherical small size droplets, this length is important to be included, in contrast to cylindrical droplets in which the influence of the Tolman length is negligible. We demonstrate that the usual convenient way to exclude linear tension in the general case can give wrong results. Here, we consider cylindrical droplets, since their contact angle does not depend on the droplet size in the range of few to 10ths of nanometres. The droplets are stabilised due to the periodic boundary conditions. This allows us to propose a new parameterisation for nanoscale droplets, which is independent the size of the droplets or its shape, minimising at the same time the calculation procedure. With the proposed methodology, we can extract the epsilon parameter of the interaction potential between a liquid and a solid from the nanoscaled molecular simulation with only as input the macrosized experimental wetting angle for a given temperature. 相似文献
4.
Butana and Kenana breeds from Sudan are part of the East African zebu Bos indicus type of cattle. Unlike other indigenous zebu cattle in Africa, they are unique due to their reputation for high milk production and are regarded as dairy cattle, the only ones of their kind on the African continent. In this study, we sequenced the complete mitochondrial DNA (mtDNA) D‐loop of 70 animals to understand the maternal genetic variation, demographic profiles and history of the two breeds in relation to the history of cattle pastoralism on the African continent. Only taurine mtDNA sequences were identified. We found very high mtDNA diversity but low level of maternal genetic structure within and between the two breeds. Bayesian coalescent‐based analysis revealed different historical and demographic profiles for the two breeds, with an earlier population expansion in the Butana vis a vis the Kenana. The maternal ancestral populations of the two breeds may have diverged prior to their introduction into the African continent, with first the arrival of the ancestral Butana population. We also reveal distinct demographic history between the two breeds with the Butana showing a decline in its effective population size (Ne) in the recent past ~590 years. Our results provide new insights on the early history of cattle pastoralism in Sudan indicative of a large ancient effective population size. 相似文献
5.
Conservation genetics considerations in fishery management 总被引:1,自引:0,他引:1
N. Ryman 《Journal of fish biology》1991,39(SA):211-224
6.
Aina Hazimah Bahaman Azzmer Azzar Abdul Hamid Khairul Bariyyah Abd Halim Yilmaz Kaya Mohamed Faraj Edbeib 《Journal of biomolecular structure & dynamics》2020,38(14):4246-4258
Abstract Fungi of the Trichoderma species are valued industrial enzymes in support of the ‘zero-waste’ technology to convert agro-industrial biomass into valuable products, i.e. nanocellulose (NC). In this study, an in silico approach using substrate docking and molecular dynamic (MD) simulation was used to predict the order of which the multilayers of cellulosic polymers, i.e. lignin, hemicellulose and cellulose in oil palm leaves (OPL) are degraded by fungal enzymes, endocellulase and exocellulase. The study aimed to establish the catalytic tendencies of the enzymes to optimally degrade the cellulosic components of OPL for high yield production of NC. Energy minimized endocellulase and exocellulase models revealed satisfactory scores of PROCHECK (90.0% and 91.2%), Verify3D (97.23% and 98.85%) and ERRAT (95.24% and 91.00%) assessments. Active site prediction by blind docking, COACH meta-server and multiple sequence alignment indicated the catalytic triads for endocellulase and exocellulase were Ser116–His205–Glu249 and Ser382–Arg124–Asp385, respectively. Binding energy of endocellulase docked with hemicellulose (?6.0 ? kcal mol?1) was the most favourable followed by lignin (?5.6 ? kcal mol?1) and cellulose (?4.4 ? kcal mol?1). Exocellulase, contrarily, bonded favorably with lignin (?8.7 ? kcal mol?1), closely followed by cellulose (?8.5 ? kcal mol?1) and hemicellulose (?8.4 ? kcal mol?1). MDs simulations showed that interactions of complexes, endocellulase–hemicellulose and the exocellulase–cellulose being the most stable. Thus, the findings of the study successfully identified the specific actions of sugar-acting enzymes for NC production. Communicated by Ramaswamy H. Sarma 相似文献
7.
8.
We used water-soluble styryl pyridinium dyes that fluoresce at the membrane-water interface to study vesicle traffic in endothelial
cells. Cultured endothelial cells derived from bovine and human pulmonary microvessels were incubated in styryl probes, washed
to remove dye from the plasmalemmal outer face, and observed by digital fluorescence microscopy. Vesicles that derived from
plasmalemma by endocytosis were filled with the styryl dye. These vesicles were distributed throughout the cytosol as numerous
particles of heterogeneous diameter and brightness. Vesicle formation was activated 2-fold following addition of extracellular
albumin whereas a control protein, immunoglobulin G, had no effect. Dye uptake was abrogated by labeling at low temperatures
and inhibitors of phosphoinositide-3-kinase (PI 3-kinase). Tyrosine kinase inhibitors (genistein and herbimycin A) prevented
the albumin-induced vesicle formation. Cytochalasin B prevented vesicle redistribution indicating involvement of actin filaments
in translocation of endosomes away from sites of vesicle formation. Styryl dye was lost from cells by exocytosis as evident
by the disappearance of discrete fluorescent particles. N-ethylmaleimide and botulinum toxin types A and B caused cells to accumulate increased number of vesicles suggesting that exocytosis was regulated by NSF-dependent
SNARE mechanism. The results suggest that phosphoinositide metabolism regulates endocytosis in endothelial cells and that
extracellular albumin activates endocytosis by a mechanism involving tyrosine phosphorylation, whereas exocytosis is a distinct
process regulated by the SNARE machinery. The results support the hypothesis that albumin regulates its internalization and
release in vascular endothelial cells via activation of specific endocytic and exocytic pathways. 相似文献
9.
Ryan J. Haasl Bret A. Payseur 《Evolution; international journal of organic evolution》2014,68(9):2737-2744
Long dinucleotide repeats found in exons present a substantial mutational hazard: mutations at these loci occur often and generate frameshifts. Here, we provide clear and compelling evidence that exonic dinucleotides experience strong selective constraint. In humans, only 18 exonic dinucleotides have repeat lengths greater than six, which contrasts sharply with the genome‐wide distribution of dinucleotides. We genotyped each of these dinucleotides in 200 humans from eight 1000 Genomes Project populations and found a near‐absence of polymorphism. More remarkably, divergence data demonstrate that repeat lengths have been conserved across the primate phylogeny in spite of what is likely considerable mutational pressure. Coalescent simulations show that even a very low mutation rate at these loci fails to explain the anomalous patterns of polymorphism and divergence. Our data support two related selective constraints on the evolution of exonic dinucleotides: a short‐term intolerance for any change to repeat length and a long‐term prevention of increases to repeat length. In general, our results implicate purifying selection as the force that eliminates new, deleterious mutants at exonic dinucleotides. We briefly discuss the evolution of the longest exonic dinucleotide in the human genome—a 10 x CA repeat in fibroblast growth factor receptor‐like 1 (FGFRL1)—that should possess a considerably greater mutation rate than any other exonic dinucleotide and therefore generate a large number of deleterious variants. 相似文献
10.