A network representation of protein structures: Implications for protein stability

This study views each protein structure as a network of noncovalent connections between amino acid side chains. Each amino acid in a protein structure is a node, and the strength of the noncovalent interactions between two amino acids is evaluated for edge determination. The protein structure graphs (PSGs) for 232 proteins have been constructed as a function of the cutoff of the amino acid interaction strength at a few carefully chosen values. Analysis of such PSGs constructed on the basis of edge weights has shown the following: 1), The PSGs exhibit a complex topological network behavior, which is dependent on the interaction cutoff chosen for PSG construction. 2), A transition is observed at a critical interaction cutoff, in all the proteins, as monitored by the size of the largest cluster (giant component) in the graph. Amazingly, this transition occurs within a narrow range of interaction cutoff for all the proteins, irrespective of the size or the fold topology. And 3), the amino acid preferences to be highly connected (hub frequency) have been evaluated as a function of the interaction cutoff. We observe that the aromatic residues along with arginine, histidine, and methionine act as strong hubs at high interaction cutoffs, whereas the hydrophobic leucine and isoleucine residues get added to these hubs at low interaction cutoffs, forming weak hubs. The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins. They are also found to contribute to the additional stability of the thermophilic proteins when compared to their mesophilic counterparts and hence could be crucial for the folding and stability of the unique three-dimensional structure of proteins. Based on these results, we also predict a few residues in the thermophilic and mesophilic proteins that can be mutated to alter their thermal stability.

High-Throughput Flexible Constraint Length Viterbi Decoders on De Bruijn, Shuffle-Exchange and Butterfly Connected Architectures

Flexible constraint length channel decoders are required for software defined radios. This paper presents a novel scalable scheme for realizing flexible constraint length Viterbi decoders on a de Bruijn interconnection network. Architectures for flexible decoders using the flattened butterfly and shuffle-exchange networks are also described. It is shown that these networks provide favourable substrates for realizing flexible convolutional decoders. Synthesis results for the three networks are provided and a comparison is performed. An architecture based on a 2D-mesh, which is a topology having a nominally lesser silicon area requirement, is also considered as a fourth point for comparison. It is found that of all the networks considered, the de Bruijn network offers the best tradeoff in terms of area versus throughput.

Electronic structure and bonding of beta-rhombohedral boron using cluster fragment approach

Theoretical studies using density functional theory are carried out to understand the electronic structure and bonding and electronic properties of elemental beta-rhombohedral boron. The calculated band structure of ideal beta-rhombohedral boron (B-105) shows valence electron deficiency and depicts metallic behavior. This is in contrast to the experimental result that it is a semiconductor. To understand this ambiguity we discuss the electronic structure and bonding of this allotrope with cluster fragment approach using our recently proposed mno rule. This helps us to comprehend in greater detail the structure of B-105 and materials which are closely related to beta-rhombohedral boron. The molecular structures B12H12-2, B28H21+1, BeB27H21, LiB27H21-1, CB27H21+2, B57H36+3, Be3B54H36, and Li2CB54H36, and corresponding solids Li8Be3B102 and Li10CB102 are arrived at using these ideas and studied using first principles density functional theory calculations.

An analytical approach to the study of cooperation in wireless ad hoc networks

In wireless ad hoc networks, nodes communicate with far off destinations using intermediate nodes as relays. Since wireless nodes are energy constrained, it may not be in the best interest of a node to always accept relay requests. On the other hand, if all nodes decide not to expend energy in relaying, then network throughput will drop dramatically. Both these extreme scenarios (complete cooperation and complete noncooperation) are inimical to the interests of a user. In this paper, we address the issue of user cooperation in ad hoc networks. We assume that nodes are rational, i.e., their actions are strictly determined by self interest, and that each node is associated with a minimum lifetime constraint. Given these lifetime constraints and the assumption of rational behavior, we are able to determine the optimal share of service that each node should receive. We define this to be the rational Pareto optimal operating point. We then propose a distributed and scalable acceptance algorithm called Generous TIT-FOR-TAT (GTFT). The acceptance algorithm is used by the nodes to decide whether to accept or reject a relay request. We show that GTFT results in a Nash equilibrium and prove that the system converges to the rational and optimal operating point.

Simulation of wavelength/time multiple-pulses-per-row fiber-optic CDMA network

Passive wavelength/time fiber-optic code division multiple access (WIT FO-CDMA) network is a viable option for highspeed access networks. Constructions of 2-D codes, suitable for incoherent WIT FO-CDMA, have been proposed to reduce the time spread of the 1-D sequences. The 2-D constructions can be broadly classified as 1) hybrid codes and 2) matrix codes. In our earlier work [141, we had proposed a new family of wavelength/time multiple-pulses-per-row (W/T MPR) matrix codes which have good cardinality, spectral efficiency and at the same time have the lowest off-peak autocorrelation and cross-correlation values equal to unity. In this paper we propose an architecture for a WIT MPR FO-CDAM network designed using the presently available devices and technology. A complete FO-CDMA network of ten users is simulated, for various number of simultaneous users and shown that 0 --> 1 errors can occur only when the number of interfering users is at least equal to the threshold value.

Flow driven electronic transport in carbon nan otubes

The flow of a liquid on single-walled carbon nanotube bundles induces an electrical signal (voltage/current) in the sample along the direction of the flow. The electrical response is found to be logarithmic in the flow speed over a wide range. The magnitude of the flow induced electrical signal generated depends sensitively on the ionic conductivity and the polar nature of the liquid, and electrical biasing of the nanotubes can control its direction. Our measurements suggest that the dominant mechanism responsible for this highly sub-linear response should involve a direct forcing of the free charge carriers in the nanotubes by the fluctuating Coulombic field of the liquid flowing past it.

Analysis of connectivity map: Control to glutamate injured and phenobarbital treated neuronal network

We study the responses of a cultured neural network when it is exposed to epileptogenesis glutamate injury causing epilepsy and subsequent treatment with phenobarbital by constructing connectivity map of neurons using correlation matrix. This study is particularly useful in understanding the pharmaceutical drug induced changes in the neuronal network properties with insights into changes at the systems biology level. (C) 2010 American Institute of Physics. [doi:10.1063/1.3398025]

Generic Routing Rules and a Scalable Access Enhancement for the Network-on-Chip RECONNECT

RECONNECT is a Network-on-Chip using a honeycomb topology. In this paper we focus on properties of general rules applicable to a variety of routing algorithms for the NoC which take into account the missing links of the honeycomb topology when compared to a mesh. We also extend the original proposal [5] and show a method to insert and extract data to and from the network. Access Routers at the boundary of the execution fabric establish connections to multiple periphery modules and create a torus to decrease the node distances. Our approach is scalable and ensures homogeneity among the compute elements in the NoC. We synthesized and evaluated the proposed enhancement in terms of power dissipation and area. Our results indicate that the impact of necessary alterations to the fabric is negligible and effects the data transfer between the fabric and the periphery only marginally.

Influence of Oxide Particle Network Morphology on Ion Solvation and Transport in ``Soggy Sand''Electrolytes

The role of oxide surface chemical composition and solvent on ion solvation and ion transport of ``soggy sand'' electrolytes are discussed here. A ``soggy sand'' electrolyte system comprising dispersions of hydrophilic/hydrophobic functionalized aerosil silica in lithium perchlorate methoxy polyethylene glycol solution was employed for the study. Static and dynamic rheology measurements show formation of an attractive particle network in the case of the composite with unmodified aerosil silica (i.e., with surface silanol groups) as well as composites with hydrophobic alkane groups. While particle network in the composite with hydrophilic aerosil silica (unmodified) were due to hydrogen bonding, hydrophobic aerosil silica particles were held together via van der Waals forces. The network strength in the latter case (i.e., for hydrophobic composites) were weaker compared with the composite with unmodified aerosil silica. Both unmodified silica as well as hydrophobic silica composites displayed solid-like mechanical strength. No enhancement in ionic conductivity compared to the liquid electrolyte was observed in the case of the unmodified silica. This was attributed to the existence of a very strong particle network, which led to the ``expulsion'' of all conducting entities from the interfacial region between adjacent particles. The ionic conductivity for composites with hydrophobic aerosil particles displayed ionic conductivity dependent on the size of the hydrophobic chemical moiety. No spanning attractive particle network was observed for aerosil particles with surfaces modified with stronger hydrophilic groups (than silanol). The composite resembled a sol, and no percolation in ionic conductivity was observed.

Spectrophotometric and potentiometric investigations of copper (II)-Ethanolamine complexes - Part III. diethanolamine (Gaussian analysis of electronic spectra in mono and diethanolamine systems)

Spectrophotometric and potentiometric investigations have been carried out on copper-diethanolamine system. Job plots at 900, 900 and 580 mμ have indicated the formation of CuD++, CuD2++ and CuD3++. The n- pA curves obtained indicate the formation of CuD++, CuD2++, CuD3++, CuDOH+, CuD2OH+ and CuD3OH+. The n- pA curves have been analyzed to obtain the stability constants of these complexes. Absorption curves of pure complexes have been computed by a graphical method. Gaussian analysis of the absorption curves of pure and hydroxy complexes show the presence of a second band, indicating that the structure is that of a distorted octahedron.

Excited-state structures of molecules with nearby electronic states

Vibronic coupling among the nearby excited electronic states via the in-plane and the out-of-plane nuclear motions is examined in benzene, pyrazine, formaldehyde and thioformaldehyde. Results reveal that in benzene the structure distorts via the most active nuclear bending (planar) motion while in the other molecules the structures distort through an out-of-plane bending motion in their respective lowest excited states.

Electronic structures of electron donor-acceptor complexes: results from ultraviolet photoelectron spectroscopy and molecular orbital calculations

HeI photoelectron spectra of 1:1 electron donor-acceptor complexes are discussed in the light of molecular orbital calculations. The complexes discussed include those formed by BH3, BF3 and SO2. Some systematics have been found in the ionization energy shifts of the complexes compared to the free components and these are related to the strength of the donor-acceptor bond. Hel spectra of hydrogen bonded complexes are discussed in comparison with results from MO calculations. Limitations of such studies as well as scope for further investigations are indicated.

Solvent effect on the electronic absorption spectra of polyaniline

The electronic absorption peak at around 2 eV of polyaniline (in the emeraldine base form) solution is found to be highly sensitive to the dielectric constant of the solvent, showing a bathochromic shift. An increase in electron density on the imine nitrogen of the polymer, on ‘2 eV’ excitation, has been concluded.