Conformation of substituted polyacetylenes in solution : relationship between electronic properties and local order

A study of the chain conformation in solutions of polyphenylacetylene and poly(2-octyne) has been performed. The two polymers differ in many ways : polyphenylacetylene gives a red solution while poly(2-octyne) is transparent and, a marked difference on the chain rigidity is observed : the statistical length are 45 Å and 135 Å respectively. From the study of these two systems, one deduces that curvature fluctuations play a minor role on the π electrons localization, and that the torsion between monomer units is the pertinent parameter to understand the chain conformation and the π electrons localization.

Results from PAMELA, ATIC and FERMI: Pulsars or dark matter?

It is well known that dark matter dominates the dynamics of galaxies and clusters of galaxies. Its constituents remain a mystery despite an assiduous search for them over the past three decades. Recent results from the satellite-based PAMELA experiment show an excess in the positron fraction at energies between 10 and 100 GeV in the secondary cosmic ray spectrum. Other experiments, namely ATIC, HESS and FERMI, show an excess in the total electron (e(+) + e(-)) spectrum for energies greater than 100 GeV. These excesses in the positron fraction as well as the electron spectrum can arise in local astrophysical processes like pulsars, or can be attributed to the annihilation of the dark matter particles. The latter possibility gives clues to the possible candidates for the dark matter in galaxies and other astrophysical systems. In this article, we give a report of these exciting developments.

Search Strategies for Multiple UAV Search and Destroy Missions

Multiple UAVs are deployed to carry out a search and destroy mission in a bounded region. The UAVs have limited sensor range and can carry limited resources which reduce with use. The UAVs perform a search task to detect targets. When a target is detected which requires different type and quantities of resources to completely destroy, then a team of UAVs called as a coalition is formed to attack the target. The coalition members have to modify their route to attack the target, in the process, the search task is affected, as search and destroy tasks are coupled. The performance of the mission is a function of the search and the task allocation strategies. Therefore, for a given task allocation strategy, we need to devise search strategies that are efficient. In this paper, we propose three different search strategies namely; random search strategy, lanes based search strategy and grid based search strategy and analyze their performance through Monte-Carlo simulations. The results show that the grid based search strategy performs the best but with high information overhead.

Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Frontier Based Multiple Goal Search in Unknown Environments

We present a frontier based algorithm for searching multiple goals in a fully unknown environment, with only information about the regions where the goals are most likely to be located. Our algorithm chooses an ``active goal'' from the ``active goal list'' generated by running a Traveling Salesman Problem (Tsp) routine with the given centroid locations of the goal regions. We use the concept of ``goal switching'' which helps not only in reaching more number of goals in given time, but also prevents unnecessary search around the goals that are not accessible (surrounded by walls). The simulation study shows that our algorithm outperforms Multi-Heuristic LRTA* (MELRTA*) which is a significant representative of multiple goal search approaches in an unknown environment, especially in environments with wall like obstacles.

Multiple UAV Coalitions for a Search and Prosecute Mission

Unmanned aerial vehicles (UAVs) have the potential to carry resources in support of search and prosecute operations. Often to completely prosecute a target, UAVs may have to simultaneously attack the target with various resources with different capacities. However, the UAVs are capable of carrying only limited resources in small quantities, hence, a group of UAVs (coalition) needs to be assigned that satisfies the target resource requirement. The assigned coalition must be such that it minimizes the target prosecution delay and the size of the coalition. The problem of forming coalitions is computationally intensive due to the combinatorial nature of the problem, but for real-time applications computationally cheap solutions are required. In this paper, we propose decentralized sub-optimal (polynomial time) and decentralized optimal coalition formation algorithms that generate coalitions for a single target with low computational complexity. We compare the performance of the proposed algorithms to that of a global optimal solution for which we need to solve a centralized combinatorial optimization problem. This problem is computationally intensive because the solution has to (a) provide a coalition for each target, (b) design a sequence in which targets need to be prosecuted, and (c) take into account reduction of UAV resources with usage. To solve this problem we use the Particle Swarm Optimization (PSO) technique. Through simulations, we study the performance of the proposed algorithms in terms of mission performance, complexity of the algorithms and the time taken to form the coalition. The simulation results show that the solution provided by the proposed algorithms is close to the global optimal solution and requires far less computational resources.

Anomalous X-ray scattering study of local structures in the superionic conducting class (CuI)(0.3)(Cu2O)(0.35)(MoO3)(0.35)

The anomalous X-ray scattering (AXS) method using Cu and Mo K absorption edges has been employed for obtaining the local structural information of superionic conducting glass having the composition (CuI)(0.3)(Cu2O)(0.35)(MoO3)(0.35). The possible atomic arrangements in near-neighbor region of this glass were estimated by coupling the results with the least-squares analysis so as to reproduce two differential intensity profiles for Cu and Mo as well as the ordinary scattering profile. The coordination number of oxygen around Mo is found to be 6.1 at the distance of 0.187 nm. This implies that the MoO6 octahedral unit is a more probable structural entity in the glass rather than MoO4 tetrahedra which has been proposed based on infrared spectroscopy. The pre-peak shoulder observed at about 10 nm(-1) may be attributed to density fluctuation originating from the MoO6 octahedral units connected with the corner sharing linkage, in which the correlation length is about 0.8 nm. The value of the coordination number of I- around Cu+ is estimated as 4.3 at 0.261 nm, suggesting an arrangement similar to that in molten CuI.

Local polynomial convexity of the union of two totally-real surfaces at their intersection

We consider the following question: Let S (1) and S (2) be two smooth, totally-real surfaces in C-2 that contain the origin. If the union of their tangent planes is locally polynomially convex at the origin, then is S-1 boolean OR S-2 locally polynomially convex at the origin? If T (0) S (1) a (c) T (0) S (2) = {0}, then it is a folk result that the answer is yes. We discuss an obstruction to the presumed proof, and provide a different approach. When dim(R)(T0S1 boolean AND T0S2) = 1, we present a geometric condition under which no consistent answer to the above question exists. We then discuss conditions under which we can expect local polynomial convexity.

Automated Multi-Agent Search Using Centroidal Voronoi Configuration

This paper addresses the problem of automated multiagent search in an unknown environment. Autonomous agents equipped with sensors carry out a search operation in a search space, where the uncertainty, or lack of information about the environment, is known a priori as an uncertainty density distribution function. The agents are deployed in the search space to maximize single step search effectiveness. The centroidal Voronoi configuration, which achieves a locally optimal deployment, forms the basis for the proposed sequential deploy and search strategy. It is shown that with the proposed control law the agent trajectories converge in a globally asymptotic manner to the centroidal Voronoi configuration. Simulation experiments are provided to validate the strategy. Note to Practitioners-In this paper, searching an unknown region to gather information about it is modeled as a problem of using search as a means of reducing information uncertainty about the region. Moreover, multiple automated searchers or agents are used to carry out this operation optimally. This problem has many applications in search and surveillance operations using several autonomous UAVs or mobile robots. The concept of agents converging to the centroid of their Voronoi cells, weighted with the uncertainty density, is used to design a search strategy named as sequential deploy and search. Finally, the performance of the strategy is validated using simulations.

Genetic search: Analysis using fitness moments

Genetic Algorithms are efficient and robust search methods that are being employed in a plethora of applications with extremely large search spaces. The directed search mechanism employed in Genetic Algorithms performs a simultaneous and balanced, exploration of new regions in the search space and exploitation of already discovered regions.This paper introduces the notion of fitness moments for analyzing the working of Genetic Algorithms (GAs). We show that the fitness moments in any generation may be predicted from those of the initial population. Since a knowledge of the fitness moments allows us to estimate the fitness distribution of strings, this approach provides for a method of characterizing the dynamics of GAs. In particular the average fitness and fitness variance of the population in any generation may be predicted. We introduce the technique of fitness-based disruption of solutions for improving the performance of GAs. Using fitness moments, we demonstrate the advantages of using fitness-based disruption. We also present experimental results comparing the performance of a standard GA and GAs (CDGA and AGA) that incorporate the principle of fitness-based disruption. The experimental evidence clearly demonstrates the power of fitness based disruption.

Unwinding of heterologous DNA by RecA protein during the search for homologous sequences

The search for homologous sequences promoted by RecA protein in vitro involves a presynaptic filament and naked duplex DNA, the multiple contacts of which produce nucleoprotein networks or coaggregates. The single-stranded DNA within the presynaptic filaments, however, is extended to an axial spacing 1.5 times that of B-form DNA. To investigate this paradoxical difference between the spacing of bases in the RecA presynaptic filament versus the target duplex DNA, we explored the effect of heterologous contacts on the conformation of DNA, and vice versa. In the presence of wheat germ topoisomerase I, RecA presynaptic filaments induced a rapid, limited reduction in the linking number of heterologous circular duplex DNA. This limited unwinding of heterologous duplex DNA, termed heterologous unwinding, was detected within 30 seconds and reached a steady state within a few minutes. Presynaptic filaments that were formed in the presence of ATP?S and separated from free RecA protein by gel filtration also generated a ladder of topoisomers upon incubation with relaxed duplex DNA and topoisomerase. The inhibition of heterologous contacts by 60 mImage -NaCl or 5 mImage -ADP resulted in a corresponding decrease in heterologous unwinding. In reciprocal fashion, the stability or number of heterologous contacts with presynaptic filaments was inversely related to the linking number of circular duplex DNA. These observations show that heterologous contacts with the presynaptic filament cause a limited unwinding of the duplex DNA, and conversely that the ability of the DNA to unwind stabilizes transient heterologous contacts.

BSSB: BLAST Server for Structural Biologists

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processing BLAST output, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed tool BLAST Server for Structural Biologists (BSSB), which maps a BLAST output onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject protein is represented using a three-color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three-dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence-structure correlation. Furthermore, the additional structure-level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.

Sensitivity Enhancement in Solid-State Separated Local Field NMR Experiments by the Use of Adiabatic Cross-Polarization

Measurement of dipolar couplings using separated local field (SLF) NMR experiment is a powerful tool for structural and dynamics studies of oriented molecules such as liquid crystals and membrane proteins in aligned lipid bilayers. Enhancing the sensitivity of such SLF techniques is of significant importance in present-day solid-state NMR methodology. The present study considers the use of adiabatic cross-polarization for this purpose, which is applied for the first time to one of the well-known SLF techniques, namely, polarization inversion spin exchange at the magic angle (PISEMA). The experiments have been carried out on a single crystal of a model peptide, and a dramatic enhancement in signal-to-noise up to 90% has been demonstrated.