28 research outputs found

    Correlated disorder in entropic crystals

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    We report computational evidence of a new type of disordered phase in crystals resulting from entropy driven self-assembly of hard convex polyhedra. The disorder was reflected in the orientations of the anisotropic particles and not in the positions of the centers of geometry. Despite the lack of order, particle orientations were not random and exhibited strong correlations. The correlations were manifested in terms of ``quantized'' rotational motions in a fixed number of absolute orientations, while maintaining equal populations and specific measure of pairwise angular differences among the discrete values. This gave rise to a discretely mobile phase in the low density solid and a quenched disordered state at high pressure. This finding can be interpreted as the simplest example of correlated disorder in crystalline materials.Comment: 15 pages, 4 figures in the main text, 11 figures in the supporting informatio

    Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

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    Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. © 2014 Das et al

    Conformational Transitions in ATP-Driven Calcium Pump SERCA

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    Event Tracking: A systematic method for analyzing nucleation and growth in hierarchical self-assembly

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    Molecular self-assembly has garnered significant attention in the field of biomaterials and nanotechnology due its potential for creating novel materials with diverse applications. The entire process is guided by either classical nucleation and growth or formation of multiple nucleus and their growth and finally the fusion of the self- assembled states. Systematic way to track this nucleation, growth and fusion process is still unknown. We have developed an algorithm to systematically identify all the possible molecular events. The events provide immediate information when a cluster or individual molecule combines with another cluster or molecule, or when a cluster or molecule detaches from another, during each stage of the mechanism. By comprehensively examining the entire process, we can gain a clearer understanding of the molecular mechanisms involved in the assembly process. We applied this algorithm to self-assembly of some ultrashort peptides. Through a systematic analysis, we identify commonalities and differences in the self-assembly mechanism of various ultrashort peptides. This comparative analysis contributes to a deeper understanding of the mechanisms governing ultrashort peptide self-assembly, offering valuable guidance for the rational design of biomaterials which can serve various technological and biomedical purposes

    Na+/K+-ATPase Pumping Mechanism: Insights from Simulations

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    Not AvailableAs the world is moving towards ‘knowledge economy’, training and capacity building has become an integral part of all organizations. The trainers themselves need to undergo training programmes to increase their efficiency. The present study aims to investigate the impact of five trainers’ training programmes in the inland fishery sector of India based on participants’ perceptions and changes in human capital, i.e., knowledge, attitude, and skill. The training effectiveness index was devised for this purpose consisting of six parameters namely, expectation fulfillment, the overall grading of the programme, the extent of satisfaction, change in knowledge, attitude, and skill level of the participants. The statistically significant change in knowledge level in all programmes and in attitude level in two programmes was recorded. The effectiveness scores ranged from 71.76 to 80.66 percent. The motivation for participation, perceived challenges, suggestions for improvement, and future action plans were also noted. Based on the findings a three-stage training cycle has been recommended by the authors for improving the efficiency of training programmes. Some of the recommended measures are conducting Training Need Analysis (TNA), application of simulation method for skill-building, the inclusion of more practical and field-oriented sessions, carrying out microlab in the beginning of the training for building positive effect, post-training follow up with the mother organizations and analyzing the impact of training on job performance. The findings are expected to aid in designing more efficient training programmes in the inland fishery sector in the future.Not Availabl