Dynamics of loop formation in a semiflexible polymer

The dynamics of loop formation by linear polymer chains has been a topic of several theoretical and experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible chains has been extensively studied by many groups. However, in the more realistic case of semiflexible polymers, not much results are available. In a recent study [K. P. Santo and K. L. Sebastian, Phys. Rev. E 73, 031923 (2006)], we investigated opening dynamics of semiflexible loops in the short chain limit and presented results for opening rates as a function of the length of the chain. We presented an approximate model for a semiflexible polymer in the rod limit based on a semiclassical expansion of the bending energy of the chain. The model provided an easy way to describe the dynamics. In this paper, using this model, we investigate the reverse process, i.e., the loop formation dynamics of a semiflexible polymer chain by describing the process as a diffusion-controlled reaction. We make use of the ``closure approximation'' of Wilemski and Fixman [G. Wilemski and M. Fixman, J. Chem. Phys. 60, 878 (1974)], in which a sink function is used to represent the reaction. We perform a detailed multidimensional analysis of the problem and calculate closing times for a semiflexible chain. We show that for short chains, the loop formation time tau decreases with the contour length of the polymer. But for longer chains, it increases with length obeying a power law and so it has a minimum at an intermediate length. In terms of dimensionless variables, the closing time is found to be given by tau similar to L-n exp(const/L), where n=4.5-6. The minimum loop formation time occurs at a length L-m of about 2.2-2.4. These are, indeed, the results that are physically expected, but a multidimensional analysis leading to these results does not seem to exist in the literature so far.

Formation of a novel surface structure encoded by Salmonella Pathogenicity Island 2.

The type III secretion system (T3SS) encoded by Salmonella Pathogenicity Island 2 (SPI2) is essential for virulence and intracellular proliferation of Salmonella enterica. We have previously identified SPI2-encoded proteins that are secreted and function as a translocon for the injection of effector proteins. Here, we describe the formation of a novel SPI2-dependent appendage structure in vitro as well as on the surface of bacteria that reside inside a vacuole of infected host cells. In contrast to the T3SS of other pathogens, the translocon encoded by SPI2 is only present singly or in few copies at one pole of the bacterial cell. Under in vitro conditions, appendages are composed of a filamentous needle-like structure with a diameter of 10 nm that was sheathed with secreted protein. The formation of the appendage in vitro is dependent on acidic media conditions. We analyzed SPI2-encoded appendages in infected cells and observed that acidic vacuolar pH was not required for induction of SPI2 gene expression, but was essential for the assembly of these structures and their function as translocon for delivery of effector proteins.

Racemization at proline residues during peptide bond formation : A study of diastereomeric mixtures of synthetic alamethicin fragments by 270 MHz 1H NMR

The stepwise synthesis of amino terminal pentapeptide of alamethicin, Z-Aib-Pro-Aib-Ala-Aib-OMe, by the dicyclohexylcarbodiimide mediated couplings leads to extensive racemization at the Ala and Pro residues. Racemization is largely suppressed by the use of additives like N-hydroxysuccinimide and 1-hydroxybenzotriazole. The presence of diastereomeric peptides may be detected by the observation of additional methyl ester and benzylic methylene signals in the 270 MHz 1H NMR spectra. Unambiguous spectral assignment of the signals to the diastereomers has been carried out by the synthesis and NMR studies of the D-Ala tetra and pentapeptides. The racemization at Pro is of particular relevance in view of the reported lack of inversion at C-terminal Pro on carboxyl activation.

Formation of linear plasmid multimers promoted by the phage lambda Red-system in lon mutants of Escherichia coli

We report here the formation of plasmid linear multimers promoted by the Red-system of phage lambda using a multicopy plasmid comprised of lambda red alpha and red beta genes, under the control of the lambda cI857 repressor. Our observations have revealed that the multimerization of plasmid DNA is dependent on the red beta and recA genes, suggesting a concerted role for these functions in the formation of plasmid multimers. The formation of multimers occurred in a recBCD+ sbcB+ xthA+ lon genetic background at a higher frequency than in the isogenic lon+ host cells. The multimers comprised tandem repeats of monomer plasmid DNA. Treatment of purified plasmid DNA with exonuclease III revealed the presence of free double-chain ends in the molecules. Determination of the size of multimeric DNA, by pulse field gel electrophoresis, revealed that the bulk of the DNA was in the range 50-240 kb, representing approximately 5-24 unit lengths of monomeric plasmid DNA. We provide a conceptual framework for Red-system-promoted formation and enhanced accumulation of plasmid linear multimers in lon mutants of E. coli.

Mechanics of Deformation under Traction and Friction of a Micrometric Monolithic MoS2 Particle in Comparison with those of an Agglomerate of Nanometric MoS2 Particles

Tribology of small inorganic nanoparticles in suspension in a liquid lubricant is often impaired because these particles agglomerate even when organic dispersants are used. In this paper we use lateral force microscopy to study the deformation mechanism and dissipation under traction of two extreme configurations (1) a large MoS2 particle (similar to 20 mu m width) of about 1 mu m height and (2) an agglomerate (similar to 20 mu m width), constituting 50 nm MoS2 crystallites, of about 1 mu m height. The agglomerate records a friction coefficient which is about 5-7 times that of monolithic particle. The paper examines the mechanisms of material removal for both the particles using continuum modeling and microscopy and infers that while the agglomerate response to traction can be accounted for by the bulk mechanical properties of the material, intralayer and interlayer basal planar slips determine the friction and wear of monolithic particles. The results provide a rationale for selection of layered particles, for suspension in liquid lubricants.

Microtribology and Friction-Induced Material Transfer in Layered MoS2 Nanoparticles Sprayed on a Steel Surface

Frictional performance of molybdenum disulfide (MoS2) particles sprayed on a substrate is investigated in a ball-on-disc tribometer. The ability of large (similar to 2 mu m) and small (similar to 50 nm) particles to generate low-friction transfer film is investigated with a view to elucidate the requirement for film formation. Particle migration, particle stability in the contact region, oxidation potential, and particle adhesion to the substrate are explored within a span of operating parametersp; normal load, and sliding velocity. It is found that the larger particles are able to migrate to the contact to raise a homogeneous but nonuniform low-friction transfer film that flows plastically to yield large contact areas, which aid in wear protection. Within the present load and speed range, the inability of small particles to stay in the contact region and undergo basal slip militates against the formation of a low-friction transfer film.

Accurate Parameter Estimation of Contaminant Transport Inverse Problem using Particle Swarm Optimization

Swarm Intelligence techniques such as particle swarm optimization (PSO) are shown to be incompetent for an accurate estimation of global solutions in several engineering applications. This problem is more severe in case of inverse optimization problems where fitness calculations are computationally expensive. In this work, a novel strategy is introduced to alleviate this problem. The proposed inverse model based on modified particle swarm optimization algorithm is applied for a contaminant transport inverse model. The inverse models based on standard-PSO and proposed-PSO are validated to estimate the accuracy of the models. The proposed model is shown to be out performing the standard one in terms of accuracy in parameter estimation. The preliminary results obtained using the proposed model is presented in this work.

Crystallite size effects in stacking faulted nickel hydroxide and its electrochemical behaviour

P-Nickel hydroxide comprises a long range periodic arrangement of atoms with a stacking sequence of AC AC AC-having an ideal composition Ni(OH)(2). Variation in the preparative conditions can lead to the changes in the stacking sequence (AC AC BA CB AC AC or AC AC AB AC AC) This type of variation in stacking sequence can result in the formation of stacking fault in nickel hydroxide. The stability of the stacking fault depends on the free energy content of the sample. Stacking faults in nickel hydroxide is essential for better electrochemical activity. Also there are reports correlating particle size to the better electrochemical activity. Here we present the effect of crystallite size on the stacking faulted nickel hydroxide samples. The electrochemical performance of stacking faulted nickel hydroxide with small crystallite size exchanges 0.8e/Ni, while the samples with larger crystallite size exchange 0.4e/Ni. Hence a right combination of crystallite size and stacking fault content has to be controlled for good electrochemical activity of nickel hydroxide. (C) 2008 Elsevier B.V. All rights reserved.

A Bayesian incentive compatible mechanism for decentralized supply chain formation

In this paper we consider a decentralized supply chain formation problem for linear multi-echelon supply chains when the managers of the individual echelons are autonomous, rational, and intelligent. At each echelon, there is a choice of service providers and the specific problem we solve is that of determining a cost-optimal mix of service providers so as to achieve a desired level of end-to-end delivery performance. The problem can be broken up into two sub-problems following a mechanism design approach: (1) Design of an incentive compatible mechanism to elicit the true cost functions from the echelon managers; (2) Formulation and solution of an appropriate optimization problem using the true cost information. In this paper we propose a novel Bayesian incentive compatible mechanism for eliciting the true cost functions. This improves upon existing solutions in the literature which are all based on the classical Vickrey-Clarke-Groves mechanisms, requiring significant incentives to be paid to the echelon managers for achieving dominant strategy incentive compatibility. The proposed solution, which we call SCF-BIC (Supply Chain Formation with Bayesian Incentive Compatibility), significantly reduces the cost of supply chain formation. We illustrate the efficacy of the proposed methodology using the example of a three echelon manufacturing supply chain.

A Shapley value analysis to coordinate the formation of procurement

In this paper we address the problem of forming procurement networks for items with value adding stages that are linearly arranged. Formation of such procurement networks involves a bottom-up assembly of complex production, assembly, and exchange relationships through supplier selection and contracting decisions. Recent research in supply chain management has emphasized that such decisions need to take into account the fact that suppliers and buyers are intelligent and rational agents who act strategically. In this paper, we view the problem of Procurement Network Formation (PNF) for multiple units of a single item as a cooperative game where agents cooperate to form a surplus maximizing procurement network and then share the surplus in a fair manner. We study the implications of using the Shapley value as a solution concept for forming such procurement networks. We also present a protocol, based on the extensive form game realization of the Shapley value, for forming these networks.

Oxide Particle Surface Chemistry and Ion Transport in "Soggy Sand" Electrolytes

The crucial role of oxide surface chemical composition on ion transport in "soggy sand" electrolytes is discussed in a systematic manner. A prototype soggy sand electrolytic system comprising aerosil silica functionalized with various hydrophilic and hydrophobic moieties dispersed in lithium perchlorate-ethylene glycol solution was used for the study. Detailed rheology studies show that the attractive particle network in the case of the composite with unmodified aerosil silica (with surface silanol groups) is most favorable for percolation in ionic conductivity, as well as rendering the composite with beneficial elastic mechanical properties: Though weaker in strength compared to the composite with unmodified aerosil particles, attractive particle networks are also observed in composites of aerosil particles with surfaces partially substituted with hydrophobic groups. The percolation in ionic conductivity is, however, dependent on the size of the hydrophobic moiety. No spanning attractive particle network was formed for aerosil particles with surfaces modified with stronger hydrophilic groups (than silanol), and as a result, no percolation in ionic conductivity was observed. The composite with hydrophilic particles was a sol, contrary to gels obtained in the case of unmodified aerosil, and partially substituted with hydrophobic groups.

Performance evaluation of elitist-mutated multi-objective particle swarm optimization for integrated water resources management

Optimal allocation of water resources for various stakeholders often involves considerable complexity with several conflicting goals, which often leads to multi-objective optimization. In aid of effective decision-making to the water managers, apart from developing effective multi-objective mathematical models, there is a greater necessity of providing efficient Pareto optimal solutions to the real world problems. This study proposes a swarm-intelligence-based multi-objective technique, namely the elitist-mutated multi-objective particle swarm optimization technique (EM-MOPSO), for arriving at efficient Pareto optimal solutions to the multi-objective water resource management problems. The EM-MOPSO technique is applied to a case study of the multi-objective reservoir operation problem. The model performance is evaluated by comparing with results of a non-dominated sorting genetic algorithm (NSGA-II) model, and it is found that the EM-MOPSO method results in better performance. The developed method can be used as an effective aid for multi-objective decision-making in integrated water resource management.

The illustrative use of thiosulfate in the formation of new three-dimensional hybrid structures

Examples of 3D cadmium thiosulfate based inorganic-organic hybrid compounds have been shown to be active photocatalysts using sunlight.

Formation of ω-Al7Cu2Fe phase during laser processing of quasicrystal-forming Al-Cu-Fe alloy

The formation of an ω-Al7Cu2Fe phase during laser cladding of quasicrystal-forming Al65Cu23.3Fe11.7 alloy on a pure aluminium substrate is reported. This phase is found to nucleate at the periphery of primary icosahedral-phase particles. A large number of ω-phase particles form an envelope around the icosahedral phase. On the outer side, they form an interface with an agr-Al solid solution. Detailed transmission electron microscopic observations show that the ω phase exhibits an orientation relationship with the icosahedral phase. Analysis of experimental results suggests that the ω phase forms by precipitation on an icosahedral phase by heterogeneous nucleation and grows into the aluminium-rich melt until supersaturation is exhausted. The microstructural observations are explained in terms of available models of phase transformations.

Gibbs Energy of Formation of MnO: Measurement and Assessment

Based on the measurements of Alcock and Zador, Grundy et al. estimated an uncertainty of the order of +/- 5 kJ mol(-1) for the standard Gibbs energy of formation of MnO in a recent assessment. Since the evaluation of thermodynamic data for the higher oxides Mn3O4, Mn2O3, and MnO2 depends on values for MnO, a redetermination of its Gibbs energy of formation was undertaken in the temperature range from 875 to 1300 K using a solid-state electrochemical cell incorporating yttria-doped thoria (YDT) as the solid electrolyte and Fe + Fe1-delta O as the reference electrode. The cell can be presented as Pt, Mn + MnO/YDT/Fe + Fe1+delta O, Pt Since the metals Fe and Mn undergo phase transitions in the temperature range of measurement, the reversible emf of the cell is represented by the three linear segments. Combining the emf with the oxygen potential for the reference electrode, the standard Gibbs energy of formation of MnO from alpha-Mn and gaseous diatomic oxygen in the temperature range from 875 to 980 K is obtained as: Delta G(f)(o)/Jmol(-1)(+/- 250) = -385624 + 73.071T From 980 to 1300 K the Gibbs energy of formation of MnO from beta-Mn and oxygen gas is given by: Delta G(f)(o)/Jmol(-1)(+/- 250) = -387850 + 75.36T The new data are in excellent agreement with the earlier measurements of Alcock and Zador. Grundy et al. incorrectly analyzed the data of Alcock and Zador showing relatively large difference (+/- 5 kJ mol(-1)) in Gibbs energies of MnO from their two cells with Fe + Fe1-delta O and Ni + NiO as reference electrodes. Thermodynamic data for MnO is reassessed in the light of the new measurements. A table of refined thermodynamic data for MnO from 298.15 to 2000 K is presented.