The rheology of chain molecules under shear

The rheology of chain molecules is a subject that comprises a wide variety of complex physical phenomena, challenging scientific questions, and fundamentally important practical applications. Computer simulation, molecular dynamics in particular, is a powerful tool to provide insight into these subjects on a molecular level. In this work, nonequilibrium molecular dynamics (NEMD) is employed to study linear and branched alkane chains in the melt state under transient and steady-state shearing conditions. This study focuses on three isomers of C30H62 (n-triacontane, squalane, and 9-n-octyldocosane) as well as a linear short-chain polyethylene (C100H202)- A transferable united atom potential is used to model these alkane chains, and the simulations of planar Couette flow are performed using the SLLOD algorithm and a multitimestep simulation technique implemented on massively parallel computer architectures. The strain rates studied in this work (108-1012 s-1) are extremely difficult to study experimentally yet typical of the severe conditions commonly found in engines and other machinery. Compared to experiment, NEMD and the united atom model underpredict the kinematic viscosities of n-triacontane and 9-n-octyldocosane but accurately predict the values for squalane (within 15%) at temperatures of 311 and 372 K. In addition, the predicted kinematic viscosity index values for both 9-n-octyldocosane and squalane are in quantitative agreement with experiment and represent the first such predictions by molecular simulation. Thus, this same general potential model and computational approach can be used to predict this important lubricant property for potential lubricants prior to their synthesis, offering the possibility of simulation guided lubricant design. Simulations of C100H202 under steady-state shearing conditions reveal a pronounced minimum in the hydrostatic pressure at an intermediate strain rate that is associated with a minimum in the intermolecular potential energy as well as transitions in the strain-rate-dependent behavior of several other viscous and structural properties of the system. Upon onset of shear, the stress overshoot curves calculated for C100 are in good quantitative agreement with Doi-Edwards theory if the terminal relaxation time is assumed to have the same strain-rate dependence as the calculated self-diffusion coefficient in the flow direction. This shear-enhanced diffusion offers a possible mechanism for strain-rate-dependent relaxation times in the fast flows of polymers

MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling

Background Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm. Results After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively. Conclusions MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base

Controls on vegetation structure in southwestern ponderosa pine forests, 1941 and 2004

Long-term studies can broaden our ecological understanding and are particularly important when examining contingent effects that involve changes to dominance by long-lived species. Such a change occurred during the last century in Southwestern (USA) ponderosa pine (Pinus ponderosa) forests. We used five livestock grazing exclosures established in 1912 to quantify vegetation structure in 1941 and 2004. Our objectives were to (1) assess the effects of historical livestock grazing on overstory structure and age distribution, (2) assess the effects of recent livestock grazing and overstory on understory vegetation, and (3) quantify and explain changes in understory vegetation between 1941 and 2004. In 1941, canopy cover of tree regeneration was significantly higher inside exclosures. In 2004, total tree canopy cover was twice as high, density was three times higher, trees were smaller, and total basal area was 40% higher inside exclosures. Understory species density, herbaceous plant density, and herbaceous cover were negatively correlated with overstory vegetation in both years. Most understory variables did not differ between grazing treatments in 1941 but were lower inside exclosures in 2004. Differences between grazing treatments disappeared once overstory effects were accounted for, indicating that they were due to the differential overstory response to historical livestock grazing practices. Between 1941 and 2004, species density declined by 34%, herbaceous plant density by 37%, shrub cover by 69%, total herbaceous cover by 59%, graminoid cover by 39%, and forb cover by 82%. However, these variables did not differ between grazing treatments or years once overstory effects were accounted for, indicating that the declines were driven by the increased dominance of the overstory during this period. Our results demonstrate that historical livestock grazing practices are an aspect of land-use history that can affect ecosystem development. Grazing history must be considered when extrapolating results from one site to another. In addition, the understory vegetation was more strongly controlled by the ponderosa pine overstory than by recent livestock grazing or by temporal dynamics, indicating that overstory effects must be accounted for when examining understory responses in this ecosystem

Archaeogenetic evidence of ancient Nubian barley evolution from six to two-row indicates local adaptation

Background Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years. Methodology and Findings We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure. Conclusions The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures

Effects of long-term livestock grazing and habitat on understory vegetation

The herbaceous understory stratum contains most of the plant diversity in ponderosa pine (Pinus ponderosa P. & C. Lawson var. scopulorum Engelm.) forests of the American Southwest and provides critical food and habitat for many wildlife species. During the last century, this stratum has been affected by livestock grazing and by increased dominance of overstory trees. We sampled a unique grazing exclosure to examine the relative importance of long-term livestock grazing (grazed or ungrazed) and habitat (park or tree) on the understory community. We sampled 3 plots of 192 contiguous quadrats (each quadrat 0.5 m2) in each of the 4 treatment combinations, for a total of 2304 quadrats. Species-area curves were generated by aggregating quadrats into nonoverlapping areas at grain sizes of 0.5 to 576 m2. The effects of habitat and grazing on species density were evident at very different scales. Species density was higher in park than tree plots at scales ≤32 m2 but did not differ between habitats at larger scales. Species density differed minimally between grazed and ungrazed treatments at small grains, but grazed plots contained more species than ungrazed plots at larger grains. Grazing treatments differed at smaller grains (to 4–8 m2) than did habitats (to 32 m2), with respect to density of native species and graminoids. Grazed plots had more exotic species than ungrazed plots at all grain sizes, though few exotics were present. Twenty-two species were identified as indicator species associated with habitats and/or grazing treatments. Evaluations of plant community response to treatments would be improved by accounting for the grain at which data have been collected and analyzed and by identifying indicator species associated with various treatments. These data would enable more-informed conservation and management decisions

Study protocol: computerised cognitive testing in a cohort of people with frontotemporal dementia

Introduction: The term frontotemporal dementia (FTD) refers to a heterogeneous group of neurodegenerative disorders affecting the frontal and temporal lobes. Cognitively, impairment of executive function and social cognition predominates across the FTD spectrum, although other domains can be affected. Traditionally, cognition is tested through standard ‘pen and paper’ tasks in FTD. However, recent attempts have been made across other neurodegenerative disorders such as Alzheimer’s disease to develop computerised batteries that allow more accurate and sensitive detection of cognitive impairment. / Methods and analysis: This paper describes the development of a novel battery of tests for a tablet computer, particularly focused on FTD. It consists of 12 different tasks which aim to tap into information processing speed, various aspects of executive function, social cognition, semantic knowledge, calculation and visuospatial skills. Future studies will focus on validating the battery in a healthy control cohort, comparing it against a standard ‘pen and paper’ psychometric battery, and finally testing it within an FTD cohort, including those with genetic forms of FTD where we will be able to assess its ability to detect very early cognitive deficits prior to the onset of symptoms. / Ethics and dissemination: Normative data will be produced in the initial validation study (approved by the UCL Ethics Committee, project ID 17691/002) and will be made available online

Long-term vegetation studies in the southwest

In this paper, we describe several long-term studies in the ponderosa pine (Pinus ponderosa) forests of the American Southwest, focusing on the unique insights and contributions of these studies. Many of the studies that we discuss were established by staff from the Fort Valley Experiment Station (FVES; http://www.rmrs.nau.edu/fortvalley/)