Biological water: Femtosecond dynamics of macromolecular hydration

The unique features of a macromolecule and water as a solvent make the issue of solvation unconventional, with questions about the static versus dynamic nature of hydration and the, physics of orientational and translational diffusion at the boundary. For proteins, the hydration shell that covers the surface is critical to the stability of its structure and function. Dynamically speaking, the residence time of water at the surface is a signature of its mobility and binding. With femtosecond time resolution it is possible to unravel the shortest residence times which are key for the description of the hydration layer, static or dynamic. In this article we review these issues guided by experimental studies, from this laboratory, of polar hydration dynamics at the surfaces of two proteins (Subtilisin Carlsberg (SC) and Monellin). The natural probe tryptophan amino acid was used for the interrogation of the dynamics, and for direct comparison we also studied the behavior in bulk water - a complete hydration in 1 ps. We develop a theoretical description of solvation and relate the theory to the experimental observations. In this - theoretical approach, we consider the dynamical equilibrium in the hydration shell, defining the rate processes for breaking and making the transient hydrogen bonds, and the effective friction in the layer which is defined by the translational and orientational motions of water molecules. The relationship between the residence time of water molecules and the observed slow component in solvation dynamics is a direct one. For the two proteins studied, we observed a "bimodal decay" for the hydration correlation function, with two primary relaxation times: ultrafast, typically 1 ps or less, and longer, typically 15-40 ps, and both are related to the residence time at the protein surface, depending on the binding energies. We end by making extensions to studies of the denatured state of the protein, random coils, and the biomimetic micelles, and conclude with our thoughts on the relevance of the dynamics of native structures to their functions.

Topological phases, Majorana modes and quench dynamics in a spin ladder system

We explore the salient features of the `Kitaev ladder', a two-legged ladder version of the spin-1/2 Kitaev model on a honeycomb lattice, by mapping it to a one-dimensional fermionic p-wave superconducting system. We examine the connections between spin phases and topologically non-trivial phases of non-interacting fermionic systems, demonstrating the equivalence between the spontaneous breaking of global Z(2) symmetry in spin systems and the existence of isolated Majorana modes. In the Kitaev ladder, we investigate topological properties of the system in different sectors characterized by the presence or absence of a vortex in each plaquette of the ladder. We show that vortex patterns can yield a rich parameter space for tuning into topologically non-trivial phases. We introduce and employ a new topological invariant for explicitly determining the presence of zero energy Majorana modes at the boundaries of such phases. Finally, we discuss dynamic quenching between topologically non-trivial phases in the Kitaev ladder and, in particular, the post-quench dynamics governed by tuning through a quantum critical point.

Freezing of classical fluids in a quenched random potential

The phase diagram of a hard-sphere fluid in the presence of a random pinning potential is studied analytically and numerically. In the analytic work, replicas are introduced for averaging over the quenched disorder, and the hypernetted chain approximation is used to calculate density correlations in the replicated liquid. The freezing transition of the liquid into a nearly crystalline state is studied using a density-functional approach, and the liquid to glass transition is studied using a phenomenological replica symmetry breaking approach. In the numerical work, local minima of a discretized version of the Ramakrishnan-Yussouff free-energy functional are located and the phase diagram in the density-disorder plane is obtained from an analysis of the relative stability of these minima. Both approaches lead to similar results for the phase diagram. The first-order liquid to crystalline solid transition is found to change to a continuous liquid to glass transition as the strength of the disorder is increased above a threshold value.

Cavitation in holographic sQGP

We study the possibility of cavitation in the non-conformal N = 2* SU(N) theory which is a mass deformation of N = 4 SU(N) Yang-Mills theory. The second order transport coefficients are known from the numerical work using AdS/CFT by Buchel and collaborators. Using these and the approach of Rajagopal and Tripuraneni, we investigate the flow equations in a (1 + 1)-dimensional boost invariant set up. We find that the string theory model does not exhibit cavitation before phase transition is reached. We give a semi-analytic explanation of this finding. (C) 2011 Elsevier B.V. All rights reserved.

Guessing and compression subject to distortion

The problem of guessing a random string is revisited. The relation-ship between guessing without distortion and compression is extended to the case when source alphabet size is countably in¯nite. Further, similar relationship is established for the case when distortion allowed by establishing a tight relationship between rate distortion codes and guessing strategies.

Potential and Electric Field Profiles for Transmission line Insulators

Transmission of bulk power at high voltages over very long distances has become very imperative. At present, throughout the globe, this task has been mostly performed by overhead transmission lines. The dual task of mechanically supporting and electrically isolating the live phase conductors from the support tower is performed by string insulators. Whether in clean condition or under polluted conditions, the electrical stress distribution along the insulators governs the possible flashover, which is quite detrimental to the system. However, a reliable data on stress distribution in commonly employed string insulators are rather scarce. Considering this, the present work has made an attempt to study accurately, the field distribution in 220 kV strings for six different types of porcelain/ceramic insulators (Normal and Antifog discs) used for high voltage transmission. The surface charge simulation method is employed for the required field computation. Voltage and electric stress distribution is deduced and compared across different types of discs. A comparison on normalised surface resistance, which is an indicator for the stress concentration under polluted condition, is also attempted.

Dynamically Reconfigurable Regular Expression Matching Architecture

Regular Expressions are generic representations for a string or a collection of strings. This paper focuses on implementation of a regular expression matching architecture on reconfigurable fabric like FPGA. We present a Nondeterministic Finite Automata based implementation with extended regular expression syntax set compared to previous approaches. We also describe a dynamically reconfigurable generic block that implements the supported regular expression syntax. This enables formation of the regular expression hardware by a simple cascade of generic blocks as well as a possibility for reconfiguring the generic blocks to change the regular expression being matched. Further,we have developed an HDL code generator to obtain the VHDL description of the hardware for any regular expression set. Our optimized regular expression engine achieves a throughput of 2.45 Gbps. Our dynamically reconfigurable regular expression engine achieves a throughput of 0.8 Gbps using 12 FPGA slices per generic block on Xilinx Virtex2Pro FPGA.

Ultrasonic Lamb wave based monitoring of corrosion type of damage in plate using a circular array of piezoelectric transducers

In this paper we propose a concept and report experimental results based on a circular array of Piezoelectric Wafer Active Sensors (PWASs) for rapid localization and parametric identification of corrosion type damage in metallic plates. Implementation of this circular array of PWASs combines the use of ultrasonic Lamb wave propagation technique and an algorithm based on symmetry breaking in the signal pattern to locate and monitor the growth of a corrosion pit on a metallic plate. Wavelet time-frequency maps of the sensor signals are employed to obtain an insight regarding the effect of corrosion growth on the Lamb wave transmission in time-frequency scale. We present here a method to eliminate the time scale, which helps in identifying easily the signature of damage in the measured signals. The proposed method becomes useful in determining the approximate location of the damage with respect to the location of three neighboring sensors in the circular array. A cumulative damage index is computed from the wavelet coefficients for varying damage sizes and the results appear promising. Damage index is plotted against the damage parameters for frequency sweep of the excitation signal (a windowed sine signal). Results of corrosion damage are compared with circular holes of various sizes to demonstrate the applicability of present method to different types of damage. (C) 2011 Elsevier Ltd. All rights reserved.

Possible Neutrino-Antineutrino Oscillation Under Gravity and its Consequences

We show that under gravity the effective masses for neutrino and antineutrino are different which opens a possible window of neutrino-antineutrino oscillation even if the rest masses of the corresponding eigenstates are same. This is due to CPT violation and possible to demonstrate if the neutrino mass eigenstates are expressed as a combination of neutrino and antineutrino eigenstates, as of the neutral kaon system, with the plausible breaking of lepton number conservation. In early universe, in presence of various lepton number violating processes, this oscillation might lead to neutrino-antineutrino asymmetry which resulted baryogenesis from the B-L symmetry by electro-weak sphaleron processes. On the other hand, for Majorana neutrinos, this oscillation is expected to affect the inner edge of neutrino dominated accretion disks around a compact object by influencing the neutrino sphere which controls the accretion dynamics, and then the related type-II supernova evolution and the r-process nucleosynthesis.

Classical integrability in the BTZ black hole

Using the fact the BTZ black hole is a quotient of AdS(3) we show that classical string propagation in the BTZ background is integrable. We construct the flat connection and its monodromy matrix which generates the non-local charges. From examining the general behaviour of the eigen values of the monodromy matrix we determine the set of integral equations which constrain them. These equations imply that each classical solution is characterized by a density function in the complex plane. For classical solutions which correspond to geodesics and winding strings we solve for the eigen values of the monodromy matrix explicitly and show that geodesics correspond to zero density in the complex plane. We solve the integral equations for BMN and magnon like solutions and obtain their dispersion relation. We show that the set of integral equations which constrain the eigen values of the monodromy matrix can be identified with the continuum limit of the Bethe equations of a twisted SL(2, R) spin chain at one loop. The Landau-Lifshitz equations from the spin chain can also be identified with the sigma model equations of motion.

Instabilities of soft elastic microtubes filled with viscous fluids: Pearls, wrinkles, and sausage strings

A linear stability analysis is presented to study the self-organized instabilities of a highly compliant elastic cylindrical shell filled with a viscous liquid and submerged in another viscous medium. The prototype closely mimics many components of micro-or nanofluidic devices and biological processes such as the budding of a string of pearls inside cells and sausage-string formation of blood vessels. The cylindrical shell is considered to be a soft linear elastic solid with small storage modulus. When the destabilizing capillary force derived from the cross-sectional curvature overcomes the stabilizing elastic and in-plane capillary forces, the microtube can spontaneously self-organize into one of several possible configurations; namely, pearling, in which the viscous fluid in the core of the elastic shell breaks up into droplets; sausage strings, in which the outer interface of the mircrotube deforms more than the inner interface; and wrinkles, in which both interfaces of the thin-walled mircrotube deform in phase with small amplitudes. This study identifies the conditions for the existence of these modes and demonstrates that the ratios of the interfacial tensions at the interfaces, the viscosities, and the thickness of the microtube play crucial roles in the mode selection and the relative amplitudes of deformations at the two interfaces. The analysis also shows asymptotically that an elastic fiber submerged in a viscous liquid is unstable for Y = gamma/(G(e)R) > 6 and an elastic microchannel filled with a viscous liquid should rupture to form spherical cavities (pearling) for Y > 2, where gamma, G(e), and R are the surface tension, elastic shear modulus, and radius, respectively, of the fiber or microchannel.

Possibility of chaos in interval friction experiments of martensites

Wuttig and Suzuki's model on anelastic nonlinearities in solids in the vicinity of martensite transformations is analysed numerically. This model shows chaos even in the absence of applied forcing field as a function of a temperature dependent parameter. Even though the model exhibits sustained oscillations as a function of the amplitude of the forcing term, it does not exactly capture the features of the experimental time series. We have improved the model by adding a symmetry breaking term. The improved model shows period doubling bifurcation as a function of the amplitude of the forcing term. The solutions of our improved model shows good resemblance with the nonsymmetric period four oscillation seen in the experiment. (C) 1999 Elsevier Science B.V. All rights reserved.

Simulation of Potential and Electric Field Profiles for transmission line Insulators

Since the end of second world war, extra high voltage ac transmission has seen its development. The distances between generating and load centres as well as the amount of power to be handled increased tremendously for last 50 years. The highest commercial voltage has increased to 765 kV in India and 1,200 kV in many other countries. The bulk power transmission has been mostly performed by overhead transmission lines. The dual task of mechanically supporting and electrically isolating the live phase conductors from the support tower is performed by string insulators. Whether in clean condition or under polluted conditions, the electrical stress distribution along the insulators governs the possible flashover, which is quite detrimental to the system. Hence the present investigation aims to study accurately, the field distribution for various types of porcelain/ceramic insulators (Normal and Antifog discs) used for high-voltage transmission. The surface charge simulation method is employed for the field computation. A comparison on normalised surface resistance, which is an indicator for the stress concentration under polluted condition, is also attempted.

Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative `Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed `3interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Nanoindentation as a probe for mechanically-induced molecular migration in layered organic donor-acceptor complexes

Nanoindentation and scratch experiments on 1:1 donor-acceptor complexes, 1 and 2, of 1,2,4,5-tetracyanobenzene with pyrene and phenanthrene, respectively, reveal long-range molecular layer gliding and large interaction anisotropy. Due to the layered arrangements in these crystals, these experiments that apply stress in particular directions result in the breaking of interlayer interactions, thus allowing molecular sheets to glide over one another with ease. Complex 1 has a layered crystal packing wherein the layers are 68° skew under the (002) face and the interlayer space is stabilized by van der Waals interactions. Upon indenting this surface with a Berkovich tip, pile-up of material was observed on just one side of the indenter due to the close angular alignment of the layers with the half angle of the indenter tip (65.35°). The interfacial differences in the elastic modulus (21 ) and hardness (16 ) demonstrate the anisotropic nature of crystal packing. In 2, the molecular stacks are arranged in a staggered manner; there is no layer arrangement, and the interlayer stabilization involves C-H�N hydrogen bonds and ��� interactions. This results in a higher modulus (20 ) for (020) as compared to (001), although the anisotropy in hardness is minimal (4 ). The anisotropy within a face was analyzed using AFM image scans and the coefficient of friction of four orthogonal nanoscratches on the cleavage planes of 1 and 2. A higher friction coefficient was obtained for 2 as compared to 1 even in the cleavage direction due to the presence of hydrogen bonds in the interlayer region making the tip movement more hindered. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.