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.

Optimal multicommodity flow through the complete graph with random edge capacities

We consider a multicommodity flow problem on a complete graph whose edges have random, independent, and identically distributed capacities. We show that, as the number of nodes tends to infinity, the maximumutility, given by the average of a concave function of each commodity How, has an almost-sure limit. Furthermore, the asymptotically optimal flow uses only direct and two-hop paths, and can be obtained in a distributed manner.

Neutral-point balancing of neutral-point-clamped three-level inverter with a front end switched rectifier DC source for the full modulationn range

A switched rectifier DC voltage source three-level neutral-point-clamped (NPC) converter topology is proposed here to alleviate the inverter from capacitor voltage balancing in three-level drive systems. The proposed configuration requires only one DC link with a voltage of half of that needed in a conventional NPC inverter. To obtain a rated DC link voltage, the rectifier DC source is alternately connected in parallel to one of the two series capacitors using two switches and two diodes with device voltage ratings of half the total DC bus voltage. The frequency at which the voltage source is switched is independent of the inverter and will not affect its operation since the switched voltage source in this configuration balances the capacitors automatically. The proposed configuration can also be used as a conventional two-level inverter in the lower modulation index range, thereby increasing the reliability of the drivesystem. A space-vector-based PWM scheme is used to verify this proposed topology on a laboratory system.

Anomalous temperature dependence of Fermi-edge singularity in modulation-doped AlGaAs/InGaAs/GaAs hetero-structures

The temperature and power dependence of Fermi-edge singularity (FES) in high-density two-dimensional electron gas, specific to pseudomorphic AlxGa1-xAs/InGa1-yAs/GaAs heterostructures is studied by photoluminescence (PL). In all these structures, there are two prominent transitions E-11 and E-21 considered to be the result of electron-hole recombination from first and second electron sub-bands with that of first heavy-hole sub-band. FES is observed approximately 5-10 meV below the E-21 transition. At 4.2 K, FES appears as a lower energy shoulder to the E-21 transition. The PL intensity of all the three transitions E-11, FES and E-21 grows linearly with excitation power. However, we observe anomalous behavior of FES with temperature. While PL intensity of E-11 and E-21 decrease with increasing temperature, FES transition becomes stronger initially and then quenches-off slowly (till 40K). Though it appears as a distinct peak at about 20 K, its maximum is around 7 - 13 K.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of mn K-edge XANES data

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K-edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3. The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

Local structure of Sr(2)FeMoxW1-xO(6) double perovskites studied by EXAFS

Sr2FeMoO6 double perovskits display low field MR at a relatively high temperature and unusual ferromagnetic properties. These compounds depicts metal to insulator transition increasing x above x(c) similar to 0.25. A comparative analysis of the near edge regions (XANES) suggests that iron is Fe3+ in the metallic range. Checking the end compounds, we found that the doped samples can be viewn as inhomogeneous distributions of the end compounds. This could help to distinguish between the two scenarios proposed to explain the metal to insulator transition. Moreover, the local atomic structure of Sr2FeMoxW1-xO6 as a function of composition (0 <= x <= 1) has been investigated by Extended X-ray absorption spectroscopy (EXAFS) a the Fe, Mo, Sr K-edges andW L-III-edge.

Design of rectangular reinforced concrete slabs supported on all the sides with a short discontinuous edge

Bending moment coefficients for the design of rectangular reinforced concrete panels supported on four sides with a short discontinuous edge are derived using the strip theory. The moment fields resulting from the use of proposed coefficients are examined in terms of the moment volume for possible savings in reinforcement and compared with other codified procedures. The strip coefficients averaged over the corresponding sides of the panel, besides resulting in considerable savings in reinforcement, are found to be identical with the coefficients predicted by simple yield line theory using an orthotropic layout of reinforcement.

Long-range synthon Aufbau modules (LSAM) in crystal structures: systematic changes in C6H6-nFn (0 <= n <= 6) fluorobenzenes

We discuss the assembly of a three-dimensional molecular crystal in terms of short-range supramolecular synthons that spontaneously organize themselves according to Aufbau principles into long-range geometries characteristic of the molecules themselves. For this purpose we have examined the systematic changes in the known crystal structures of a family of fluorobenzenes, C6H6-nFn, where 0 <= n <= 6. Crystal assembly is initiated by forming long-range synthon Aufbau modules (LSAM) that carry the imprint of the synthons. For example, when 1 <= n <= 5 the short-range synthons use H center dot center dot center dot F interactions to form the LSAMs. In the n = 0 and n = 6 compounds, the synthons are H center dot center dot center dot C and F center dot center dot center dot C interactions, respectively. The LSAMs are usually one-dimensional. In this study we show that these 1D LSAMs assemble into 2D quasi-hexagonal close-packed layers. The 3D crystal structure is obtained from the various kinds of close-packing known for these 2D layers. The final stages of this 1D -> 2D -> 3D assembly seem to be more influenced by the packing of LSAMs than by any other factor. In these final stages, there may not be so much influence exerted by the stronger short-range synthons. We discuss the evolution of these fluorobenzene crystal structures in terms of putative LSAMs and the purely geometric relationships between the n and (6 - n) compounds that can thus be expected. Such particle-hole pairs show structural similarities. Our discussion is quantified by the interpretation of intermolecular distances in terms of atomic sizes and with qualitative predictions of magnetic model systems.

Long-range synthon Aufbau modules (LSAM) in crystal structures: systematic changes in C6H6-nFn (0 <= n <= 6) fluorobenzenes

We discuss the assembly of a three-dimensional molecular crystal in terms of short-range supramolecular synthons that spontaneously organize themselves according to Aufbau principles into long-range geometries characteristic of the molecules themselves. For this purpose we have examined the systematic changes in the known crystal structures of a family of fluorobenzenes, C6H6-nFn, where 0 <= n <= 6. Crystal assembly is initiated by forming long-range synthon Aufbau modules (LSAM) that carry the imprint of the synthons. For example, when 1 <= n <= 5 the short-range synthons use H center dot center dot center dot F interactions to form the LSAMs. In the n = 0 and n = 6 compounds, the synthons are H center dot center dot center dot C and F center dot center dot center dot C interactions, respectively. The LSAMs are usually one-dimensional. In this study we show that these 1D LSAMs assemble into 2D quasi-hexagonal close-packed layers. The 3D crystal structure is obtained from the various kinds of close-packing known for these 2D layers. The final stages of this 1D -> 2D -> 3D assembly seem to be more influenced by the packing of LSAMs than by any other factor. In these final stages, there may not be so much influence exerted by the stronger short-range synthons. We discuss the evolution of these fluorobenzene crystal structures in terms of putative LSAMs and the purely geometric relationships between the n and (6 - n) compounds that can thus be expected. Such particle-hole pairs show structural similarities. Our discussion is quantified by the interpretation of intermolecular distances in terms of atomic sizes and with qualitative predictions of magnetic model systems.

A comparative study of dynamic,ductile fracture initiation in two specimen configurations

In this work a single edge notched plate (SEN(T)) subjected to a tensile stress pulse is analysed, using a 2D plane strain dynamic finite element procedure. The interaction of the notch with a pre-nucleated hole ahead of it is examined. The background material is modelled by the Gurson constitutive law and ductile failure by microvoid coalescence in the ligament connecting the notch and the hole is simulated. Both rate independent and rate dependent material behaviour is considered. The notch tip region is subjected to a range of loading rates j by varying the peak value and the rise time of the applied stress pulse. The results obtained from these simulations are compared with a three point bend (TPB) specimen subjected to impact loading analysed in an earlier work [3] The variation of J at fracture initiation, J(c), with average loading rate j is obtained from the finite element simulations. It is found that the functional relationship between J(c) and j is fairly independent of the specimen geometry and is only dependent on material behaviour.

Limit Analysis of Slabs with Free Edge

The general method earlier developed by the writers for obtaining valid lower bound solutions to slabs under uniformly distributed load and supported along all edges is extended to the slabs with a free edge. Lower bound solutions with normal moment criterion are presented for six cases of orthotropically reinforced slabs, with one of the short edges being free and the other three edges being any combination of fixed and simply supported conditions. The expressions for moment field and collapse load are given for each slab. The lower bounds have been compared with the corresponding upper bound values obtained from the yield line theory with simple straight yield line modes of failure. They are also compared with Nielsen’s solutions available for two cases with isotropic reinforcement.

Nature of Pb in superconducting cuprates containing lead: A Pb L3 x‐ray absorption near‐edge spectroscopy study

X‐ray absorption near‐edge spectroscopy studies show that Pb in superconducting Tl0.5Pb0.5CaSr2Cu2O7+δ is essentially in the 4+ state while it is in the 2+ state in Pb2Sr2Ca1−xLnxCu3O8+δ.

Effect of interaction of macrocracks on the stress intensity factor in a beam

Beams with a central edge crack, as well as other noncentral vertical and inclined edge cracks distributed symmetrically, subjected to three-point as well as four-point bending, are analysed using the finite element technique. Values of stress intensity factor K1 at the central crack tip for a crack-to-beam depth ratio Image equal to 0.5, are calculated for various cracked-beam configurations, using the compliance calibration technique as well as method of strain energy release rate. These are compared with the value of K1 for the case of a beam with central edge crack alone. Results of the present parametric study are used to specify the range of values pertaining to basic parameters such as crack-to-beam depth ratios, geometry and position with respect to central edge crack, of other macrocracks for which interaction exists. Accordingly, the macrocracks are classified as either interacting or noninteracting types. Hence for noninteracting types of cracks, analytical expressions available for the determination of K1 in the case of beam with a central edge crack alone, are applicable.

Fractional quantum Hall edge: Effect of nonlinear dispersion and edge roton

According to Wen's theory, a universal behavior of the fractional quantum Hall edge is expected at sufficiently low energies, where the dispersion of the elementary edge excitation is linear. A microscopic calculation shows that the actual dispersion is indeed linear at low energies, but deviates from linearity beyond certain energy, and also exhibits an "edge roton minimum." We determine the edge exponent from a microscopic approach, and find that the nonlinearity of the dispersion makes a surprisingly small correction to the edge exponent even at energies higher than the roton energy. We explain this insensitivity as arising from the fact that the energy at maximum spectral weight continues to show an almost linear behavior up to fairly high energies. We also study, in an effective-field theory, how interactions modify the exponent for a reconstructed edge with multiple edge modes. Relevance to experiment is discussed.

Faster Algorithms for All-pairs Approximate Shortest Paths in Undirected Graphs

Let G - (V, E) be a weighted undirected graph having nonnegative edge weights. An estimate (delta) over cap (u, v) of the actual distance d( u, v) between u, v is an element of V is said to be of stretch t if and only if delta(u, v) <= (delta) over cap (u, v) <= t . delta(u, v). Computing all-pairs small stretch distances efficiently ( both in terms of time and space) is a well-studied problem in graph algorithms. We present a simple, novel, and generic scheme for all-pairs approximate shortest paths. Using this scheme and some new ideas and tools, we design faster algorithms for all-pairs t-stretch distances for a whole range of stretch t, and we also answer an open question posed by Thorup and Zwick in their seminal paper [J. ACM, 52 (2005), pp. 1-24].