Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations

Recently developed synthetic membrane pores composed of folded DNA enrich the current range of natural and engineered protein pores and of nonbiogenic channels. Here we report all-atom molecular dynamics simulations of a DNA nanotube (DNT) pore scaffold to gain fundamental insight into its atomic structure, dynamics, and interactions with ions and water. Our multiple simulations of models of DNTs that are composed of a six-duplex bundle lead to a coherent description. The central tube lumen adopts a cylindrical shape while the mouth regions at the two DNT openings undergo gating-like motions which provide a possible molecular explanation of a lower conductance state observed in our previous experimental study on a membrane-spanning version of the DNT (ACS Nano 2015, 9, 1117-26). Similarly, the central nanotube lumen is filled with water and ions characterized by bulk diffusion coefficients while the gating regions exhibit temporal fluctuations in their aqueous volume. We furthermore observe that the porous nature of the walls allows lateral leakage of ions and water. This study will benefit rational design of DNA nanopores of enhanced stability of relevance for sensing applications, of nanodevices with tunable gating properties that mimic gated ion channels, or of nanopores featuring defined permeation behavior

Household Livelihoods, Marketing And Resource Impacts: A Case Study Of Bark Products In Eastern Zimbabwe

An IES Working Paper.The bark of Warburgia salutaris, locally known as muranga, is a medicine of great traditional significance in Zimbabwe. However, trees of this species are at or near extinction in the wild in Zimbabwe. In this paper, the economics of the re-introduction of this rare medicinal species in some relatively moist, high altitude sites in south-eastern Zimbabwe are examined. The analysis builds on the information base provided by a recent pilot project of Warburgia re-introduction, as well as on market price data from a survey of current medicinal bark markets and on assumptions regarding the prospective future production and use of Warburgia leaves and bark by farmers and healers. The economic analysis, strongly suggests that expanded Warburgia production, at least on a small scale, in the remote, hilly region of southeastern Zimbabwe is very economically attractive and conducive to improving rural incomes and livelihoods of small-holders. This conclusion holds true in private feasibility terms, for both small-scale farmers and healer-growers, and in terms of social cost benefit analysis wherein seedling subsidies are removed.Funding for the study was provided by Canadian International Development Agency (CIDA) through the Agro-forestry Southern Africa project and the World Wide Fund for Nature (WWF) People and Plants Initiative

Evaluation of a modified multipurpose cassava processing machine for size reduction

The production of cassava (Manihot esculenta) is considered an important alternative to a reduction in food scarcity around the world. Kenya is rapidly gaining prominence due to the declining production of staple foods, especially maize and wheat. Though still considered a poor man’s food, the usage of cassava has greatly diversified in terms of both industrial and domestic applications. This coupled with the introduction of improved varieties and better farming options calls for innovative ways of handling the increasing volumes of fresh cassava tubers to minimize post-harvest losses. One of the important postharvest processes is size reduction which is achieved by either chipping or grating. Improved production methods alone are not adequate to solve the issues of field losses in cassava production. Factors affecting the efficiency of size reduction operation include operator experience, disc type, disc speed, cutting clearance and moisture content. Conventionally, this has been done manually but due to the inherent problems, the use of machines is being encouraged through the development and adoption of chipping/grating machines. In this study, the machine developed was dual-powered and allowed conversion from a chipper to a grater and vice versa as need be. It has a capacity of 162.15kg/h and 81.62 kg/h when chipping and grating respectively. The chipping process consumed less power averaging 0.0034 kW/kg compared to 0.0075 kW/kg used in the grating and these chips dried faster than manually worked cassava. Keywords: Cassava, post-harvest, chipping, grating, dual power DOI: 10.7176/ISDE/13-1-06 Publication date:June 30th 202

Evaluation of a Modified Multipurpose Cassava Processing Machine for Size Reduction

The production cassava (Manihot esculenta) is considered an important alternative to reduction in food scarcity around the world. In Kenya, it is rapidly gaining prominence due to the declining production of staple foods, especially maize and wheat. Though still considered a poor man’s food, the usage of cassava has greatly diversified in terms of both industrial and domestic applications. This coupled with the introduction of improved varieties and better farming options calls for innovative ways of handling the increasing volumes of fresh cassava tubers to minimize post-harvest losses. One of the important postharvest processes is size reduction which is achieved by either chipping or grating. Improved production methods alone are not adequate to solve the issues of field losses in cassava production. Factors affecting the efficiency of size reduction operation include operator experience, disc type, disc speed, cutting clearance and moisture content. Conventionally, this has been done manually but due to the inherent problems, use of machines is being encouraged through the development and adoption of chipping/grating machines. In this study the machine developed was dual powered and allowed conversion from a chipper to grater and vice versa as need be. It has a capacity of 162.15kg/h and 81.62 kg/h when chipping and grating respectively. The chipping process consumed less power averaging 0.0034kW/kg compared to 0.0075 kW/kg used in the grating and these chips dried faster than manually worked cassava. Keywords: Cassava, post-harvest, chipping, grating, dual power DOI: 10.7176/JBAH/13-8-03 Publication date:May 31st 202

UV femtosecond laser cleaning of encrusted historical stained-glasses

Laser irradiation enables the removal of unwanted surface deposits from different materials in a safe and controllable manner. Laser parameters should be carefully selected to achieve the removal of the target contaminants without inducing damage to the substrate. Ultra-short pulse lasers have opened new opportunities for safe and controlled decontamination of cultural heritage materials because the thickness of material that is affected by the laser is limited. In this study, an ultraviolet femtosecond pulsed laser was used for the removal of unwanted encrustation formed on the surface of an historical colourless stained-glass sample from the Cuenca Cathedral in Spain. One of the sides of this glass exhibits a reddish-brown grisaille that also has to be preserved. A laser cleaning process has been designed to avoid heat accumulation while controlling the thickness of ablated material. In this context, a multi-step process was selected in order to be able to eliminate, in a controlled way, the crust layer without damaging the grisaille layer, or the glass substrate. In this case, laser irradiation in beam scanning mode with a pulse repetition frequency of 10 kHz proved to be effective for the safe cleaning of the glass. The latter was analysed before and after laser cleaning by optical and confocal microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, X-ray fluorescence, and Raman spectroscopy, confirming that the crust layer was effectively eliminated without damaging the surface

L-H Mode Transitions in the National Spherical Torus Experiment

Edge data from plasmas in the National Spherical Torus Experiment (NSTX) [S. Kaye et al., Fusion Technology 36 (1999) 16] have been compared to theories of transport suppression that have been used to develop a physics framework for low-confinement (L) to high-confinement (H) mode transitions. The NSTX data were obtained in low aspect ratio (R/a approximately equal to 1.3) discharges taken from a variety of discharge phases, including L-modes, L-H transitions, and H-modes with and without edge localized modes (ELMs). The comparisons show that the group of points taken just before the L-H mode transition are well mixed with the purely L-mode group to within the measurement uncertainties, indicating that changes in these parameters leading up to the transition are subtle. One of the theory parameters, alpha{sub MHD} = -R{sub q}{sup 2}dbeta{sub t/dr}, does show a clear threshold alpha{sub MHD} = 1 to 2 between the H-mode grouping of points and those remaining in the L-mode or taken just prior to the transition. Additionally, there is no evidence for an edge temperature threshold necessary for transitioning into the H-mode. NSTX data indicate further a possible connection between L-H transitions and non-ambipolar beam ion losses

Practical computational toolkits for dendrimers and dendrons structure design

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface (GUI) toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.Peer reviewe

Modeling of lithium granule injection in NSTX using M3D-C1

In this paper, we present simulations of pedestal control by lithium granule injection (LGI) in NSTX. A model for small granule ablation has been implemented in the M3D-C1 code (Jardin et al 2012 Comput. Sci. Discovery 5 014002), allowing the simulation of realistic lithium granule injections. 2D and 3D simulations of Li injections in NSTX H-mode plasmas are performed and the effect of granule size, injection angle and velocity on the pedestal gradient increase is studied. The amplitude of the local pressure perturbation caused by the granules is found to be highly dependent on the solid granule size. Adjusting the granule injection velocity allows one to inject more particles at the pedestal top. 3D simulations show the destabilization of high order MHD modes whose amplitude is directly linked to the localized pressure perturbation, which is found to depend on the toroidal localization of the granule density source