Network properties of protein-decoy structures

Convergence of the vast sequence space of proteins into a highly restricted fold/conformational space suggests a simple yet unique underlying mechanism of protein folding that has been the subject of much debate in the last several decades. One of the major challenges related to the understanding of protein folding or in silico protein structure prediction is the discrimination of non-native structures/decoys from the native structure. Applications of knowledge-based potentials to attain this goal have been extensively reported in the literature. Also, scoring functions based on accessible surface area and amino acid neighbourhood considerations were used in discriminating the decoys from native structures. In this article, we have explored the potential of protein structure network (PSN) parameters to validate the native proteins against a large number of decoy structures generated by diverse methods. We are guided by two principles: (a) the PSNs capture the local properties from a global perspective and (b) inclusion of non-covalent interactions, at all-atom level, including the side-chain atoms, in the network construction accommodates the sequence dependent features. Several network parameters such as the size of the largest cluster, community size, clustering coefficient are evaluated and scored on the basis of the rank of the native structures and the Z-scores. The network analysis of decoy structures highlights the importance of the global properties contributing to the uniqueness of native structures. The analysis also exhibits that the network parameters can be used as metrics to identify the native structures and filter out non-native structures/decoys in a large number of data-sets; thus also has a potential to be used in the protein `structure prediction' problem.

Scaling analysis: Equivalence of convective and radiative heating of levitated droplet

This letter develops theoretical relationships for equilibrium timescale and temperature scale of a vaporizing droplet in a convective and a radiative environment. The transient temperature normalized by the respective scales exhibits a unified profile for both modes of heating. The analysis allows for the prediction of the required laser flux to show its equivalence in a corresponding heated gas stream. The theoretical equivalence shows good agreement with experiments across a range of droplet sizes. Simple experiments can be conducted in a levitator to extrapolate information in realistic convective environments like combustion and spray drying. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4720092]

Flux tube model signals for baryon correlations in heavy ion collisions

The flux tube model offers a pictorial description of what happens during the deconfinement phase transition in QCD. The three-point vertices of a flux tube network lead to formation of baryons upon hadronization. Therefore, correlations in the baryon number distribution at the last scattering surface are related to the preceding pattern of the flux tube vertices in the quark-gluon plasma, and provide a signature of the nearby deconfinement phase transition. I discuss the nature of the expected signal, and how to extract it from the experimental data for heavy ion collisions at RHIC and LHC.

Causality analysis of groundwater dynamics based on a Vector Autoregressive model in the semi-arid basin of Gundal (South India)

Causal relationships existing between observed levels of groundwater in a semi-arid sub-basin of the Kabini River basin (Karnataka state, India) are investigated in this study. A Vector Auto Regressive model is used for this purpose. Its structure is built on an upstream/downstream interaction network based on observed hydro-physical properties. Exogenous climatic forcing is used as an input based on cumulated rainfall departure. Optimal models are obtained thanks to a trial approach and are used as a proxy of the dynamics to derive causal networks. It appears to be an interesting tool for analysing the causal relationships existing inside the basin. The causal network reveals 3 main regions: the Northeastern part of the Gundal basin is closely coupled to the outlet dynamics. The Northwestern part is mainly controlled by the climatic forcing and only marginally linked to the outlet dynamic. Finally, the upper part of the basin plays as a forcing rather than a coupling with the lower part of the basin allowing for a separate analysis of this local behaviour. The analysis also reveals differential time scales at work inside the basin when comparing upstream oriented with downstream oriented causalities. In the upper part of the basin, time delays are close to 2 months in the upward direction and lower than 1 month in the downward direction. These time scales are likely to be good indicators of the hydraulic response time of the basin which is a parameter usually difficult to estimate practically. This suggests that, at the sub-basin scale, intra-annual time scales would be more relevant scales for analysing or modelling tropical basin dynamics in hard rock (granitic and gneissic) aquifers ubiquitous in south India. (c) 2012 Elsevier B.V. All rights reserved.

Markov chain modeling of evolution of strains in reinforced concrete flexural beams

From the analysis of experimentally observed variations in surface strains with loading in reinforced concrete beams, it is noted that there is a need to consider the evolution of strains (with loading) as a stochastic process. Use of Markov Chains for modeling stochastic evolution of strains with loading in reinforced concrete flexural beams is studied in this paper. A simple, yet practically useful, bi-level homogeneous Gaussian Markov Chain (BLHGMC) model is proposed for determining the state of strain in reinforced concrete beams. The BLHGMC model will be useful for predicting behavior/response of reinforced concrete beams leading to more rational design.

1-D Hydrogen bonded water in Cu(II)-picolinate coordination polymer: synthesis, crystal structure, and thermogravimetric analysis

A new Cu(II)-picolinate complex was synthesized and characterized by single crystal X-ray crystallography. The complex crystallizes in the centrosymmetric triclinic space group P (1) over bar (no. 2). Picolinate in the complex extends the neutral unit into a 1-D chain through mu(2)-bridging carboxylate. The complex has a hydrogen bonding acceptor in the second coordination sphere allowing lattice water to assemble neighboring chains. Water self-assembles to form a zig-zag 1-D chain. The adjacent chains are assembled by C-H center dot center dot center dot O interactions result in the formation 2-D hydrogen bonded network. The overall hydrogen bonding between water chain and Cu-picolinate network yields a 3-D hydrogen bonded coordination network. X-ray structural analysis, FTIR and thermal analysis have been used to characterize the reported compound in the solid state.

Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a ``spatial motif'' and several ``fold specific hot spots'' that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.

Non-Stationary Semi-Markov Decision Processes on a Finite Horizon

We introduce and study a class of non-stationary semi-Markov decision processes on a finite horizon. By constructing an equivalent Markov decision process, we establish the existence of a piecewise open loop relaxed control which is optimal for the finite horizon problem.

A novel Q-learning algorithm with function approximation for constrained Markov decision processes

We present a novel multi-timescale Q-learning algorithm for average cost control in a Markov decision process subject to multiple inequality constraints. We formulate a relaxed version of this problem through the Lagrange multiplier method. Our algorithm is different from Q-learning in that it updates two parameters - a Q-value parameter and a policy parameter. The Q-value parameter is updated on a slower time scale as compared to the policy parameter. Whereas Q-learning with function approximation can diverge in some cases, our algorithm is seen to be convergent as a result of the aforementioned timescale separation. We show the results of experiments on a problem of constrained routing in a multistage queueing network. Our algorithm is seen to exhibit good performance and the various inequality constraints are seen to be satisfied upon convergence of the algorithm.

An analysis on WDM components in flat gain regions of EDFA

Wavelength-division multiplexing (WDM) technology, by which multiple optical channels can be simultaneously transmitted at different wavelengths through a single optical fiber, is a useful means of making full use of the low-loss characteristics of optical fibers over a wide-wavelength region. The present day multifunction RADARs with multiple transmit receive modules requires various kinds of signal distribution for real time operation. If the signal distribution can be achieved through optical networks by using Wavelength Division Multiplexing (WDM) methods, it results in a distribution scheme with less hardware complexity and leads to the reduction in the weight of the antenna arrays In addition, being an Optical network it is free from Electromagnetic interference which is a crucial requirement in an array environment. This paper discusses about the analysis performed on various WDM components of distribution optical network for radar applications. The analysis is performed by considering the feasible constant gain regions of Erbium doped fiber amplifier (EDFA) in Matlab environment. This will help the user in the selection of suitable components for WDM based optical distribution networks.

Stability analysis of aperiodic messages scheduled in the dynamic segment of flex ray protocol

In a cyber physical system like vehicles number of signals to be communicated in a network system has an increasing trend. More and more mechanical and hydraulic parts are replaced by electronic control units and infotainment and multimedia applications has increased in vehicles. Safety critical hard real time messages and aperiodic messages communicated between electronic control units have been increased in recent times. Flexray is a high bandwidth protocol consisting of static segment for supporting hard real time messages and a dynamic segment for transmitting soft and non real time messages. In this paper, a method to obtain the stability region for the random arrival of messages in each electronic control units which is scheduled in the dynamic segment of Flexray protocol is presented. Number of mini slots available in the dynamic segment of Flexray restricts the arrival rate of tasks to the micro controllers or the number of micro controllers connected to the Flexray bus. Stability region of mathematical model of the system is compared with the Flexray protocol simulation results.

Static analysis for checking data format compatibility of programs

Large software systems are developed by composing multiple programs. If the programs manip-ulate and exchange complex data, such as network packets or files, it is essential to establish that they follow compatible data formats. Most of the complexity of data formats is associated with the headers. In this paper, we address compatibility of programs operating over headers of network packets, files, images, etc. As format specifications are rarely available, we infer the format associated with headers by a program as a set of guarded layouts. In terms of these formats, we define and check compatibility of (a) producer-consumer programs and (b) different versions of producer (or consumer) programs. A compatible producer-consumer pair is free of type mismatches and logical incompatibilities such as the consumer rejecting valid outputs gen-erated by the producer. A backward compatible producer (resp. consumer) is guaranteed to be compatible with consumers (resp. producers) that were compatible with its older version. With our prototype tool, we identified 5 known bugs and 1 potential bug in (a) sender-receiver modules of Linux network drivers of 3 vendors and (b) different versions of a TIFF image library.

An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Game theoretic analysis of collusions in nonneutral networks

This paper studies the impact of exclusive contracts between a content provider (CP) and an internet service provider (ISP) in a nonneutral network. We consider a simple linear demand function for the CPs. We studywhen an exclusive contract is benefcial to the colluding pair and evaluate its impact on the noncolluding players at equilibrium. For the case of two CPs and one ISP we show that collusion may not always be benefcial. We derive an explicit condition in terms of the advertisement revenues of the CPs that tells when a collusion is proftable to the colluding entities.

Measurement Based Impromptu Deployment of a Multi-Hop Wireless Relay Network

We study the problem of optimal sequential (''as-you-go'') deployment of wireless relay nodes, as a person walks along a line of random length (with a known distribution). The objective is to create an impromptu multihop wireless network for connecting a packet source to be placed at the end of the line with a sink node located at the starting point, to operate in the light traffic regime. In walking from the sink towards the source, at every step, measurements yield the transmit powers required to establish links to one or more previously placed nodes. Based on these measurements, at every step, a decision is made to place a relay node, the overall system objective being to minimize a linear combination of the expected sum power (or the expected maximum power) required to deliver a packet from the source to the sink node and the expected number of relay nodes deployed. For each of these two objectives, two different relay selection strategies are considered: (i) each relay communicates with the sink via its immediate previous relay, (ii) the communication path can skip some of the deployed relays. With appropriate modeling assumptions, we formulate each of these problems as a Markov decision process (MDP). We provide the optimal policy structures for all these cases, and provide illustrations of the policies and their performance, via numerical results, for some typical parameters.