Acetylene chain reaction on hydrogenated boron nitride monolayers: a density functional theory study

Spin-polarized first-principles total-energy calculations have been performed to investigate the possible chain reaction of acetylene molecules mediated by hydrogen abstraction on hydrogenated hexagonal boron nitride monolayers. Calculations have been done within the periodic density functional theory (DFT), employing the PBE exchange correlation potential, with van der Waals corrections (vdW-DF). Reactions at two different sites have been considered: hydrogen vacancies on top of boron and on top of nitrogen atoms. As previously calculated, at the intermediate state of the reaction, when the acetylene molecule is attached to the surface, the adsorption energy is of the order of ?0.82 eV and ?0.20 eV (measured with respect to the energy of the non interacting molecule-substrate system) for adsorption on top of boron and nitrogen atoms, respectively. After the hydrogen abstraction takes place, the system gains additional energy, resulting in adsorption energies of ?1.52 eV and ?1.30 eV, respectively. These results suggest that the chain reaction is energetically favorable. The calculated minimum energy path (MEP) for hydrogen abstraction shows very small energy barriers of the order of 5 meV and 22 meV for the reaction on top of boron and nitrogen atoms, respectively. Finally, the density of states (DOS) evolution study helps to understand the chain reaction mechanism.

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Graphical abstract Acetylene chain reaction on hydrogenated boron nitride monolayers

     

Spin states of Mn(III) meso-tetraphenylporphyrin chloride assessed by density functional methods

The present work assessed several exchange-correlation functionals (including GGA, meta-GGA and hybrid functionals), in combination with a variety of basis sets and effective core potentials (ECP) for their ability to predict the ground spin state of Mn(III) meso-tetraphenylporphyrin chloride complex, labeled Mn(III)TPPCl, for which experimental data support the quintet high spin state. Geometry optimization of Mn(III)TPPCl was performed for three possible spin states (singlet state, LS; triplet state, IS; and quintet state, HS) at the TPSSh level using the LANL2DZ ECP for Mn and the 6-311G(d) basis set for C, N, Cl and H. Afterwards, single-point energy calculations were conducted by applying 18 exchange-correlation functionals (BLYP, B3LYP, PW91, BPW91, BP86, OLYP, OPBE, OPW91, O3LYP, PBE0, PBEh1PBE, HSEH1PBE, TPSS, TPSSh, M06 L, M06, M062X and M06HF). The influence of the basis set for the metal center was assessed using a smaller group of functionals and varying between the Pople basis set 6-31G(d), its newer formulation m6-31G(d) and the larger Def2-QZVP basis set. All functionals in combination with Pople basis sets predict the quintet state as the ground spin state. In addition, the BLYP, BP86, BPW91, PW91, PBEh1PBE, TPSS and TPSSh functionals predicted the IS lying at most ~60 kJ mol^?1 above the HS, which agrees with the reference data. Results including Def2-QZVP basis set were inconsistent, since only BLYP and B3LYP predict HS as the ground spin state. The recommended methodology for the treatment of such systems seems to be exchange-correlations functionals with few or none Hartree-Fock exchange and modest size basis sets.

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Graphical Abstract MnTPPCl molecule and the energy ordering of its spin states assessed by 18 functionals

     

Learning the deformation mechanism of poly(vinylidine fluoride-co-chlorotrifluoroethylene): an insight into strain-induced microstructure evolution via molecular dynamics

Learning the micro-mechanisms of fluorinated polymers during mechanical response is more difficult than that of common polymers due to the unique intrinsic characteristics of the fluorine element. In this paper, we applied molecular dynamics simulations to study deformation mechanisms of poly(vinylidine fluoride-co-chlorotrifluoroethylene) during uniaxial tension. We analyzed the variations of individual energy components and structural distribution curves versus strain in addition to the commonly used stress-strain curves and microstructure evolutions during stretching. The elastic limit is ??=?0.02, ??=?0.06 is the yield point, ??=?0.24 is the termination of the softening, necking occurs at 0.24?<???<?0.5, strain hardening occurs at 0.5?<???<?2.6, and ??=?2.6 is the damage or brake point. The elastic behavior of the material does not rely on strain rate, the obvious effect of strain rate can be seen at the yield region and strain softening region, and the stress values are not influenced by strain rates at the softening and hardening stages. Overall, total potential energy is mainly correlated with non-bonded energy, and the proportion of ΔE_coul overwhelms all the others. The energy components are ordered: ΔE_coul?>?ΔE_vdwl >?>?ΔE_angle?>?ΔE_dihed?>?ΔE_bond. The chain conformation at yield point is almost unchanged compared with the pre-stretching conformation. The chain conformations at the end of strain softening changes more obviously than that at yield point. The molecular chains maintain random coil structure before strain hardening, and switch into a stretch chain conformation gradually during strain hardening. The maximum change in bond angle during the stretching process is F-C-H, the largest change in bond length is the C-Cl bond, and the largest change in dihedral angle is H-C-C-H. The change of non-bonded interaction in the poly(VDF-co-CTFE) system is much larger than the bonding interaction, and the main factor affecting bonding interaction is the change of angles.

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Graphical abstract Poly(vinylidine fluoride-co-chlorotrifluoroethylene) during tension?

     

Link between generalized nonidempotency and complexity measures

The nonidempotency measure of Löwdin is found to be proportional to the disequilibrium. It is shown that there exists a simple relationship between the LMC (López-Ruiz–Mancini–Calbet) and the generalized statistical complexities and the generalized nonidempotency measure of Löwdin. Results are illustrated for an exactly solvable two-electron model atom.     

Exploration of the binding affinities between ecdysone agonists and EcR/USP by docking and MM-PB/GBSA approaches

Ecdysone receptor (EcR) is a significant target in the identification of new environmentally friendly pesticides. There are two types of ecdysone agonists: steroidal ecdysone agonists and dibenzoylhydrazines (DBHs). In this study, various modeling methods (homology modeling, molecular docking, MD simulation, binding free energy calculation, and per-residue binding free energy decomposition) were utilized to study the different binding mechanisms of two types of ecdysone agonists. Our theoretical results indicated that the relative binding potencies of DBHs can be ranked sufficiently accurately using the MOE docking method. However, MM/PBSA calculations more accurately predicted the binding affinities between steroidal ecdysone agonists and EcR-LBD. To identify the key residues involved in ecdysone agonist binding, the binding free energy (ΔG _Bind) was decomposed into the energy contributions of individual residues. The results revealed that nine residues—Ile339, Thr343, Met380, Met381, Tyr403, Tyr408, Asp419, Gln503, and Asn504—determined the binding affinities of the DBHs. Glu309, Met342, Arg383, Arg387, and Leu396 were important influences on the binding affinities of the steroidal ecdysone agonists.

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Graphical abstract The ecdysone receptor (EcR) is related to insect growth and has been shown to be a useful target for insecticides

     

Mathematical deconvolution uncovers the genetic regulatory signal of cancer cellular heterogeneity on resistance to paclitaxel

Drug resistance remains a major problem in combating malignancies, resulting critical the resistance to paclitaxel used in the treatment of many different cancers. Elucidating the cellular heterogeneity composition of tumours may be relevant to designing more effective treatment strategies on drug resistance. In particular, such heterogeneity correlates with the measurement of gene expression below the population level. However, experimental assays capturing differential response are limited and cannot discern the variation in gene expression specific to different cellular types in tumour populations. These limitations led us to consider a mathematical modelling approach, in which the gene expression of cellular subpopulations is recovered by deconvolution. Mathematically, the deconvolution is a multi-linear regression-based problem. We combined herein data on cellular subpopulation frequency composition with gene expression values from 16 tumour lines (8 resistant and 8 sensitive to paclitaxel treatment) to find genes that are differentially expressed between paclitaxel resistant and paclitaxel sensitive tumour lines in different cellular subpopulations. The results indicate that many genes differentially expressed between paclitaxel resistant and sensitive cancer lines are only detected when considering their heterogeneous cellular composition. Overall, our methodology is thought to keep in mind phenotypic heterogeneity improving our resolution in the identification of biomarkers on resistance to chemo-therapeutic agents.     

<Emphasis Type="Italic">Sex combs reduced</Emphasis> (<Emphasis Type="Italic">Scr</Emphasis>) regulatory region of <Emphasis Type="Italic">Drosophila</Emphasis> revisited

The Hox gene Sex combs reduced (Scr) is responsible for the differentiation of the labial and prothoracic segments in Drosophila. Scr is expressed in several specific tissues throughout embryonic development, following a complex path that must be coordinated by an equally complex regulatory region. Although some cis-regulatory modules (CRMs) have been identified in the Scr regulatory region (~75 kb), there has been no detailed and systematic study of the distinct regulatory elements present within this region. In this study, the Scr regulatory region was revisited with the aim of filling this gap. We focused on the identification of Initiator elements (IEs) that bind segmentation factors, Polycomb response elements (PREs) that are recognized by the Polycomb and Trithorax complexes, as well as insulators and tethering elements. To this end, we summarized all currently available information, mainly obtained from high throughput ChIP data projects. In addition, a bioinformatic analysis based on the evolutionary conservation of regulatory sequences using the software MOTEVO was performed to identify IE and PRE candidates in the Scr region. The results obtained by this combined strategy are largely consistent with the CRMs previously identified in the Scr region and help to: (i) delimit them more accurately, (ii) subdivide two of them into different independent elements, (iii) identify a new CRM, (iv) identify the composition of their binding sites and (v) better define some of their characteristics. These positive results indicate that an approach that integrates functional and bioinformatic data might be useful to characterize other regulatory regions.     

Utility of traditional and alternative EMG-based measures of fatigue during low-moderate level isometric efforts.

Traditional electromyographic (EMG) measures (e.g., amplitude, mean and median frequencies of the power spectra) have demonstrated inconsistent abilities in monitoring localized muscle fatigue at relatively low effort levels. In the present study, several alternative EMG-based fatigue indices were evaluated, derived using a logarithmic representation of the power spectrum, the fractal dimension of the raw signal, and a Poisson distribution fit to the power spectrum. These methods, along with traditional approaches, were applied to EMG data obtained from three separate experiments. In the first two experiments, 24 participants performed sustained isometric shoulder abductions and torso extensions at 30% of maximum voluntary strength (MVC). In the third experiment, another group of 12 participants performed similar shoulder exercises at 15% and 30% MVC, with repeatability assessed at 15% MVC. Both traditional and alternative EMG measures were analyzed for their 'utility', in terms of sensitivity to fatigue, variability, repeatability, and predictive ability. Results demonstrated that parameters derived from fractal analysis and the Poisson distribution demonstrated high utility. These alternative approaches appear promising as fatigue indices for low level isometric tasks.     

Deletion of many yeast introns reveals a minority of genes that require splicing for function

Splicing regulates gene expression and contributes to proteomic diversity in higher eukaryotes. However, in yeast only 283 of the 6000 genes contain introns and their impact on cell function is not clear. To assess the contribution of introns to cell function, we initiated large-scale intron deletions in yeast with the ultimate goal of creating an intron-free model eukaryote. We show that about one-third of yeast introns are not essential for growth. Only three intron deletions caused severe growth defects, but normal growth was restored in all cases by expressing the intronless mRNA from a heterologous promoter. Twenty percent of the intron deletions caused minor phenotypes under different growth conditions. Strikingly, the combined deletion of all introns from the 15 cytoskeleton-related genes did not affect growth or strain fitness. Together, our results show that although the presence of introns may optimize gene expression and provide benefit under stress, a majority of introns could be removed with minor consequences on growth under laboratory conditions, supporting the view that many introns could be phased out of Saccharomyces cerevisiae without blocking cell growth.     

Does a short period of lower limb strength training improve performance in field-based tests of running and agility in young professional soccer players?

The present study assessed the effects of specific leg strength training (as part of a broader exercise program) on running speed and agility in young professional soccer players. Twenty-six male players (ages 17 to 19 years) were divided into 3 groups. The reference group (Re) performed individual technical work only, the coordination group (Co) performed a circuit designed to promote agility, coordination, and balance control (together with some technical work) and the Squat group (Sq) underwent 3 series of 3 squat repetitions (at 90% of the individual maximum value) and a sprint, before competition of the agility circuit and some technical work. These specific training programs were performed 5 times a week for 3 weeks. Before the experimental session and at the end of each week, all players were assessed using 4 types of tests, (agility, a shuttle test with changes of direction, and 2 sprints over 10 and 7.32 meters, respectively), with completion time being the only performance parameter recorded. Our results indicate that in the short sprints or shuttle sprint with changes in direction, lower limb strengthening did not improve performance. Performance improved in all 3 groups in the agility test but more so in the reference and coordination groups. It appears that soccer-specific training composed of exercise circuits specifically adapted to the different types of effort actually used in match play can enhance agility and coordination.