AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

Background: Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, AlignHUSH for HMM-HMM alignment has been developed which is capable of recognizing distantly related domain families The method uses structural information, in the form of predicted secondary structure probabilities, and hydrophobicity of amino acids to align HMMs of two sets of aligned sequences. The effect of using adjoining column(s) information has also been investigated and is found to increase the sensitivity of HMM-HMM alignments and remote homology detection. Results: We have assessed the performance of AlignHUSH using known evolutionary relationships available in SCOP. AlignHUSH performs better than the best HMM-HMM alignment methods and is observed to be even more sensitive at higher error rates. Accuracy of the alignments obtained using AlignHUSH has been assessed using the structure-based alignments available in BaliBASE. The alignment length and the alignment quality are found to be appropriate for homology modeling and function annotation. The alignment accuracy is found to be comparable to existing methods for profile-profile alignments. Conclusions: A new method to align HMMs has been developed and is shown to have better sensitivity at error rates of 10% and above when compared to other available programs. The proposed method could effectively aid obtaining clues to functions of proteins of yet unknown function. A web-server incorporating the AlignHUSH method is available at http://crick.mbu.iisc.ernet.in/similar to alignhush/

Asymmetric and symmetric rolling of magnesium: Evolution of microstructure, texture and mechanical properties

In the present study, asymmetric rolling was carried out for incorporating a shear component during the rolling at different temperatures, and was compared with conventional (symmetric) rolling. The microstructures were investigated using electron back-scatter diffraction (EBSD). The strain incorporated was compared with the help of grain orientation spread (GOS). GOS was eventually used as a criterion to partition the microstructure for separating the deformed and the dynamically recrystallized (DRX) grains. The texture of the partitioned DRX grains was shifted by similar to 30 degrees along the c-axis from the deformed grains. The mechanism of dynamic recrystallization (DRX) has been identified as continuous dynamic recovery and recrystallization (CDRR). The partitioned deformed grains for the higher temperature rolled specimens exhibited a texture similar to the room temperature rolled specimen. The asymmetric rolling introduces a shear component which shifts the texture fibre by similar to 5-10 degrees from the conventional rolling texture. This led to an increase in ductility with little compromise on strength. (c) 2012 Elsevier B.V. All rights reserved.

Combining product information and process information to build virtual assembly situations for knowledge acquisition

Assembly is an important part of the product development process. To avoid potential issues during assembly in specialized domains such as aircraft assembly, expert knowledge to predict such issues is helpful. Knowledge based systems can act as virtual experts to provide assistance. Knowledge acquisition for such systems however, is a challenge, and this paper describes one part of an ongoing research to acquire knowledge through a dialog between an expert and a knowledge acquisition system. In particular this paper discusses the use of a situation model for assemblies to present experts with a virtual assembly and help them locate the specific context of the knowledge they provide to the system.

How to run a campaign: Optimal control of SIS and SIR information epidemics

Information spreading in a population can be modeled as an epidemic. Campaigners (e.g., election campaign managers, companies marketing products or movies) are interested in spreading a message by a given deadline, using limited resources. In this paper, we formulate the above situation as an optimal control problem and the solution (using Pontryagin's Maximum Principle) prescribes an optimal resource allocation over the time of the campaign. We consider two different scenarios-in the first, the campaigner can adjust a direct control (over time) which allows her to recruit individuals from the population (at some cost) to act as spreaders for the Susceptible-Infected-Susceptible (SIS) epidemic model. In the second case, we allow the campaigner to adjust the effective spreading rate by incentivizing the infected in the Susceptible-Infected-Recovered (SIR) model, in addition to the direct recruitment. We consider time varying information spreading rate in our formulation to model the changing interest level of individuals in the campaign, as the deadline is reached. In both the cases, we show the existence of a solution and its uniqueness for sufficiently small campaign deadlines. For the fixed spreading rate, we show the effectiveness of the optimal control strategy against the constant control strategy, a heuristic control strategy and no control. We show the sensitivity of the optimal control to the spreading rate profile when it is time varying. (C) 2014 Elsevier Inc. All rights reserved.

Analysis of microstructure and texture evolution in pure magnesium during symmetric and asymmetric rolling

Asymmetric rolling of commercially pure magnesium was carried out at three different temperatures: room temperature, 200 degrees C and 350 degrees C. Systematic analysis of microstructures, grain size distributions, texture and misorientation distributions were performed using electron backscattered diffraction in a field emission gun scanning electron microscope. The results were compared with conventional (symmetric) rolling carried out under the same conditions of temperature and strain rate. Simulations of deformation texture evolution were performed using the viscoplastic self-consistent polycrystal plasticity model. The main trends of texture evolution are faithfully reproduced by the simulations for the tests at room temperature. The deviations that appear for the textures obtained at high temperature can be explained by the occurrence of dynamic recrystallization. Finally, the mechanisms of texture evolution in magnesium during asymmetric and symmetric rolling are explained with the help of ideal orientations, grain velocity fields and divergence maps displayed in orientation space.

Role of information and communication in redefining unmanned aerial vehicle autonomous control levels

Autonomous mission control, unlike automatic mission control which is generally pre-programmed to execute an intended mission, is guided by the philosophy of carrying out a complete mission on its own through online sensing, information processing, and control reconfiguration. A crucial cornerstone of this philosophy is the capability of intelligence and of information sharing between unmanned aerial vehicles (UAVs) or with a central controller through secured communication links. Though several mission control algorithms, for single and multiple UAVs, have been discussed in the literature, they lack a clear definition of the various autonomous mission control levels. In the conventional system, the ground pilot issues the flight and mission control command to a UAV through a command data link and the UAV transmits intelligence information, back to the ground pilot through a communication link. Thus, the success of the mission depends entirely on the information flow through a secured communication link between ground pilot and the UAV In the past, mission success depended on the continuous interaction of ground pilot with a single UAV, while present day applications are attempting to define mission success through efficient interaction of ground pilot with multiple UAVs. However, the current trend in UAV applications is expected to lead to a futuristic scenario where mission success would depend only on interaction among UAV groups with no interaction with any ground entity. However, to reach this capability level, it is necessary to first understand the various levels of autonomy and the crucial role that information and communication plays in making these autonomy levels possible. This article presents a detailed framework of UAV autonomous mission control levels in the context of information flow and communication between UAVs and UAV groups for each level of autonomy.

Information-theoretic and communication-theoretic optimal power allocation for fading channels

In this paper we review the most peculiar and interesting information-theoretic and communications features of fading channels. We first describe the statistical models of fading channels which are frequently used in the analysis and design of communication systems. Next, we focus on the information theory of fading channels, by emphasizing capacity as the most important performance measure. Both single-user and multiuser transmission are examined. Further, we describe how the structure of fading channels impacts code design, and finally overview equalization of fading multipath channels.

Information content of molecular graph and prediction of gas phase thermal entropy of organic compounds

Entropy is a fundamental thermodynamic property that has attracted a wide attention across domains, including chemistry. Inference of entropy of chemical compounds using various approaches has been a widely studied topic. However, many aspects of entropy in chemical compounds remain unexplained. In the present work, we propose two new information-theoretical molecular descriptors for the prediction of gas phase thermal entropy of organic compounds. The descriptors reflect the bulk and size of the compounds as well as the gross topological symmetry in their structures, all of which are believed to determine entropy. A high correlation () between the entropy values and our information-theoretical indices have been found and the predicted entropy values, obtained from the corresponding statistically significant regression model, have been found to be within acceptable approximation. We provide additional mathematical result in the form of a theorem and proof that might further help in assessing changes in gas phase thermal entropy values with the changes in molecular structures. The proposed information-theoretical molecular descriptors, regression model and the mathematical result are expected to augment predictions of gas phase thermal entropy for a large number of chemical compounds.

Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency

Information is encoded in neural circuits using both graded and action potentials, converting between them within single neurons and successive processing layers. This conversion is accompanied by information loss and a drop in energy efficiency. We investigate the biophysical causes of this loss of information and efficiency by comparing spiking neuron models, containing stochastic voltage-gated Na+ and K+ channels, with generator potential and graded potential models lacking voltage-gated Na+ channels. We identify three causes of information loss in the generator potential that are the by-product of action potential generation: (1) the voltage-gated Na+ channels necessary for action potential generation increase intrinsic noise and (2) introduce non-linearities, and (3) the finite duration of the action potential creates a `footprint' in the generator potential that obscures incoming signals. These three processes reduce information rates by similar to 50% in generator potentials, to similar to 3 times that of spike trains. Both generator potentials and graded potentials consume almost an order of magnitude less energy per second than spike trains. Because of the lower information rates of generator potentials they are substantially less energy efficient than graded potentials. However, both are an order of magnitude more efficient than spike trains due to the higher energy costs and low information content of spikes, emphasizing that there is a two-fold cost of converting analogue to digital; information loss and cost inflation.