RevelsMD: Reduced Variance Estimators of the Local Structure in Molecular Dynamics

RevelsMD is a new open source Python library, which uses reduced variance force sampling based estimators to calculate 3D particle densities and radial distribution functions from molecular dynamics simulations. This short note describes the scientific background of the code, its utility and how it fits within the current zeitgeist in computational chemistry and materials science.Comment: 3 page note describing an open source cod

A Cl- cotransporter selective for NH4+ over K+ in glial cells of bee retina

There appears to be a flux of ammonium (NH4+/NH3) from neurons to glial cells in most nervous tissues. In bee retinal glial cells, NH4+/NH3 uptake is at least partly by chloride-dependant transport of the ionic form NH4+. Transmembrane transport of NH4+ has been described previously on transporters on which NH4+ replaces K+, or, more rarely, Na+ or H+, but no transport system in animal cells has been shown to be selective for NH4+ over these other ions. To see if the NH4+-Cl− cotransporter on bee retinal glial cells is selective for NH4+ over K+ we measured ammonium-induced changes in intracellular pH (pHi) in isolated bundles of glial cells using a fluorescent indicator. These changes in pHi result from transmembrane fluxes not only of NH4+, but also of NH3. To estimate transmembrane fluxes of NH4+, it was necessary to measure several parameters. Intracellular pH buffering power was found to be 12 mM. Regulatory mechanisms tended to restore intracellular [H+] after its displacement with a time constant of 3 min. Membrane permeability to NH3 was 13 μm s−1. A numerical model was used to deduce the NH4+ flux through the transporter that would account for the pHi changes induced by a 30-s application of ammonium. This flux saturated with increasing [NH4+]o; the relation was fitted with a Michaelis-Menten equation with Km ≈ 7 mM. The inhibition of NH4+ flux by extracellular K+ appeared to be competitive, with an apparent Ki of ∼15 mM. A simple standard model of the transport process satisfactorily described the pHi changes caused by various experimental manipulations when the transporter bound NH4+ with greater affinity than K+. We conclude that this transporter is functionally selective for NH4+ over K+ and that the transporter molecule probably has a greater affinity for NH4+ than for K+

Accurate Estimation of Diffusion Coefficients and their Uncertainties from Computer Simulation

Self-diffusion coefficients, $D^*$, are routinely estimated from molecular dynamics simulations by fitting a linear model to the observed mean-squared displacements (MSDs) of mobile species. MSDs derived from simulation suffer from statistical noise, which introduces uncertainty in the resulting estimate of $D^*$. An optimal scheme for estimating $D^*$ will minimise this uncertainty, i.e., will have high statistical efficiency, and will give an accurate estimate of the uncertainty itself. We present a scheme for estimating $D^*$ from a single simulation trajectory with high statistical efficiency and accurately estimating the uncertainty in the predicted value. The statistical distribution of MSDs observable from a given simulation is modelled as a multivariate normal distribution using an analytical covariance matrix for an equivalent system of freely diffusing particles, which we parameterise from the available simulation data. We then perform Bayesian regression to sample the distribution of linear models that are compatible with this model multivariate normal distribution, to obtain a statistically efficient estimate of $D^*$ and an accurate estimate of the associated statistical uncertainty

Measuring agri-food supply chain performance: insights from the Peruvian kiwicha industry

Purpose: Agri-food firms face many challenges when assessing and managing their performance. The purpose of this research is to determine important factors for an integrated agri-food supply chain performance measurement system. Design/methodology/approach: This research uses the Peruvian kiwicha supply chain as a meaningful context to examine critical factors affecting agri-food supply chain performance. The research uses interpretative structural modelling (ISM) with fuzzy MICMAC methods to suggest a hierarchical performance measurement model. Findings: The resulting kiwicha supply chain performance management model provides insights for managers and academic theory regarding managing competing priorities within the agri-food supply chain. Originality/value: The model developed in this research has been validated by cooperative kiwicha associations based in Puno, Peru, and further refined by experts. Moreover, the results obtained through ISM and fuzzy MICMAC methods could help decision-makers from any agri-food supply chain focus on achieving high operational performance by integrating key performance measurement factors

Soybean production and conversion of tropical forest in the Brazilian Amazon: The case of Vilhena, Rondônia

The recent rise in Brazilian soybean production has generated concern among the environmental community and some authors that natural tropical environments of the Amazon Basin are being converted to soybean fields. Proponents of soybean production counter that soybeans represent a viable agricultural commodity for the region; environmental concern is unwarranted, because new soybean fields are replacing already deforested or otherwise transformed lands. Both arguments have been made without comprehensive study and measure of land-use/land-cover (LULC) in areas undergoing expansion of soybean production. This case study, conducted in the municipality of Vilhena, Rondônia, Brazil, in the southwestern Amazon Basin, uses remote sensing to evaluate the LULC accompanying this municipality's large growth in soybean production from 1996 to 2001. Forests are being converted for soybean production, but most of the production increase appears attributable to slight expansion of already existing fields, conversion of already deforested land, and higher yields

Strong exciton-photon coupling with colloidal nanoplatelets in an open microcavity

Colloidal semiconductor nanoplatelets exhibit quantum size effects due to their thickness of only few monolayers, together with strong optical band-edge transitions facilitated by large lateral extensions. In this article we demonstrate room temperature strong coupling of the light and heavy hole exciton transitions of CdSe nanoplatelets with the photonic modes of an open planar microcavity. Vacuum Rabi splittings of $66 \pm 1$ meV and $58 \pm 1$ meV are observed for the heavy and light hole excitons respectively, together with a polariton-mediated hybridisation of both transitions. By measuring the concentration of platelets in the film we compute the transition dipole moment of a nanoplatelet exciton to be $\mu = (575 \pm 110)$ D. The large oscillator strength and fluorescence quantum yield of semiconductor nanoplatelets provide a perspective towards novel photonic devices, combining polaritonic and spinoptronic effects.Comment: 9 pages, 4 figure