Coupled dynamics of sequence selection and compactification in mean-field hetero-polymers

We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the competing demands of functionality and reproducibility of the polymer's folded structure. Since reproducibility is defined in terms of properties of the folding process, one is led to the analysis of the coupled dynamics of (fast) polymer folding and (slow) genetic sequence selection. For the present mean-field model this analysis can be carried out using the finite-dimensional replica method, leading to exact results for (first- and second-order) transitions and to rich phase diagrams.Comment: 21 pages, 7 figure

Solvable Lattice Gas Models of Random Heteropolymers at Finite Density: II. Dynamics and Transitions to Compact States

In this paper we analyse both the dynamics and the high density physics of the infinite dimensional lattice gas model for random heteropolymers recently introduced in \cite{jort}. Restricting ourselves to site-disordered heteropolymers, we derive exact closed deterministic evolution equations for a suitable set of dynamic order parameters (in the thermodynamic limit), and use these to study the dynamics of the system for different choices of the monomer polarity parameters. We also study the equilibrium properties of the system in the high density limit, which leads to a phase diagram exhibiting transitions between swollen states, compact states, and regions with partial compactification. Our results find excellent verification in numerical simulations, and have a natural and appealing interpretation in terms of real heteropolymers.Comment: 12 pages, 8 eps figures, revised version (to be published in EPJ

New Binuclear Nickel(II) Species

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Dynamic Response and Static Analysis of RCC Space Frames Supporting High Speed Centrifugal Machines with Coupled Soil-Structure Interaction

The paper reviews the current state of the art on the dynamic and static analyses of RCC space frames supporting high speed centrifugal machines e.g. large turbogenerators and compressors. The need to include the effects of soil-structure interaction formulations on overall behaviour of various analytical models are highlighted, At the same time, the uncertainties involved in evaluating essential geotechnical parameters and paucity of reliable and elaborate information from the machine manufacturers are discussed. The analysis and design aspects of this inter-disciplinary problem are illustrated with two typical design case studies selected from authors’ own experience in this specialised field. The paper also discusses the usefulness, if any, of such rigorous analysis and identifies various shortcomings which still persist in finalising realistic design data and adopting suitable models to represent machine foundation-soil system

Optimisation of Process Variables in Sintering through Statistical design of Experiments

An attempt has been made to quantify the effects of the variables on strength in sintering of iron ore/blue dust received from Bailadila, NMDC. For this, the method of design 2n factorial experiment is used to obtain a response surface equation. Results indicate if the coke breeze increases in the range of variation of the variable in sintering, the strength increases but strength decreases when moisture increases from lower level to higher level. Blue dust does no effect the strength. The optimum levi (-4: variables for the maximon strength of the sinter produ(A is determined by the method of hexagonal design of experjnent. The results indicate that for a basicity of 1.9 an acceptable quality of sinter can be produced. Blue dust amounting to 40.0% of all the iron ore fines taken together can be incorporated in the raw mixture without imparting the strength of the finished sinter

A solvable model of the genesis of amino-acid sequences via coupled dynamics of folding and slow genetic variation

We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and long-range polarity-driven forces. Our solution is based on the diagonalization of replicated transfer matrices, and leads in the thermodynamic limit to explicit predictions regarding phase transitions and phase diagrams at genetic equilibrium. The predicted phenomenology allows for natural physical interpretations, and finds satisfactory support in numerical simulations.Comment: 51 pages, 13 figures, submitted to J. Phys.

Ineficient water pricing and incentives for conservation

We use two randomized controlled trials in Bangladesh to study a simple water conservation technology for rice production called "Alternate Wetting and Drying (AWD)." Despite proven results in agronomic trials, our first experiment shows that AWD only saves water and increases profits in villages where farmers pay a marginal price for water, but not when they pay fixed seasonal charges. The second RCT randomly distributed debit cards that can be used to pay volumetric prices for irrigation water. This low-cost, scalable intervention causes farmers to place more value on the water-saving technology. Demand for the technology becomes less price-sensitive

Dielectronic recombination and stability of warm gas in AGN

Understanding the thermal equilibrium (stability) curve may offer insights into the nature of the warm absorbers often found in active galactic nuclei. Its shape is determined by factors like the spectrum of the ionizing continuum and the chemical composition of the gas. We find that the stability curves obtained under the same set of the above mentioned physical factors, but using recently derived dielectronic recombination rates, give significantly different results, especially in the regions corresponding to warm absorbers, leading to different physical predictions. Using the current rates we find a larger probability of having thermally stable warm absorber at 10^5 \kel than previous predictions and also a greater possibility for its multiphase nature. the results obtained with the current dielectronic recombination rate coefficients are more reliable because the warm absorber models along the stability curve have computed coefficient values, whereas previous calculations relied on guessed averages for the same due to lack of available data.Comment: 5 pages, 3 figures, Accepted for publication in MNRAS Letters. The definitive version is available at http://www3.interscience.wiley.com/cgi-bin/hom

Phosphorylation of the regulatory light chain of myosin in striated muscle: methodological perspectives

Copyright © The Author(s) 2016. Phosphorylation of the regulatory light chain (RLC) of myosin modulates cellular functions such as muscle contraction, mitosis, and cytokinesis. Phosphorylation defects are implicated in a number of diseases. Here we focus on striated muscle where changes in RLC phosphorylation relate to diseases such as hypertrophic cardiomyopathy and muscular dystrophy, or age-related changes. RLC phosphorylation in smooth muscle and non-muscle cells are covered briefly where relevant. There is much scientific interest in controlling the phosphorylation levels of RLC in vivo and in vitro in order to understand its physiological function in striated muscles. A summary of available and emerging in vivo and in vitro methods is presented. The physiological role of RLC phosphorylation and novel pathways are discussed to highlight the differences between muscle types and to gain insights into disease processes.Ministry of Education of Singapore (Moe Tier 2 2012-T2-2-105) and start-up grant