A global optimization approach for searching low energy conformations of proteins

De novo protein structure prediction and understanding the protein folding mechanism is an outstanding challenge of Biological Physics. Relying on the thermodynamic hypothesis of protein folding it is expected that the native state of a protein can be found out if the global minimum of the free energy surface is found. To understand the energy landscape or the free energy surface is challenging. The structure and dynamics of proteins are the manifestations of the underlying potential energy surface. Here the potential energy function stands on a framework of all-atom representation and uses purely physics-based interactions. For the solvated proteins the effective free energy is defined as an implicit solvation model which includes the solvation free energy, along with a standard all-atom biomolecular forcefield. A major challenge is to search for the global minimum on this effective free energy surface. In this work the Minima Hopping Algorithm (MHOP) to find global minima on potential energy surfaces has been used for protein structure prediction or in general finding the lowest energy conformations of proteins. Here proteins have been studied both in vacuo and in the aqueous medium. For short peptides starting from a completely extended conformation we could find conformational minima which are very close to the experimentally observed structures

Sintering Characteristics And Characterisation Of Al-Mn-Ce Nanostructured Material Prepared By Mechanical Alloying

Nanomaterials are experiencing a rapid development in recent years due to their existing and/or potential applications in a wide variety of technological areas such as electronics, catalysis, ceramics, magnetic data storage, structural components etc. To meet the technological demands in these areas, the size of the materials should be reduced to the nanometer scale. As the size reduces into the nanometer range, the materials exhibit peculiar and interesting mechanical and physical properties, e.g. increased mechanical strength, enhanced diffusivity, higher specific heat and electrical resistivity compared to conventional coarse grained counterparts. There are various routesof synthesis of nanocomposites which have been discussed at length later in this paper and out of all of these we have opted for mechanical alloying as the route for synthesizing Al-Mn-Ce nanocomposite

An improved contact detection algorithm for DEM modeling of polydisperse systems: Application to coal-ash mixture fluidization

Discrete element modelling (DEM) are becoming increasingly common for modelling of particulate flows such as avalanches and landslides and in many “solids-only” unit operations like grinding and milling, as well as in numerous gas-solid applications such as pneumatic conveying, fluidized beds and circulating fluidized beds (1). In such simulations, realistic size distributions have not been taken into account in the past. In real operations, sizes of dispersed entities can vary over several orders in magnitude. This issue is particularly pronounced when one is trying to simulate polydisperse systems, such as coal-ash mixtures, wherein a single coal particle may be (in general) surrounded by many much smaller ash particles, even when the overall mass fraction of the ash may be only a few percent. Figure 1 shows the idea schematically. One of the main reasons for this challenge is the DEM calculations required contact detection in the dispersed objects. When the sizes of these objects vary to a great degree, the contact detection poses a computational bottleneck. Amongst others, notably Perkins and Williams have proposed “Double Ended Spatial Sorting” (DESS) for contact detection which is insensitive to variation in particle sizes (2). It had been shown in their contribution in that DESS has a complexity of N log(N), where N is the number of entities being simulated. Please click Additional Files below to see the full abstract

Hydrodynamic behaviour of coal and bottom ash mixtures in a fluidized bed gasifier

systems. One of the principal applications of such systems are in combustion and gasification of solid fuels (coal, pet coke, and biomass), wherein the fuel and the inorganic residue (“ash”) form a system of binary fluidization. Even though the fluid bed gasification of coal per se is a relatively well-known operation, however the technology for high ash coal (\u3e30% ash in the native coal) is still in its nascent stage. Existing knowhow on such operations cannot predict interactions of a constantly depleting coal inventory and constantly evolving ash inventory. With this backdrop we attempt here to study the dynamic behavior of coal and ash in a fluidized bed. In order to simulate a realistic bed composition of a gasifier, hydrodynamic characteristics were studied under various proportions of coal and ash on laboratory scale cold flow setup. A three-dimensional transient CFD model was set up to predict the dynamic and time-averaged profiles of coal and ash concentrations. The same were validated against chordal averaged solids holdup (coal and ash) characteristics measured using γ-ray densitometry, with a single collimated source (Cs-137) aligned with a scintillation NaI detector. The other part of the validation, involving the comparison of measured solids velocity profiles and CFD-predicted ones, is accomplished by implementing the Radioactive Particle Tracking (RPT) technique. In the latter technique, a single radioactive particle designed to mimic a single typical coal particle is tracked for a long time in the vessel using strategically placed scintillation detectors, and its position-time history is processed to yield the solids velocity field. Please click Additional Files below to see the full abstract

A Bell-Evans-Polanyi principle for molecular dynamics trajectories and its implications for global optimization

The Bell-Evans-Polanyi principle that is valid for a chemical reaction that proceeds along the reaction coordinate over the transition state is extended to molecular dynamics trajectories that in general do not cross the dividing surface between the initial and the final local minima at the exact transition state. Our molecular dynamics Bell-Evans-Polanyi principle states that low energy molecular dynamics trajectories are more likely to lead into the basin of attraction of a low energy local minimum than high energy trajectories. In the context of global optimization schemes based on molecular dynamics our molecular dynamics Bell-Evans-Polanyi principle implies that using low energy trajectories one needs to visit a smaller number of distinguishable local minima before finding the global minimum than when using high energy trajectories

Examining the roles of Bangladesh, Myanmar and Maldives in the rivalry for Indian Ocean supremacy

As India and China continue to vie for supremacy of the highly geopolitically prized Indian Ocean, Shantanu Roy-Chaudhury focuses on the roles of Bangladesh, Myanmar and Maldives and their strategic importance for both states

Sericulture as an Employment Generating Household Industry in West Bengal

Employment generation is one of the major potentials of Sericulture and Silk Industry in India. The farm and non-farm activity of this sector creates sixty lakh mandays of employment every year mostly in rural sector. The industry helps to create egalitarian distribution of income as it transfers greater share of its wealth from high end urban customers to poor artisan classes. In West Bengal, more than one lakh families are occupied with sericulture activities where Karnataka is the state with the largest number of families involved with sericulture. Despite having high level family involvement, West Bengal produces smaller quantities of raw silk compared to Karnataka as well as Andhra Pradesh. This paper investigates the reason of this low production and finds out that low productivity of land is no way responsible for that. Different Employment Models constructed in this paper suggest that ‘area of mulberry cultivation’, ‘cocoon-market’ and ‘power-looms’ are powerful factors in changing the level of employment, while the primary survey exposes factors like ‘unitary household structure’, ‘income’ ‘years of education’ and ‘numbers of female in the household’ as the significant factors in accelerating average employment per family. The spillover effect of this employment generation is studied at the end. The study finds that as a poverty eradication measure, sericulture fails to expand in rural West Bengal vis-à-vis the other prominent states. But income inequality is undoubtedly diminished with the practice in sericulture