Complex carbohydrates: 2. The modes of binding of complex carbohydrates to concanavalin A - a computer modelling approach

The probable modes of binding of some complex carbohydrates, which have the trimannosidic core structure (Man3GlcNAc2), to concanavalin A (Con A) have been determined using a computer modelling technique. These studies show that Con a can bind to the terminal mannose residues of the trimannosidic core structure and to the internal mannosyl as well as to the terminal N-acetylglucosamine residues of the N-acetylglucosamine substituted trimannosidic core structure. The oligosaccharide with terminal mannose residues can bind in its minimum energy conformers, whereas the oligosaccharide with internal mannosyl and terminal N-acetylglucosamine residues can bind only in higher energy conformers. In addition the former oligosaccharide forms more hydrogen bonds with Con A than the latter. These results suggest that, for these oligosaccharides, the terminal mannose residue has a much higher probability of reaching the binding site than either the internal mannosyl or the terminal N-acetylglucosamine residues. The substitution of a bisecting N-acetylglucosamine residue on these oligosaccharides, affects significantly the accessibility of the residues which bind to Con A and thereby reduces their binding affinity. It thus seems that the binding affinity of an oligosaccharide to Con A depends not only on the number of sugar residues which possess free 3-, 4- and 6-hydroxyl groups but also on the accessibility of these sugar residues to Con A. This study also reveals that the sugar binding site of Con A is small and that the interactions between Con A and carbohydrates are extended slightly beyond the single sugar residue that is placed in the binding site.

Analysis of two degrees of freedom systems through weighted mean square linearization approach

In this paper a study of the free, forced and self-excited vibrations of non-linear, two degrees of freedom systems is reported. The responses are obtained by linearizing the nonlinear equations using the weighted mean square linearization approach. The scope of this approach, in terms of the type of non-linearities the method can tackle, is also discussed.

Analysis of two degrees of freedom systems through weighted mean square linearization approach

In this paper a study of the free, forced and self-excited vibrations of non-linear, two degrees of freedom systems is reported. The responses are obtained by linearizing the nonlinear equations using the weighted mean square linearization approach. The scope of this approach, in terms of the type of non-linearities the method can tackle, is also discussed.

Dissipative dynamics of a harmonic oscillator: A nonperturbative approach

Starting from a microscopic theory, we derive a master equation for a harmonic oscillator coupled to a bath of noninteracting oscillators. We follow a nonperturbative approach, proposed earlier by us for the free Brownian particle. The diffusion constants are calculated analytically and the positivity of the master equation is shown to hold above a critical temperature. We compare the long time behavior of the average kinetic and potential energies with known thermodynamic results. In the limit of vanishing oscillator frequency of the system, we recover the results of the free Brownian particle.

Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks

The interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of llostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side-chains and then to compute the ligand-induced population shift. Finally, we obtain the free-energy landscape of the protein in equilibrium, characterizing the free-energy minima accessed by the protein complexes. We have chosen human tryptophanyl-tRNA synthetase (hTrpRS), a protein esponsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure.

A discrete wavelet transform approach to multiresolution complex SAR image generation

We present a signal processing approach using discrete wavelet transform (DWT) for the generation of complex synthetic aperture radar (SAR) images at an arbitrary number of dyadic scales of resolution. The method is computationally efficient and is free from significant system-imposed limitations present in traditional subaperture-based multiresolution image formation. Problems due to aliasing associated with biorthogonal decomposition of the complex signals are addressed. The lifting scheme of DWT is adapted to handle complex signal approximations and employed to further enhance the computational efficiency. Multiresolution SAR images formed by the proposed method are presented.

Simplified theory of carrier back-scattering in semiconducting carbon nanotubes: A Kane's model approach

We present a simplified yet analytical formulation of the carrier backscattering coefficient for zig-zag semiconducting single walled carbon nanotubes under diffusive regime. The electron-phonon scattering rate for longitudinal acoustic, optical, and zone-boundary phonon emissions for both inter- and intrasubband transition rates have been derived using Kane's nonparabolic energy subband model.The expressions for the mean free path and diffusive resistance have been formulated incorporating the aforementioned phonon scattering. Appropriate overlap function in Fermi's golden rule has been incorporated for a more general approach. The effect of energy subbands on low and high bias zones for the onset of longitudinal acoustic, optical, and zone-boundary phonon emissions and absorption have been analytically addressed. 90% transmission of the carriers from the source to the drain at 400 K for a 5 mu m long nanotube at 105 V m(-1) has been exhibited. The analytical results are in good agreement with the available experimental data. (c) 2010 American Institute of Physics.

A simple classical approach for the melting temperature of inert-gas nanoparticles

Like the metal and semiconductor nanoparticles, the melting temperature of free inert-gas nanoparticles decreases with decreasing size. The variation is linear with the inverse of the particle size for large nanoparticles and deviates from the linearity for small nanoparticles. The decrease in the melting temperature is slower for free nanoparticles with non-wetting surfaces, while the decrease is faster for nanoparticles with wetting surfaces. Though the depression of the melting temperature has been reported for inert-gas nanoparticles in porous glasses, superheating has also been observed when the nanoparticles are embedded in some matrices. By using a simple classical approach, the influence of size, geometry and the matrix on the melting temperature of nanoparticles is understood quantitatively and shown to be applicable for other materials. It is also shown that the classical approach can be applied to understand the size-dependent freezing temperature of nanoparticles.

Free vibration of circular plates of arbitrary thickness

Free vibration of circular plates of arbitrary thickness is investigated using the method of initial functions. State-space approach is used to derive the governing equations of the above method. The formulation is such that theories of any desired order can be obtained by deleting higher terms in the infinite-order differential equations. Numerical results are obtained for flexural and extensional vibration of circular plates. Results are also computed using Mindlin's theory and they are in agreement with the present analysis.

Complexation of siRNA with Dendrimer: A Molecular Modeling Approach

This paper reports the structural behavior and thermodynamics of the complexation of siRNA with poly(amidoamine) (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) through fully atomistic molecular dynamics (MD) simulations accompanied by free energy calculations and inherent structure determination. We have also done simulation with one siRNA and two dendrimers (2 x G3 or 2xG4) to get the microscopic picture of various binding modes. Our simulation results reveal the formation of stable siRNA-dendrimer complex over nanosecond time scale. With the increase in dendrimcr generation, the charge ratio increases and hence the binding energy between siRNA and dendrimer also increases in accordance with available experimental measurements. Calculated radial distribution functions of amines groups of various subgenerations in a given generation of dendrimer and phosphate in backbone of siRNA reveals that one dendrimer of generation 4 shows better binding with siRNA almost wrapping the dendrimer when compared to the binding with lower generation dendrimer like G3. In contrast, two dendrimers of generation 4 show binding without siRNA wrapping the den-rimer because of repulsion between two dendrimers. The counterion distribution around the complex and the water molecules in the hydration shell of siRNA give microscopic picture of the binding dynamics. We see a clear correlation between water. counterions motions and the complexation i.e. the water molecules and counterions which condensed around siRNA are moved away from the siRNA backbone when dendrimer start binding to the siRNA back hone. As siRNA wraps/bind to the dendrimer counterions originally condensed onto siRNA (Na-1) and dendrimer (Cl-) get released. We give a quantitative estimate of the entropy of counterions and show that there is gain in entropy due to counterions release during the complexation. Furthermore, the free energy of complexation of IG3 and IG4 at two different salt concentrations shows that increase in salt concentration leads to the weakening of the binding affinity of siRNA and dendrimer.

In-Network Computation in Random Wireless Networks: A PAC Approach to Constant Refresh Rates with Lower Energy Costs

We propose a method to compute a probably approximately correct (PAC) normalized histogram of observations with a refresh rate of Theta(1) time units per histogram sample on a random geometric graph with noise-free links. The delay in computation is Theta(root n) time units. We further extend our approach to a network with noisy links. While the refresh rate remains Theta(1) time units per sample, the delay increases to Theta(root n log n). The number of transmissions in both cases is Theta(n) per histogram sample. The achieved Theta(1) refresh rate for PAC histogram computation is a significant improvement over the refresh rate of Theta(1/log n) for histogram computation in noiseless networks. We achieve this by operating in the supercritical thermodynamic regime where large pathways for communication build up, but the network may have more than one component. The largest component however will have an arbitrarily large fraction of nodes in order to enable approximate computation of the histogram to the desired level of accuracy. Operation in the supercritical thermodynamic regime also reduces energy consumption. A key step in the proof of our achievability result is the construction of a connected component having bounded degree and any desired fraction of nodes. This construction may also prove useful in other communication settings on the random geometric graph.

Free vibration of rectangular beams of arbitrary depth

The state space approach is extended to the two dimensional elastodynamic problems. The formulation is in a form particularly amenable to consistent reduction to obtain approximate theories of any desired order. Free vibration of rectangular beams of arbitrary depth is investigated using this approach. The method does not involve the concept of the shear coefficientk. It takes into account the vertical normal stress and the transverse shear stress. The frequency values are calculated using the Timoshenko beam theory and the present analysis for different values of Poisson's ratio and they are in good agreement. Four cases of beams with different end conditions are considered.Die Zustandsraum-Technik wird auf zweidimensionale elastodynamische Probleme ausgedehnt. Die Formulierung ist besonders geeignet für die Aufstellung von Näherungstheorien beliebigen Grades. Freie Schwingungen von Rechteckbalken beliebiger Höhe wurden mit Hilfe dieser Technik untersucht. Das Verfahren umgeht den Begriff des Schubbeiwertsk. Es berücksichtigt die senkrechte Normalbeanspruchung und die Querkraft. Die Frequenzwerte werden mit Hilfe der Balkentheorie von Timoshenko und der vorliegenden Analyse berechnet, und zwar für verschiedene Werte der Querdehnzahl. Die berechneten Werte befinden sich in guter Übereinstimmung. Vier Fälle von Balken mit verschiedenen Endbedingungen werden untersucht.

Critical phenomena in polymer solutions: Scaling of the free energy

The thermodynamics of monodisperse solutions of polymers in the neighborhood of the phase separation temperature is studied by means of Wilson’s recursion relation approach, starting from an effective ϕ4 Hamiltonian derived from a continuum model of a many‐chain system in poor solvents. Details of the chain statistics are contained in the coefficients of the field variables ϕ, so that the parameter space of the Hamiltonian includes the temperature, coupling constant, molecular weight, and excluded volume interaction. The recursion relations are solved under a series of simplifying assumptions, providing the scaling forms of the relevant parameters, which are then used to determine the scaling form of the free energy. The free energy, in turn, is used to calculate the other singular thermodynamic properties of the solution. These are characteristically power laws in the reduced temperature and molecular weight, with the temperature exponents being the same as those of the 3d Ising model. The molecular weight exponents are unique to polymer solutions, and the calculated values compare well with the available experimental data.

Spectral approach for the soliton and periodic solutions of the nonlinear wave equation

A spectral method that obtains the soliton and periodic solutions to the nonlinear wave equation is presented. The results show that the nonlinear group velocity is a function of the frequency shift as well as of the soliton power. When the frequency shift is a function of time, a solution in terms of the Jacobian elliptic function is obtained. This solution is periodic in nature, and, to generate such an optical pulse train, one must simultaneously amplitude- and frequency-modulate the optical carrier. Finally, we extend the method to include the effect of self-steepening.

Lasing in active, sub-mean-free path-sized systems with dense, random, weak scatterers

We report enhanced emission and gain narrowing in Rhodamine 590 perchlorate dye in an aqueous suspension of polystyrene microspheres. A systematic experimental study of the threshold condition for and the gain narrowing of the stimulated emission over a wide range of dye concentrations and scatterer number densities showed several interesting features, even though the transport mean free path far exceeded the system size. The conventional diffusive-reactive approximation to radiative transfer in an inhomogeneously illuminated random amplifying medium, which is valid for a transport mean-free path much smaller than the system size, is clearly inapplicable here. We propose a new probabilistic approach for the present case of dense, random, weak scatterers involving the otherwise rare and ignorable sub-mean-free-path scatterings, now made effective by the high gain in the medium, which is consistent: with experimentally observed features. (C) 1997 Optical Society of America.