Studies on simultaneous nhibition of trypsin and chymotrypsin by horsegram Bowman-Birk inhibitor

Bowman-Birk inhibitors (BBI) isolated from plant seeds are small proteins active against trypsin and/or chymotrypsin. These inhibitors have been extensively studied in terms of their structure, interactions, function and evolution. Examination of the known three-dimensional structures of BBIs revealed similarities and subtle differences.The hydrophobic core, deduced from surface accessibility and hydrophobicity plots, corresponding to the two tandem structural domains of the double headed BBI are related by an almost exact two-fold, in contrast to the reactive site loops which depart appreciably from the two-fold symmetry. Also, the orientations of inhibitory loops in soybean and peanut inhibitors were different with respect to the rigid core. Based on the structure of Adzuki bean BBI-trypsin complex, models of trypsin and chymotryspin bound to the monomeric soybean BBI (SBI) were constructed. There were minor short contacts between the two enzymes bound to the inhibitor suggesting near independence of binding. Binding studies revealed that the inhibition of one enzyme in the presence of the other is associated with a minor negative cooperativity. In order to assess the functional significance of the reported oligomeric forms of BBI, binding of proteases to the crystallographic and non-crystallographic dimers as found in the crystal structure of peanut inhibitor were examined. It was found that all the active sites in these oligomers cannot simultaneously participate in inhibition.

Pulsatile flow of a viscous fluid in elliptical pipe of variable cross-section

The pulsatile flow of an incompressible viscous fluid in an elliptical pipe of slowly varying cross-section is considered. Asymptotic series solutions for the velocity distribution and pressure gradient are obtained in terms of Mathieu functions for a low Reynold number flow in which the volume flux is prescribed. An expression for shear stress on the boundary is derived. The physically significant quantities governing the flow are computed numerically and analysed for different types of constrictions. The effect of eccentricity and Womerslay parameter on the flow is discussed.

Crystal structures of fluorinated aryl biscarbonates and a biscarbamate: a counterpoise between weak intermolecular interactions and molecular symmetry

Conformational features and supramolecular structural organization in three aryl biscarbonates and an aryl biscarbamate with rigid acetylenic unit providing variable spacer lengths have been probed to gain insights into the packing features associated with molecular symmetry and the intermolecular interactions involving `organic' fluorine. Four structures but-2-yne-1,4-diyl bis(2,3,4,5,6-pentafluorophenylcarbonate), 1; but-2-yne-1,4-diyl bis(4-fluorophenylcarbonate), 2; but-2-yne-1,4-diyl bis(2,3,4,5,6-pentafluorophenylcarbamate), 3 and hexa-2,4-diyne-1,6-diyl bis(2,3,4,5,6-pentafluorophenylcarbonate), 4 have been analyzed in this context. Compound 1 adopts a non-centrosymmetric ``twisted'' (syn) conformation, whereas 2, 3 and 4 acquire a centrosymmetric ``extended'' (anti) conformation. Weak intermolecular interactions and in particular those involving fluorine are found to dictate this conformational variation in the crystal structure of 1. A single-crystal neutron diffraction study at 90 K was performed on 1 to obtain further insights into these interactions involving `organic' fluorine.

Symmetry Properties of the Large-Deviation Function of the Velocity of a Self-Propelled Polar Particle

A geometrically polar granular rod confined in 2D geometry, subjected to a sinusoidal vertical oscillation, undergoes noisy self-propulsion in a direction determined by its polarity. When surrounded by a medium of crystalline spherical beads, it displays substantial negative fluctuations in its velocity. We find that the large-deviation function (LDF) for the normalized velocity is strongly non-Gaussian with a kink at zero velocity, and that the antisymmetric part of the LDF is linear, resembling the fluctuation relation known for entropy production, even when the velocity distribution is clearly non-Gaussian. We extract an analogue of the phase-space contraction rate and find that it compares well with an independent estimate based on the persistence of forward and reverse velocities.

Bound states of two spin-1/2 fermions in a synthetic non-Abelian gauge field

We study the bound states of two spin-1/2 fermions interacting via a contact attraction (characterized by a scattering length) in the singlet channel in three-dimensional space in presence of a uniform non-Abelian gauge field. The configuration of the gauge field that generates a Rashba-type spin-orbit interaction is described by three coupling parameters (lambda(x),lambda(y),lambda(z)). For a generic gauge field configuration, the critical scattering length required for the formation of a bound state is negative, i.e., shifts to the ``BCS side'' of the resonance. Interestingly, we find that there are special high-symmetry configurations (e.g., lambda(x) = lambda(y) = lambda(z)) for which there is a two-body bound state for any scattering length however small and negative. Remarkably, the bound-state wave functions obtained for such configurations have nematic spin structure similar to those found in liquid He-3. Our results show that the BCS-BEC (Bose-Einstein condensation) crossover is drastically affected by the presence of a non-Abelian gauge field. We discuss possible experimental signatures of our findings both at high and low temperatures.

Exact N-Wave Solutions for the Non-Planar Burgers Equation

An exact representation of N-wave solutions for the non-planar Burgers equation u(t) + uu(x) + 1/2ju/t = 1/2deltau(xx), j = m/n, m < 2n, where m and n are positive integers with no common factors, is given. This solution is asymptotic to the inviscid solution for Absolute value of x < square-root (2Q0 t), where Q0 is a function of the initial lobe area, as lobe Reynolds number tends to infinity, and is also asymptotic to the old age linear solution, as t tends to infinity; the formulae for the lobe Reynolds numbers are shown to have the correct behaviour in these limits. The general results apply to all j = m/n, m < 2n, and are rather involved; explicit results are written out for j = 0, 1, 1/2, 1/3 and 1/4. The case of spherical symmetry j = 2 is found to be 'singular' and the general approach set forth here does not work; an alternative approach for this case gives the large time behaviour in two different time regimes. The results of this study are compared with those of Crighton & Scott (1979).

Non-Fermi liquid behavior in a mean-field study of the t-J model: Role of zero-point spin fluctuations

We present analytic results to show that the Schwinger-boson hole-fermion mean-field state exhibits non-Fermi liquid behavior due to spin-charge separation. The physical electron Green's function consists of three additive components. (a) A Fermi-liquid component associated with the bose condensate. (b) A non-Fermi liquid component which has a logarithmic peak and a long tail that gives rise to a linear density of states that is symmetric about the Fermi level and a momentum distribution function with a logarithmic discontinuity at the Fermi surface. (c) A second non-Fermi liquid component associated with the thermal bosons which leads to a constant density of states. It is shown that zero-point fluctuations associated with the spin-degrees of freedom are responsible for the logarithmic instabilities and the restoration of particle-hole symmetry close to the Fermi surface.

On the characterisation of syntactic foam core sandwich composites for compressive properties

Sandwich structures, especially those with honeycomb and grid structures as the core material, are very commonly employed in aircraft structures. There is an increasing use of closed-pore rigid syntactic foams as core materials in sandwich constructions because they possess a number of favourable properties. The syntactic foams, owing to their structure and formation, behave differently under compression compared to other traditionally used core materials. In the present study, therefore, syntactic foam core sandwich constructions are evaluated for their behaviour under compression in both edgewise and flatwise orientations. Further, the work characterises the relative performance of two sets of sandwich materials, one containing glass-epoxy and the other, glass/carbon hybrid-epoxy skins. As non-standard geometry test specimens were involved, only a comparative evaluation was contemplated in this approach. The experiments indicate that the nature of the reinforcement fabric in the skin has a bearing on the test results in edgewise orientation. Thus, the tendency towards initiation of vertical crack in the central plane of the core material, which is a typical fracture event in this kind of material, was found to occur after a delay for the specimens containing the glass fabric in the skin. Attempts are made to establish the correlation between observations made on the test specimen visually during the course of testing and the post-compression microscopic examinations of the fracture features.

Autoignition in a non-premixed medium: DNS studies on the effects of three-dimensional turbulence

Direct numerical simulation (DNS) results of autoignition in anon-premixed medium under an isotropic, homogeneous, and decaying turbulence are presented. The initial mixture consists of segregated fuel parcels randomly distributed within warm air, and the entire medium is subjected to a three-dimensional turbulence. Chemical kinetics is modeled by a four-step reduced reaction mechanism for autoignition of n-heptane/air mixture. Thus, this work overcomes the principal limitations of a previous contribution of the authors on two-dimensional DNS of autoignition with a one-step reaction model. Specific attention is focused on the differences in the effects of two- and three-dimensional turbulence on autoignition characteristics. The three-dimensional results show that ignition spots are most likely to originate at locations jointly corresponding to the most reactive mixture fraction and low scalar dissipation rate. Further, these ignition spots are found to originate at locations corresponding to the core of local vortical structures, and after ignition, the burning gases move toward the vortex periphery Such a movement is explained as caused by the cyclostrophic imbalance developed when the local gas density is variable. These results lead to the conclusion that the local ignition-zone structure does not conform to the classical stretched flamelet description. Parametric studies show that the ignition delay time decreases with an increase in turbulence intensity. Hence, these three-dimensional simulation results resolve the discrepancy between trends in experimental data and predictions from DNSs of two-dimensional turbulence. This qualitative difference between DNS results from three- and two-dimensional simulations is discussed and attributed to the effect of vortex stretching that is present in the former, but not in the latter.

BCS-BEC crossover induced by a synthetic non-Abelian gauge field

We investigate the ground state of interacting spin-1/2 fermions in three dimensions at a finite density (rho similar to k(F)(3)) in the presence of a uniform non-Abelian gauge field. The gauge-field configuration (GFC) described by a vector lambda equivalent to (lambda(x),lambda(y),lambda(z)), whose magnitude lambda determines the gauge coupling strength, generates a generalized Rashba spin-orbit interaction. For a weak attractive interaction in the singlet channel described by a small negative scattering length (k(F)vertical bar a(s)vertical bar less than or similar to 1), the ground state in the absence of the gauge field (lambda = 0) is a BCS (Bardeen-Cooper-Schrieffer) superfluid with large overlapping pairs. With increasing gauge-coupling strength, a non-Abelian gauge field engenders a crossover of this BCS ground state to a BEC (Bose-Einstein condensate) of bosons even with a weak attractive interaction that fails to produce a two-body bound state in free vacuum (lambda = 0). For large gauge couplings (lambda/k(F) >> 1), the BEC attained is a condensate of bosons whose properties are solely determined by the Rashba gauge field (and not by the scattering length so long as it is nonzero)-we call these bosons ``rashbons.'' In the absence of interactions (a(s) = 0(-)), the shape of the Fermi surface of the system undergoes a topological transition at a critical gauge coupling lambda(T). For high-symmetry GFCs we show that the crossover from the BCS superfluid to the rashbon BEC occurs in the regime of lambda near lambda(T). In the context of cold atomic systems, these results make an interesting suggestion of obtaining BCS-BEC crossover through a route other than tuning the interaction between the fermions.

Trapped fermions in a synthetic non-Abelian gauge field

On increasing the coupling strength (lambda) of a non-Abelian gauge field that induces a generalized Rashba spin-orbit interaction, the topology of the Fermi surface of a homogeneous gas of noninteracting fermions of density rho similar to k(F)(3) undergoes a change at a critical value, lambda(T) approximate to k(F) [Phys. Rev. B 84, 014512 ( 2011)]. In this paper we analyze how this phenomenon affects the size and shape of a cloud of spin-1/2 fermions trapped in a harmonic potential such as those used in cold atom experiments. We develop an adiabatic formulation, including the concomitant Pancharatnam-Berry phase effects, for the one-particle states in the presence of a trapping potential and the gauge field, obtaining approximate analytical formulas for the energy levels for some high symmetry gauge field configurations of interest. An analysis based on the local density approximation reveals that, for a given number of particles, the cloud shrinks in a characteristic fashion with increasing.. We explain the physical origins of this effect by a study of the stress tensor of the system. For an isotropic harmonic trap, the local density approximation predicts a spherical cloud even for anisotropic gauge field configurations. We show, via a calculation of the cloud shape using exact eigenstates, that for certain gauge field configurations there is a systematic and observable anisotropy in the cloud shape that increases with increasing gauge coupling lambda. The reasons for this anisotropy are explained using the analytical energy levels obtained via the adiabatic approximation. These results should be useful in the design of cold atom experiments with fermions in non-Abelian gauge fields. An important spin-off of our adiabatic formulation is that it reveals exciting possibilities for the cold-atom realization of interesting condensed matter Hamiltonians by using a non-Abelian gauge field in conjunction with another potential. In particular, we show that the use of a spherical non-Abelian gauge field with a harmonic trapping potential produces a monopole field giving rise to a spherical geometry quantum Hall-like Hamiltonian in the momentum representation.

Full spin and spatial symmetry adapted technique for correlated electronic hamiltonians: Application to an icosahedral cluster

One of the long standing problems in quantum chemistry had been the inability to exploit full spatial and spin symmetry of an electronic Hamiltonian belonging to a non-Abelian point group. Here, we present a general technique which can utilize all the symmetries of an electronic (magnetic) Hamiltonian to obtain its full eigenvalue spectrum. This is a hybrid method based on Valence Bond basis and the basis of constant z-component of the total spin. This technique is applicable to systems with any point group symmetry and is easy to implement on a computer. We illustrate the power of the method by applying it to a model icosahedral half-filled electronic system. This model spans a huge Hilbert space (dimension 1,778,966) and in the largest non-Abelian point group. The C60 molecule has this symmetry and hence our calculation throw light on the higher energy excited states of the bucky ball. This method can also be utilized to study finite temperature properties of strongly correlated systems within an exact diagonalization approach. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme

Experimental studies have observed significant changes in both structure and function of lysozyme (and other proteins) on addition of a small amount of dimethyl sulfoxide (DMSO) in aqueous solution. Our atomistic molecular dynamic simulations of lysozyme in water-DMSO reveal the following sequence of changes on increasing DMSO concentration. (i) At the initial stage (around 5% DMSO concentration) protein's conformational flexibility gets markedly suppressed. From study of radial distribution functions, we attribute this to the preferential solvation of exposed protein hydrophobic residues by the methyl groups of DMSO. (ii) In the next stage (10-15% DMSO concentration range), lysozome partially unfolds accompanied by an increase both in fluctuation and in exposed protein surface area. (iii) Between 15-20% concentration ranges, both conformational fluctuation and solvent accessible protein surface area suddenly decrease again indicating the formation of an intermediate collapse state. These results are in good agreement with near-UV circular dichroism (CD) and fluorescence studies. We explain this apparently surprising behavior in terms of a structural transformation which involves clustering among the methyl groups of DMSO. (iv) Beyond 20% concentration of DMSO, the protein starts its final sojourn towards the unfolding state with further increase in conformational fluctuation and loss in native contacts. Most importantly, analysis of contact map and fluctuation near the active site reveal that both partial unfolding and conformational fluctuations are centered mostly on the hydrophobic core of active site of lysozyme. Our results could offer a general explanation and universal picture of the anomalous behavior of protein structure-function observed in the presence of cosolvents (DMSO, ethanol, tertiary butyl alcohol, dioxane) at their low concentrations. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3694268]

Ultrasonic Guided Wave Characterization and Damage Detection in Foam-core Sandwich Panel using PWAS and LDV

Lamb wave type guided wave propagation in foam core sandwich structures and detectability of damages using spectral analysis method are reported in this paper. An experimental study supported by theoretical evaluation of the guided wave characteristics is presented here that shows the applicability of Lamb wave type guided ultrasonic wave for detection of damage in foam core sandwich structures. Sandwich beam specimens were fabricated with 10 mm thick foam core and 0.3 mm thick aluminum face sheets. Thin piezoelectric patch actuators and sensors are used to excite and sense guided wave. Group velocity dispersion curves and frequency response of sensed signal are obtained experimentally. The nature of damping present in the sandwich panel is monitored by measuring the sensor signal amplitude at various different distances measured from the center of the linear phased array. Delaminations of increasing width are created and detected experimentally by pitch-catch interrogation with guided waves and wavelet transform of the sensed signal. Signal amplitudes are analyzed for various different sizes of damages to differentiate the damage size/severity. A sandwich panel is also fabricated with a planer dimension of 600 mm x 400 mm. Release film delamination is introduced during fabrication. Non-contact Laser Doppler Vibrometer (LDV) is used to scan the panel while exciting with a surface bonded piezoelectric actuator. Presence of damage is confirmed by the reflected wave fringe pattern obtained from the LDV scan. With this approach it is possible to locate and monitor the damages by tracking the wave packets scattered from the damages.

Fermions in synthetic non-Abelian gauge potentials: rashbon condensates to novel Hamiltonians

Recent advances in the generation of synthetic gauge fields in cold atomic systems have stimulated interest in the physics of interacting bosons and fermions in them. In this paper, we discuss interacting two-component fermionic systems in uniform non-Abelian gauge fields that produce a spin-orbit interaction and uniform spin potentials. Two classes of gauge fields discussed include those that produce a Rashba spin-orbit interaction and the type of gauge fields (SM gauge fields) obtained in experiments by the Shanxi and MIT groups. For high symmetry Rashba gauge fields, a two-particle bound state exists even for a vanishingly small attractive interaction described by a scattering length. Upon increasing the strength of a Rashba gauge field, a finite density of weakly interacting fermions undergoes a crossover from a BCS like ground state to a BEC state of a new kind of boson called the rashbon whose properties are determined solely by the gauge field and not by the interaction between the fermions. The rashbon Bose-Einstein condensate (RBEC) is a quite intriguing state with the rashbon-rashbon interactions being independent of the fermion-fermion interactions (scattering length). Furthermore, we show that the RBEC has a transition temperature of the order of the Fermi temperature, suggesting routes to enhance the transition temperatures of weakly interacting superfluids by tuning the spin-orbit coupling. For the SM gauge fields, we show that in a regime of parameters, a pair of particles with finite centre-of-mass momentum is the most strongly bound. In other regimes of centre-of-mass momenta, there is no two-body bound state, but a resonance like feature appears in the scattering continuum. In the many-body setting, this results in flow enhanced pairing. Also, strongly interacting normal states utilizing the scattering resonance can be created opening the possibility of studying properties of helical Fermi liquids. This paper contains a general discussion of the physics of Feshbach resonance in a non-Abelian gauge field, where several novel features such as centre-of-mass-momentum-dependent effective interactions are shown. It is also shown that a uniform non-Abelian gauge field in conjunction with a spatial potential can be used to generate novel Hamiltonians; we discuss an explicit example of the generation of a monopole Hamiltonian.