DockYard-a repository to assist modeling of protein-protein docking

In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a limited number of protein complexes. We have created a repository called dockYard (http://pallab.serc.iisc.ernet.in/dockYard), that allows modelers interested in protein-protein interaction to access large volume of information on protein dimers and their interlogs, and also download decoys for their work if they are interested in building modeling methods. dockYard currently offers four categories of docking decoys derived from: Bound (native dimer co-crystallized), Unbound (individual subunits are crystallized, as well as the target dimer), Variants (match the previous two categories in at least one subunit with 100% sequence identity), and Interlogs (match the previous categories in at least one subunit with >= 90% or >= 50% sequence identity). The web service offers options for full or selective download based on search parameters. Our portal also serves as a repository to modelers who may want to share their decoy sets with the community.

Role of surface tension driven convection in pulsed - laser melting and solidification

Surface melting by a stationary, pulsed laser has been modelled by the finite element method. The role of the surface tension driven convection is investigated in detail. Numerical results are presented for a triangular laser pulse of durations 10, 50 and 200 ms. Though the magnitude of the velocity is high due to the surface tension forces, the present results indicate that a finite time is required for convection to affect the temperature distribution within the melt pool. The effect of convection is very significant for pulse durations longer than 10 ms.

Nonaxisymmetric convection in stationary Gas Tungsten Arc Weld Pools

Observations of surface flow patterns of steel and aluminum GTAW pools have been made using a pulsed laser visualization system. The weld pool convection is found to be three-dimensional with the azimuthal circulation depending on the location of the clamp with respect to the torch. Oscillation of steel pools and undulating motion in aluminum weld pools are also observed even with steady process parameters. Current axisymmetric numerical models are unable to explain such phenomena. A three-dimensional computational study is carried out in this study to explain the rotational flow in aluminum weld pools.

Prediction of separation factor in foam separation of proteins

A phenomenological model has been developed for predicting separation factors obtained in concentrating protein solutions using batch-foam columns. The model considers the adsorption of surface active proteins onto the air-water interface of bubbles, and drainage of liquid from the foam, which are the two predominant processes responsible for separation in foam columns. The model has been verified with data collected on casein and bovine serum albumin (BSA) solutions, for which adsorption isotherms are available in the literature. It has been found that an increase in liquid pool height above the gas distributor and the time allowed for drainage result in a better separation. Further, taller foam columns yield poorer separation at constant time of drainage. The model successfully predicts the observed results. (C) 1997 Elsevier Science Ltd.

Scaling analysis of momentum and heat transport in gas tungsten arc weld pools

A systematic procedure is outlined for scaling analysis of momentum and heat transfer in gas tungsten arc weld pools. With suitable selections of non-dimentionalised parameters, the governing equations coupled with appropriate boundary conditions are first scaled, and the relative significance of various terms appearing in them is analysed accordingly. The analysis is then used to predict the orders of magnitude of some important quantities, such as the velocity scene lit the top surface, velocity boundary layer thickness, maximum temperature increase in the pool, and time required for initiation of melting. Some of the quantities predicted from the scaling analysis can also be used for optimised selection of appropriate grid size and time steps for full numerical simulation of the process. The scaling predictions are finally assessed by comparison with numerical results quoted in the literature, and a good qualitative agreement is observed.

Spring Warming of the Eastern Arabian Sea and Bay of Bengal from Buoy Data

Observations from moored buoys during spring of 1998-2000 suggest that the warming of the mixed layer (similar to20 m deep) of the north Indian Ocean warm pool is a response to net surface heat flux Q(net) (similar to100 W m(-2)) minus penetrative solar radiation Q(pen) (similar to45 W m(-2)). A residual cooling due to vertical mixing and advection is indirectly estimated to be about 25 W m(-2). The rate of warming due to typical values of Q(net) minus Q(pen) is not very sensitive to the depth of the mixed layer if it lies between 10 m and 30 m.

A scaling analysis of momentum and heat transport in laser surface melting

In this paper, we outline a systematic procedure for scaling analysis of momentum and heat transfer in laser melted pools. With suitable choices of non-dimensionalising parameters, the governing equations coupled with appropriate boundary conditions are first scaled, and the relative significance of various terms appearing in them are accordingly analysed. The analysis is then utilised to predict the orders of magnitude of some important quantities, such as the velocity scale at the top surface, velocity boundary layer thickness, maximum temperature rise in the pool, fully developed pool-depth, and time required for initiation of melting. Using the scaling predictions, the influence of various processing parameters on the system variables can be well recognised, which enables us to develop a deeper insight into the physical problem of interest. Moreover, some of the quantities predicted from the scaling analysis can be utilised for optimised selection of appropriate grid-size and time-steps for full numerical simulation of the process. The scaling predictions are finally assessed by comparison with experimental and numerical results quoted in the literature, and an excellent qualitative agreement is observed.

Three-dimensional computational modeling of momentum, heat, and mass transfer in a laser surface alloying process

A three- dimensional, transient model is developed for studying heat transfer, fluid flow, and mass transfer for the case of a single- pass laser surface alloying process. The coupled momentum, energy, and species conservation equations are solved using a finite volume procedure. Phase change processes are modeled using a fixed-grid enthalpy-porosity technique, which is capable of predicting the continuously evolving solid- liquid interface. The three- dimensional model is able to predict the species concentration distribution inside the molten pool during alloying, as well as in the entire cross section of the solidified alloy. The model is simulated for different values of various significant processing parameters such as laser power, scanning speed, and powder feedrate in order to assess their influences on geometry and dynamics of the pool, cooling rates, as well as species concentration distribution inside the substrate. Effects of incorporating property variations in the numerical model are also discussed.

A Coalitional Game Framework for Cooperative Secondary Spectrum Access

We consider a framework in which several service providers offer downlink wireless data access service in a certain area. Each provider serves its end-users through opportunistic secondary spectrum access of licensed spectrum, and needs to pay primary license holders of the spectrum usage based and membership based charges for such secondary spectrum access. In these circumstances, if providers pool their resources and allow end-users to be served by any of the cooperating providers, the total user satisfaction as well as the aggregate revenue earned by providers may increase. We use coalitional game theory to investigate such cooperation among providers, and show that the optimal cooperation schemes can be obtained as solutions of convex optimizations. We next show that under usage based charging scheme, if all providers cooperate, there always exists an operating point that maximizes the aggregate revenue of providers, while presenting each provider a share of the revenue such that no subset of providers has an incentive to leave the coalition. Furthermore, such an operating point can be computed in polynomial time. Finally, we show that when the charging scheme involves membership based charges, the above result holds in important special cases.

A Coalition game model for spectrum pooling in wireless data access networks

We consider a setting in which several operators offer downlink wireless data access services in a certain geographical region. Each operator deploys several base stations or access points, and registers some subscribers. In such a situation, if operators pool their infrastructure, and permit the possibility of subscribers being served by any of the cooperating operators, then there can be overall better user satisfaction, and increased operator revenue. We use coalitional game theory to investigate such resource pooling and cooperation between operators.We use utility functions to model user satisfaction, and show that the resulting coalitional game has the property that if all operators cooperate (i.e., form a grand coalition) then there is an operating point that maximizes the sum utility over the operators while providing the operators revenues such that no subset of operators has an incentive to break away from the coalition. We investigate whether such operating points can result in utility unfairness between users of the various operators. We also study other revenue sharing concepts, namely, the nucleolus and the Shapely value. Such investigations throw light on criteria for operators to accept or reject subscribers, based on the service level agreements proposed by them. We also investigate the situation in which only certain subsets of operators may be willing to cooperate.

Protein Model Discrimination Using Mutational Sensitivity Derived from Deep Sequencing

A major bottleneck in protein structure prediction is the selection of correct models from a pool of decoys. Relative activities of similar to 1,200 individual single-site mutants in a saturation library of the bacterial toxin CcdB were estimated by determining their relative populations using deep sequencing. This phenotypic information was used to define an empirical score for each residue (Rank Score), which correlated with the residue depth, and identify active-site residues. Using these correlations, similar to 98% of correct models of CcdB (RMSD <= 4 angstrom) were identified from a large set of decoys. The model-discrimination methodology was further validated on eleven different monomeric proteins using simulated RankScore values. The methodology is also a rapid, accurate way to obtain relative activities of each mutant in a large pool and derive sequence-structure-function relationships without protein isolation or characterization. It can be applied to any system in which mutational effects can be monitored by a phenotypic readout.

Unconventional initiator tRNAs sustain Escherichia coli

Of all tRNAs, initiator tRNA is unique in its ability to start protein synthesis by directly binding the ribosomal P-site. This ability is believed to derive from the almost universal presence of three consecutive G-C base (3G-C) pairs in the anticodon stem of initiator tRNA. Consistent with the hypothesis, a plasmid-borne initiator tRNA with one, two, or all 3G-C pairs mutated displays negligible initiation activity when tested in a WT Escherichia coli cell. Given this, the occurrence of unconventional initiator tRNAs lacking the 3G-C pairs, as in some species of Mycoplasma and Rhizobium, is puzzling. We resolve the puzzle by showing that the poor activity of unconventional initiator tRNAs in E. coli is because of competition from a large pool of the endogenous WT initiator tRNA (possessing the 3G-C pairs). We show that E. coli can be sustained on an initiator tRNA lacking the first and third G-C pairs; thereby reducing the 3G-C rule to a mere middle G-C requirement. Two general inferences following from our findings, that the activity of a mutant gene product may depend on its abundance in the cell relative to that of the WT, and that promiscuous initiation with elongator tRNAs has the potential to enhance phenotypic diversity without affecting genomic integrity, have been discussed.

Strength of Gamma Rhythm Depends on Normalization

Neuronal assemblies often exhibit stimulus-induced rhythmic activity in the gamma range (30-80 Hz), whose magnitude depends on the attentional load. This has led to the suggestion that gamma rhythms form dynamic communication channels across cortical areas processing the features of behaviorally relevant stimuli. Recently, attention has been linked to a normalization mechanism, in which the response of a neuron is suppressed (normalized) by the overall activity of a large pool of neighboring neurons. In this model, attention increases the excitatory drive received by the neuron, which in turn also increases the strength of normalization, thereby changing the balance of excitation and inhibition. Recent studies have shown that gamma power also depends on such excitatory-inhibitory interactions. Could modulation in gamma power during an attention task be a reflection of the changes in the underlying excitation-inhibition interactions? By manipulating the normalization strength independent of attentional load in macaque monkeys, we show that gamma power increases with increasing normalization, even when the attentional load is fixed. Further, manipulations of attention that increase normalization increase gamma power, even when they decrease the firing rate. Thus, gamma rhythms could be a reflection of changes in the relative strengths of excitation and normalization rather than playing a functional role in communication or control.

Packing in molten globules and native states

Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules.

Water treatment potential in relation to phytoplankton dynamics in tropical sewage-fed urban water bodies

Urban water bodies frequently receive untreated sewage and water levels in such water bodies are maintained by daily inputs of sewage. They function as “variable-zone” anaerobic-aerobic lagoons suffering several macrophyte, biotic and abiotic stresses. We have studied two such lakes in Bangalore (Bellandur-360 ha and Varthur-220 ha) to understand whether such an occurrence could be made beneficial (maintaining water levels as well as treatment). Such hypertrophic water body receives sewage at 180-250mg/L and is discharged at 25-80mg/L COD/BOD in different seasons. In an earlier study we reported macrophyte altering the purification function of the water body. In this paper we studied the impact of phytoplankton dynamics and macrophyte cover on the functions such as organic load removal. Algal community analysis, algal biomass, macrophyte cover, water quality, nutrient status was studied seasonally during 2009-2010. Oxygen deficiency and sometimes anoxia, recorded from surface samples resulted in high quantities of NH4+-N (30-40mg/L) and phosphate (0.5-4mg/L)-characteristics of anoxic hypertrophic urban lakes. The productiveness favoured high phytoplanktonic community characterized by small cells (<10μm; Chlorella sp. - highest numbers). The lake could be clearly demarcated into an initial anaerobic zone (40% area), a facultative zone (20%) and an aerobic zone (40%) based on redox values and GIS/bathymetry. During summer the lake is covered by floating macrophytes converting the lake into an anoxic/anaerobic water pool subduing the water purification function as well as aesthetics. When macrophytes are controlled such sewage fed water bodies can be used for treating urban wastewater while also maintaining water sustainability in these semi-arid ecosystems. This paper reports the community dynamics of phytoplankton, their function and competition with macrophytes.