A bodner-partom visco-plastic dynamic sphere benchmark problem

Developing benchmark analytic solutions for problems in solid and fluid mechanics is very important for the purpose of testing and verifying computational physics codes. Our primary objective in this research is to obtain a benchmark analytic solution to the equation of motion in radially symmetric spherical coordinates. An analytic solution for the dynamic response of a sphere composed of an isotropic visco-plastic material and subjected to spherically symmetric boundary conditions is developed and implemented. The radial displacement u is computed by solving the equation of motion, a linear second-order hyperbolic PDE. The plastic strains εp and εp are computed by solving two non-linear first-order ODEs in time. We obtain a solution for u in terms of the plastic strain components and boundary conditions in the form of an infinite series. Computationally, at each time step, we set up an iteration scheme to solve the PDE-ODE system. The linear momentum equation is solved using the plastic strains from the previous iteration, then the plastic strain equations are solved numerically using the new displacement. We demonstrate the accuracy and convergence of our benchmark solution under spatial mesh, time step, and eigenmode refinement

Multiple Concentric Cylinder Model (MCCM) user's guide

A user's guide for the computer program mccm.f is presented. The program is based on a recently developed solution methodology for the inelastic response of an arbitrarily layered, concentric cylinder assemblage under thermomechanical loading which is used to model the axisymmetric behavior of unidirectional metal matrix composites in the presence of various microstructural details. These details include the layered morphology of certain types of ceramic fibers, as well as multiple fiber/matrix interfacial layers recently proposed as a means of reducing fabrication-induced, and in-service, residual stress. The computer code allows efficient characterization and evaluation of new fibers and/or new coating systems on existing fibers with a minimum of effort, taking into account inelastic and temperature-dependent properties and different morphologies of the fiber and the interfacial region. It also facilitates efficient design of engineered interfaces for unidirectional metal matrix composites

Optimization of Residual Stresses in MMC's Using Compensating/Compliant Interfacial Layers. Part 2: OPTCOMP User's Guide

A user's guide for the computer program OPTCOMP is presented in this report. This program provides a capability to optimize the fabrication or service-induced residual stresses in uni-directional metal matrix composites subjected to combined thermo-mechanical axisymmetric loading using compensating or compliant layers at the fiber/matrix interface. The user specifies the architecture and the initial material parameters of the interfacial region, which can be either elastic or elastoplastic, and defines the design variables, together with the objective function, the associated constraints and the loading history through a user-friendly data input interface. The optimization procedure is based on an efficient solution methodology for the elastoplastic response of an arbitrarily layered multiple concentric cylinder model that is coupled to the commercial optimization package DOT. The solution methodology for the arbitrarily layered cylinder is based on the local-global stiffness matrix formulation and Mendelson's iterative technique of successive elastic solutions developed for elastoplastic boundary-value problems. The optimization algorithm employed in DOT is based on the method of feasible directions

The Structure of β-Carbonic Anhydrase from the Carboxysomal Shell Reveals a Distinct Subclass with One Active Site for the Price of Two

CsoSCA (formerly CsoS3) is a bacterial carbonic anhydrase localized in the shell of a cellular microcompartment called the carboxysome, where it converts HCO-3 to CO2 for use in carbon fixation by ribulose-bisphosphate carboxylase/oxygenase (RuBisCO). CsoSCA lacks significant sequence similarity to any of the four known classes of carbonic anhydrase (α, β, γ, or δ), and so it was initially classified as belonging to a new class, ϵ. The crystal structure of CsoSCA from Halothiobacillus neapolitanus reveals that it is actually a representative member of a new subclass of β-carbonic anhydrases, distinguished by a lack of active site pairing. Whereas a typical β-carbonic anhydrase maintains a pair of active sites organized within a two-fold symmetric homodimer or pair of fused, homologous domains, the two domains in CsoSCA have diverged to the point that only one domain in the pair retains a viable active site. We suggest that this defunct and somewhat diminished domain has evolved a new function, specific to its carboxysomal environment. Despite the level of sequence divergence that separates CsoSCA from the other two subclasses of β-carbonic anhydrases, there is a remarkable level of structural similarity among active site regions, which suggests a common catalytic mechanism for the interconversion of HCO-3 and CO2. Crystal packing analysis suggests that CsoSCA exists within the carboxysome shell either as a homodimer or as extended filaments

Structural Analysis of CsoS1A and the Protein Shell of the \u3ci\u3eHalothiobacillus neapolitanus\u3c/i\u3e Carboxysome

The carboxysome is a bacterial organelle that functions to enhance the efficiency of CO2 fixation by encapsulating the enzymes ribulose bisphosphate carboxylase/ oxygenase (RuBisCO) and carbonic anhydrase. The outer shell of the carboxysome is reminiscent of a viral capsid, being constructed from many copies of a few small proteins. Here we describe the structure of the shell protein CsoS1A from the chemoautotrophic bacterium Halothiobacillus neapolitanus. The CsoS1A protein forms hexameric units that pack tightly together to form a molecular layer, which is perforated by narrow pores. Sulfate ions, soaked into crystals of CsoS1A, are observed in the pores of the molecular layer, supporting the idea that the pores could be the conduit for negatively charged metabolites such as bicarbonate, which must cross the shell. The problem of diffusion across a semiporous protein shell is discussed, with the conclusion that the shell is sufficiently porous to allow adequate transport of small molecules. The molecular layer formed by CsoS1A is similar to the recently observed layers formed by cyanobacterial carboxysome shell proteins. This similarity supports the argument that the layers observed represent the natural structure of the facets of the carboxysome shell. Insights into carboxysome function are provided by comparisons of the carboxysome shell to viral capsids, and a comparison of its pores to the pores of transmembrane protein channels

Random Walks for Spike-Timing Dependent Plasticity

Random walk methods are used to calculate the moments of negative image equilibrium distributions in synaptic weight dynamics governed by spike-timing dependent plasticity (STDP). The neural architecture of the model is based on the electrosensory lateral line lobe (ELL) of mormyrid electric fish, which forms a negative image of the reafferent signal from the fish's own electric discharge to optimize detection of sensory electric fields. Of particular behavioral importance to the fish is the variance of the equilibrium postsynaptic potential in the presence of noise, which is determined by the variance of the equilibrium weight distribution. Recurrence relations are derived for the moments of the equilibrium weight distribution, for arbitrary postsynaptic potential functions and arbitrary learning rules. For the case of homogeneous network parameters, explicit closed form solutions are developed for the covariances of the synaptic weight and postsynaptic potential distributions.Comment: 18 pages, 8 figures, 15 subfigures; uses revtex4, subfigure, amsmat

Climate Smart Agriculture in the African Context

Agriculture remains vital to the economy of most African countries and its development has significant implications for food security and poverty reduction in the region. Increase in agricultural production over the past decades has mainly been due to land area expansion, with very little change in production techniques and limited improvement in yields. Currently one in four people remains malnourished in Africa. CSA integrates all three dimensions of sustainable development and is aimed at (1) sustainably increasing agricultural productivity and incomes; (2) adapting and building resilience to climate change from the farm to national levels; and (3) developing opportunities to reduce greenhouse gas emissions from agriculture compared with past trends. It is an approach to identify the most suitable strategies according to national and local priorities and conditions to meet these three objectives. There is no such thing as an agricultural practice that is climate smart per se. Whether or not a particular practice or production system is climate smart depends upon the particular local climatic, biophysical, socio-economic and development context, which determines how far a particular practice or system can deliver on productivity increase, resilience and mitigation benefits. For Africa to reap the potential benefits CSA, concrete actions must be taken to: enhance the evidence base to underpin strategic choices, promote and facilitate wider adoption by farmers of appropriate technologies; develop institutional arrangements to support, apply and scale-out CSA from the farm level to the agricultural landscape level; manage tradeoffs in perspectives of farmers and policymakers; strengthen technical, analytical and implementation capacities; ensure policy frameworks and public investments are supportive of CSA; develop and implement effective risk-sharing schemes