Polymer drift in a solvent by force acting on one polymer end

We investigate the effect of hydrodynamic interactions on the non-equilibrium drift dynamics of an ideal flexible polymer pulled by a constant force applied at one polymer end using the perturbation theory and the renormalization group method. For moderate force, if the polymer elongation is small, the hydrodynamic interactions are not screened and the velocity and the longitudinal elongation of the polymer are computed using the renormalization group method. Both the velocity and elongation are nonlinear functions of the driving force in this regime. For large elongation we found two regimes. For large force but finite chain length L the hydrodynamic interactions are screened. For large chain lengths and a finite force the hydrodynamic interactions are only partially screened, which in three dimensions results in unusual logarithmic corrections to the velocity and the longitudinal elongation.

Puzzles of excited charm meson masses

We attempt a comprehensive analysis of the low lying charm meson states which present several puzzles, including the poor determination of masses of several non-strange excited mesons. We use the well-determined masses of the ground states and the strange first excited states to 'predict' the mass of the non-strange first excited state in the framework of heavy hadron chiral perturbation theory, an approach that is complementary to the well-known analysis of Mehen and Springer. This approach points to values for the masses of these states that are smaller than the experimental determinations. We provide a critical assessment of these mass measurements and point out the need for new experimental information. (c) 2007 Elsevier B.V. All rights reserved.

Unfolding of Plasmodium falciparum Triosephosphate Isomerase in Urea and Guanidinium Chloride: Evidence for a Novel Disulfide Exchange Reaction in a Covalently Cross-Linked Mutant†

The conformational stability of Plasmodium falciparum triosephosphate isomerase (TIMWT) enzyme has been investigated in urea and guanidinium chloride (GdmCl) solutions using circular dichroism, fluorescence, and size-exclusion chromatography. The dimeric enzyme is remarkably stable in urea solutions. It retains considerable secondary, tertiary, and quaternary structure even in 8 M urea. In contrast, the unfolding transition is complete by 2.4 M GdmCl. Although the secondary as well as the tertiary interactions melt before the perturbation of the quaternary structure, these studies imply that the dissociation of the dimer into monomers ultimately leads to the collapse of the structure, suggesting that the interfacial interactions play a major role in determining multimeric protein stability. The C-m(urea)/C-m(GdmCl) ratio (where C-m is the concentration of the denaturant required at the transition midpoint) is unusually high for triosephosphate isomerase as compared to other monomeric and dimeric proteins. A disulfide crosslinked mutant protein (Y74C) engineered to form two disulfide cross-links across the interface (13-74') and (13'-74) is dramatically destablized in urea. The unfolding transition is complete by 6 M urea and involves a novel mechanism of dimer dissociation through intramolecular thiol-disulfide exchange.

Structural Insights into the Acyl Intermediates of the Plasmodium falciparum Fatty Acid Synthesis Pathway THE MECHANISM OF EXPANSION OF THE ACYL CARRIER PROTEIN CORE

Acyl carrier protein (ACP) plays a central role in fatty acid biosynthesis. However, the molecular machinery that mediates its function is not yet fully understood. Therefore, structural studies were carried out on the acyl-ACP intermediates of Plasmodium falciparum using NMR as a spectroscopic probe. Chemical shift perturbation studies put forth a new picture of the interaction of ACP molecule with the acyl chain, namely, the hydrophobic core can protect up to 12 carbon units, and additional carbons protrude out from the top of the hydrophobic cavity. The latter hypothesis stems from chemical shift changes observed in C-alpha and C-beta of Ser-37 in tetradecanoyl-ACP. C-13, N-15-Double-filtered nuclear Overhauser effect (NOE) spectroscopy experiments further substantiate the concept; in octanoyl (C-8)- and dodecanoyl (C-12)-ACP, a long range NOE is observed within the phosphopantetheine arm, suggesting an arch-like conformation. This NOE is nearly invisible in tetradecanoyl (C-14)-ACP, indicating a change in conformation of the prosthetic group. Furthermore, the present study provides insights into the molecular mechanism of ACP expansion, as revealed from a unique side chain-to-backbone hydrogen bond between two fairly conserved residues, Ile-55 HN and Glu-48 O. The backbone amide of Ile-55 HN reports a pK(a) value for the carboxylate, similar to 1.9 pH units higher than model compound value, suggesting strong electrostatic repulsion between helix II and helix III. Charge-charge repulsion between the helices in combination with thrust from inside due to acyl chain would energetically favor the separation of the two helices. Helix III has fewer structural restraints and, hence, undergoes major conformational change without altering the overall-fold of P. falciparum ACP.

Solution of MDPS using simulation-based value iteration

This article proposes a three-timescale simulation based algorithm for solution of infinite horizon Markov Decision Processes (MDPs). We assume a finite state space and discounted cost criterion and adopt the value iteration approach. An approximation of the Dynamic Programming operator T is applied to the value function iterates. This 'approximate' operator is implemented using three timescales, the slowest of which updates the value function iterates. On the middle timescale we perform a gradient search over the feasible action set of each state using Simultaneous Perturbation Stochastic Approximation (SPSA) gradient estimates, thus finding the minimizing action in T. On the fastest timescale, the 'critic' estimates, over which the gradient search is performed, are obtained. A sketch of convergence explaining the dynamics of the algorithm using associated ODEs is also presented. Numerical experiments on rate based flow control on a bottleneck node using a continuous-time queueing model are performed using the proposed algorithm. The results obtained are verified against classical value iteration where the feasible set is suitably discretized. Over such a discretized setting, a variant of the algorithm of [12] is compared and the proposed algorithm is found to converge faster.

Optimal threshold policies for admission control in communication networks via discrete parameter stochastic approximation

The problem of admission control of packets in communication networks is studied in the continuous time queueing framework under different classes of service and delayed information feedback. We develop and use a variant of a simulation based two timescale simultaneous perturbation stochastic approximation (SPSA) algorithm for finding an optimal feedback policy within the class of threshold type policies. Even though SPSA has originally been designed for continuous parameter optimization, its variant for the discrete parameter case is seen to work well. We give a proof of the hypothesis needed to show convergence of the algorithm on our setting along with a sketch of the convergence analysis. Extensive numerical experiments with the algorithm are illustrated for different parameter specifications. In particular, we study the effect of feedback delays on the system performance.

Spectroscopic studies on n-donor + σ-acceptor systems: Alkylthioureas and thiocarbanilides

The donor-acceptor interactions of alkylthioureas and thiocarbanilides with halogens have been investigated in detail employing electronic and infra-red spectroscopy. Various correlations of the spectroscopic and thermodynamic data have been presented. Alkylthioureas are by far the strongest donors known, and give high equilibrium constants (10,000-40,000 l. mole-1) and enthalpies of formation (9-18 kcal mole-1). The perturbation of the various vibrational frequencies due to charge transfer have also been studied. Hydrogen bonding of thioureas with hydroxylic compounds have been reported.

Analysis of multiple crystal forms of Bacillus subtilis BacB suggests a role for a metal ion as a nucleant for crystallization

Bacillus subtilis BacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded beta-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalized B-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.

Helical Conformations of Hexapeptides Containing N-Terminus Diproline Segments

The role of N-terminus diproline segments in facilitating helical folding in short peptides has been investigated in a set of model hexapeptides of the type Piv-Xxx-Yyy-Aib-Leu-Aib-Phe-OMe (Piv, pivaloyl). Nine sequences have been investigated with the following N-terminus dipeptide segments: (D)Pro-Ala (4) and Pro-Psi Pro (5, Psi, pseudoproline), Ala-Ala (6), Ala-Pro (7), Pro-Ala (8), Aib-Ala (9), Ala-Aib (10). The analog sequences Piv-Pro-Pro-Ala-Leu-Aib-Phe-OMe (2) and Piv-Pro-Pro-Ala-Aib-Ala-Aib-OMe (3) have also been studied. Solid state conformations have been determined by X-ray crystallography for peptides 4, 6, and 8 and compared with the previously determined crystal structure of peptide 1 (Boc-Pro-Pro-Aib-Leu-Aib-Val-OMe); (Rai et al., JACS 2006, 128, 7916-7928). Peptides 1 and 6 adopt almost identical helical conformations with unfolding of the helix at the N-terminus Pro (1) residue. Peptide 4 reveals the anticipated (D)Pro-Ala type II' beta-turn, followed by a stretch of 3(10)-helix. Peptide 8 adopts a folded conformation stabilized by four successive 4 -> 1 intramolecular hydrogen bonds. Ala (2) adopts an alpha(L) conformation, resulting in a type II beta-turn conformation followed by a stretch of 3(10)-helix. Conformational properties in solution were probed using solvent perturbation of NH chemical shifts which permit delineation of hydrogen bonded NH groups and nuclear Overhauser effects (NOEs) between backbone protons, which are diagnostic of local residue conformations. The results suggest that continuous helical conformations are indeed significantly populated for peptides 2 and 3. Comparison of the results for peptides 1 and 2, suggest that there is a significant influence of the residue that follows diproline segments in influencing backbone folding. (C) 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94: 360-370, 2010.

Anomalous behavior of hydrodynamic modes in the two dimensional shear flow of a granular material

The growth rates of the hydrodynamic modes in the homogeneous sheared state of a granular material are determined by solving the Boltzmann equation. The steady velocity distribution is considered to be the product of the Maxwell Boltzmann distribution and a Hermite polynomial expansion in the velocity components; this form is inserted into them Boltzmann equation and solved to obtain the coeificients of the terms in the expansion. The solution is obtained using an expansion in the parameter epsilon =(1 - e)(1/2), and terms correct to epsilon(4) are retained to obtain an approximate solution; the error due to the neglect of higher terms is estimated at about 5% for e = 0.7. A small perturbation is placed on the distribution function in the form of a Hermite polynomial expansion for the velocity variations and a Fourier expansion in the spatial coordinates: this is inserted into the Boltzmann equation and the growth rate of the Fourier modes is determined. It is found that in the hydrodynamic limit, the growth rates of the hydrodynamic modes in the flow direction have unusual characteristics. The growth rate of the momentum diffusion mode is positive, indicating that density variations are unstable in the limit k--> 0, and the growth rate increases proportional to kslash} k kslash}(2/3) in the limit k --> 0 (in contrast to the k(2) increase in elastic systems), where k is the wave vector in the flow direction. The real and imaginary parts of the growth rate corresponding to the propagating also increase proportional to kslash k kslash(2/3) (in contrast to the k(2) and k increase in elastic systems). The energy mode is damped due to inelastic collisions between particles. The scaling of the growth rates of the hydrodynamic modes with the wave vector I in the gradient direction is similar to that in elastic systems. (C) 2000 Elsevier Science B.V. All rights reserved.

SPSA algorithms with measurement reuse

Four algorithms, all variants of Simultaneous Perturbation Stochastic Approximation (SPSA), are proposed. The original one-measurement SPSA uses an estimate of the gradient of objective function L containing an additional bias term not seen in two-measurement SPSA. As a result, the asymptotic covariance matrix of the iterate convergence process has a bias term. We propose a one-measurement algorithm that eliminates this bias, and has asymptotic convergence properties making for easier comparison with the two-measurement SPSA. The algorithm, under certain conditions, outperforms both forms of SPSA with the only overhead being the storage of a single measurement. We also propose a similar algorithm that uses perturbations obtained from normalized Hadamard matrices. The convergence w.p. 1 of both algorithms is established. We extend measurement reuse to design two second-order SPSA algorithms and sketch the convergence analysis. Finally, we present simulation results on an illustrative minimization problem.

Comparative study on damage identification from lso-Eigen-Value-Change contours and smeared damage model

The paper proposes two methodologies for damage identification from measured natural frequencies of a contiguously damaged reinforced concrete beam, idealised with distributed damage model. The first method identifies damage from Iso-Eigen-Value-Change contours, plotted between pairs of different frequencies. The performance of the method is checked for a wide variation of damage positions and extents. The method is also extended to a discrete structure in the form of a five-storied shear building and the simplicity of the method is demonstrated. The second method is through smeared damage model, where the damage is assumed constant for different segments of the beam and the lengths and centres of these segments are the known inputs. First-order perturbation method is used to derive the relevant expressions. Both these methods are based on distributed damage models and have been checked with experimental program on simply supported reinforced concrete beams, subjected to different stages of symmetric and un-symmetric damages. The results of the experiments are encouraging and show that both the methods can be adopted together in a damage identification scenario.

External Bias Dependent Direct To Indirect Band Gap Transition in Graphene Nanoribbon

In this work, using self-consistent tight-binding calculations. for the first time, we show that a direct to indirect band gap transition is possible in an armchair graphene nanoribbon by the application of an external bias along the width of the ribbon, opening up the possibility of new device applications. With the help of the Dirac equation, we qualitatively explain this band gap transition using the asymmetry in the spatial distribution of the perturbation potential produced inside the nanoribbon by the external bias. This is followed by the verification of the band gap trends with a numerical technique using Magnus expansion of matrix exponentials. Finally, we show that the carrier effective masses possess tunable sharp characters in the vicinity of the band gap transition points.

Capillary-gravity waves against a corrugated vertical cliff

An analysis involving a transformation of the velocity potential and a Fourier Sine Transform technique is described to study the effect of surface tension on incoming surface waves against a vertical cliff with a periodic wall perturbation. Known results are recovered as particular cases of the general problem considered. An analytical expression is derived for the surface elevation, at far distances from the shore-line, by using Watson's lemma and a representative table of numerical values of the coefficients of the resulting asymptotic expansion is also presented.

Coupling of surface acoustic waves propagating in two separated piezoelectric media

The coupling of surface acoustic waves propagating in two separated piezoelectric media is studied using the perturbation theory of Auld. The results of the analysis are applied to two configurations using Bi12GeO20 and CdS crystals. It is found that the loss due to coupling is about 7 dB at 50 MHz in the cases of (111)-cut, [110]-prop. Bi12GeO20 and Y-cut, 60°-X prop. CdS combination. On étudie le couplage des ondes acoustiques de surface se propageant sur deux milieux piezo-eléctriques par la théorie de perturbation de Auld. Les resultats d'analyse sont appliqué's aux deux configurations des cristanx Bi12GeO20 et CdS. On trouve que la perte par couplage est environ de 7 dB a 50 MHz dans le cas de combination de (111)-coupe, [110]-prop. Bi12GeO20 et Y-coupe, 60°-X prop. CdS.