Homologous pairing between nucleosome cores on a linear duplex DNA and nucleoprotein filaments of RecA protein-single stranded DNA

The ability of E coli recA protein to promote homologous pairing with linear duplex DNA bound to HU protein (Nucleosome cores) was found to be differentially affected. The formation of paranemic joint molecules was not affected whereas the formation of plectomic joint molecules was inhibited from the start of the reaction. The formation of paranemic joint molecules between nucleoprotein filaments of recA protein-circular single stranded DNA and closed circular duplex DNA is believed to generate positive supercoiling in the duplex DNA. We found that the positively superhelical duplex DNA was inert in the formation of joint molecules but could be converted into an active substrate, in situ, by the action of wheat germ topoisomerase I. These observations initiate an understanding of the structural features of E coli chromosome such as DNA supercoiling and nucleosome-like structures in homologous recombination.

Amino Acid Based MOFs: Synthesis, Structure, Single Crystal to Single Crystal Transformation, Magnetic and Related Studies in a Family of Cobalt and Nickel Aminoisophthales

Four new 5-aminoisophthalates of cobalt and nickel have been prepared employing hydro/solvothermal methods: [Co2(C8H5NO4)2(C4H4N2)(H2O)2]·3H2O (I), [Ni2(C8H5NO4)2(C4H4N2)(H2O)2]·3H2O (II), [Co2(H2O)(μ3-OH)2(C8H5NO4)] (III), and [Ni2(H2O)(μ3-OH)2(C8H5NO4)] (IV). Compounds I and II are isostructural, having anion-deficient CdCl2 related layers bridged by a pyrazine ligand, giving rise to a bilayer arrangement. Compounds III and IV have one-dimensional M−O(H)−M chains connected by the 5-aminoisophthalate units forming a three-dimensional structure. The coordinated as well as the lattice water molecules of I and II could be removed and inserted by simple heating−cooling cycles under the atmospheric conditions. The removal of the coordinated water molecule is accompanied by changes in the coordination environment around the M2+ (M = Co, Ni) and color of the samples (purple to blue, Co; green to dark yellow, Ni). This change has been examined by a variety of techniques that include in situ single crystal to single crystal transformation studies and in situ IR and UV−vis spectroscopic studies. Magnetic studies indicate antiferromagnetic behavior in I and II, a field-induced magnetism in III, and a canted antiferromagnetic behavior in IV.

A Model of Anomalous Chain Translocation Dynamics

A model of polymer translocation based on the stochastic dynamics of the number of monomers on one side of a pore-containing surface is formulated in terms of a one-dimensional generalized Langevin equation, in which the random force is assumed to be characterized by long-ranged temporal correlations. The model is introduced to rationalize anomalies in measured and simulated values of the average time of passage through the pore, which in general cannot be satisfactorily accounted for by simple Brownian diffusion mechanisms. Calculations are presented of the mean first passage time for barrier crossing and of the mean square displacement of a monomeric segment, in the limits of strong and weak diffusive bias. The calculations produce estimates of the exponents in various scaling relations that are in satisfactory agreement with available data.

A numerical study of crack tip constraint in ductile single crystals

In this work, the effect of crack tip constraint on near-tip stress and deformation fields in a ductile FCC single crystal is studied under mode I, plane strain conditions. To this end, modified boundary layer simulations within crystal plasticity framework are performed, neglecting elastic anisotropy. The first and second terms of the isotropic elastic crack tip field, which are governed by the stress intensity factor K and T-stress, are prescribed as remote boundary conditions and solutions pertaining to different levels of T-stress are generated. It is found that the near-tip deformation field, especially, the development of kink or slip shear bands, is sensitive to the constraint level. The stress distribution and the size and shape of the plastic zone near the crack tip are also strongly influenced by the level of T-stress, with progressive loss of crack tip constraint occurring as T-stress becomes more negative. A family of near-tip fields is obtained which are characterized by two terms (such as K and T or J and a constraint parameter Q) as in isotropic plastic solids.

A Single Mammalian Mitochondrial Translation Initiation Factor Functionally Replaces Two Bacterial Factors

The mechanism of translation in eubacteria and organelles is thought to be similar. In eubacteria, the three initiation factors IF1, IF2, and IF3 are vital. Although the homologs of IF2 and IF3 are found in mammalian mitochondria, an IF1 homolog has never been detected. Here, we show that bovine mitochondrial IF2 (IF2mt) complements E. coli containing a deletion of the IF2 gene (E. coli ΔinfB). We find that IF1 is no longer essential in an IF2mt-supported E. coli ΔinfB strain. Furthermore, biochemical and molecular modeling data show that a conserved insertion of 37 amino acids in the IF2mt substitutes for the function of IF1. Deletion of this insertion from IF2mt supports E. coli for the essential function of IF2. However, in this background, IF1 remains essential. These observations provide strong evidence that a single factor (IF2mt) in mammalian mitochondria performs the functions of two eubacterial factors, IF1 and IF2.

CAE-based prediction of projectile residual velocity for impact on single and multi-layered metallic armour plates

The present, paper deals with the CAE-based study Of impact of jacketed projectiles on single- and multi-layered metal armour plates using LS-DYNA. The validation of finite element modelling procedure is mainly based on the mesh convergence study using both shell and solid elements for representing single-layered mild steel target plates. It, is shown that the proper choice of mesh density and the strain rate-dependent material properties are essential for all accurate prediction of projectile residual velocity. The modelling requirements are initially arrived at by correlating against test residual velocities for single-layered mild steel plates of different depths at impact velocities in the ran.-c of approximately 800-870 m/s. The efficacy of correlation is adjudged, in terms of a 'correlation index', defined in the paper: for which values close to unity are desirable. The experience gained for single-layered plates is next; used in simulating projectile impacts on multi-layered mild steel target plates and once again a high degree of correlation with experimental residual velocities is observed. The study is repeated for single- and multi-layered aluminium target plates with a similar level of success in test residual velocity prediction. TO the authors' best knowledge, the present comprehensive study shows in particular for the first time that, with a. proper modelling approach, LS-DYNA can be used with a great degree of confidence in designing perforation-resistant single and multi-layered metallic armour plates.

A novel single pot synthesis of binuclear copper(II) complexes of macrocyclic and macroacyclic compartmental ligands: Structures and magnetic properties

Two binuclear copper(II) complexes one (complex 1) with a macrocyclic ligand (H(2)L1) and other (complex 2) with a macroacyclic (end-off type) compartmental ligand (HL2) have been synthesized from single pot template synthesis involving copper(II) nitrate, 1,2diaminoethane, 4-methyl-2,6-diformylphenol, and sodium azide. Structure analysis of complex I reveals that there are actually two half molecules present in the asymmetric unit and so two complexes (molecule-I and molecule-II) are present in unit cell, although they show slight differences. The two Cu(II) centers are in distorted square pyramidal coordination environment with two endogenous phenoxo bridges provided by the phenolate of H(2)L1 I having Cu-Cu separations of 2.9133(10) angstrom and 2.9103(10) in the two molecules. In complex 2 the coordination environments around two Cu(II) centers are asymmetric, Cu1 is in distorted square pyramidal environment whereas, the coordination environment around Cu2 is distorted octahedral. The two Cu(II) centers in complex 2 are connected by two different kinds of bridges, one is endogenous phenoxo bridge provided by the phenolate of the ligand HL2 and the other is exogenous azido bridge (mu-(1),(l) type) with Cu-Cu distance of 3.032(10) angstrom. Variable temperature magnetic studies show that two Cu(II) centers in both the complexes are strongly antiferromagnetically coupled with J = -625 +/- 5 cm(-1) and J = -188.6 +/- 1cm(-1) for complex 1 and 2, respectively. (C) 2006 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.

Binding of nucleobases with single-walled carbon nanotubes: Theory and experiment

We report the binding energy of various nucleobases (guanine (G), adenine (A), thymine (T) and cytosine (C)) with (5,5) single-walled carbon nanotube (SWNT) calculated using first-principle Hartre–Fock method (HF) together with classical force field. The binding energy without including the solvation effects of water decreases in the order G>A>T>C. The inclusion of solvation energy changes the order of binding preference to be G>T>A>C. Using isothermal titration (micro) calorimetry experiments, we also show the relative binding affinity to be T>A>C, in agreement with our calculations.

Melting of an Anchored Bilayer: Phase Transitions in the Organic-Inorganic Hybrid Pervoskite (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 (n=11, 13, 15, 17)

The conformation, organization, and phase transitions of alkyl chains in organic-inorganic hybrids based on the double pervoskite-slab lead iodides, (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 (n = 11, 13, 15, 17) have been investigated by X-ray diffraction, calorimetry, and infrared vibrational spectroscopy. In these hybrid solids, double pervoskite (CH3NH3)Pb2I7 slabs are interleaved with alkyl ammonium chains with the anchored alkyl chains arranged as tilted bilayers and adopting a planar all-trans conformation at room temperature. The (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 compounds exhibit a single reversible phase transition above room temperature with the associated enthalpy change varying linearly with alkyl chain length. This transition corresponds to the melting in two-dimensions of the alkyl chains of the anchored bilayer and is characterized by increased conformational disorder of the methylene units of the chain and loss of tilt angle coherence leading to an increase in the interslab spacing. By monitoring features in the infrared spectra that are characteristic of the global conformation of the alkyl chains, a quantitative relation between conformational disorder and melting of the anchored bilayer is established. It is found that, irrespective of the alkyl chain length, melting occurs when at least 60% of the chains in the anchored bilayer of (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 have one or more gauche defects. This concentration is determined by the underlying lattice to which the alkyl chains are anchored.

Crack Tip Fields in a Single Edge Notched Aluminum Single Crystal Specimen

We report a combined experimental and computational study of a low constraint aluminum single crystal fracture geometry and investigate the near-tip stress and strain fields. To this end, a single edge notched tensile (SENT) specimen is considered. A notch, with a radius of 50 µm, is taken to lie in the (010) plane and its front is aligned along the [101] direction. Experiments are conducted by subjecting the specimen to tensile loading using a special fixture inside a scanning electron microscope chamber. Both SEM micrographs and electron back-scattered diffraction (EBSD) maps are obtained from the near-tip region. The experiments are complemented by performing 3D and 2D plane strain finite element simulations within a continuum crystal plasticity framework assuming an isotropic hardening response characterized by the Pierce–Asaro–Needleman model. The simulations show a distinct slip band forming at about 55 deg with respect to the notch line corresponding to slip on (11-bar 1)[011] system, which corroborates well with experimental data. Furthermore, two kink bands occur at about 45 deg and 90 deg with respect to the notch line within which large rotations in the crystal orientation take place. These predictions are in good agreement with the EBSD observations. Finally, the near-tip angular variations of the 3D stress and plastic strain fields in the low constraint SENT fracture geometry are examined in detail.

Boson-fermion duality in SU(m vertical bar n) supersymmetric Haldane-Shastry spin chain

By using the Y(gl(m|n)) super Yangian symmetry of the SU(m|n) supersymmetric Haldane-Shastry spin chain, we show that the partition function of this model satisfies a duality relation under the exchange of bosonic and fermionic spin degrees of freedom. As a byproduct of this study of the duality relation, we find a novel combinatorial formula for the super Schur polynomials associated with some irreducible representations of the Y(gl(m|n)) Yangian algebra. Finally, we reveal an intimate connection between the global SU(m|n) symmetry of a spin chain and the boson-fermion duality relation. (C) 2007 Elsevier B.V. All rights reserved.

Single top quark events at Fermilab

According to a press release dated 9 March 2009, the two experiments CDF (Collider Detector at Fermilab) and DZero have announced the discovery of ‘single top quark’ events, which represent a spectacular discovery and confirmation of the standard model of elementary particle physics. The results of their findings are now available as preprints which have been submitted for publication in Physical Review Letters1,2.

Jointly optimal power control and routing for a single cell, dense, ad hoc wireless network

We consider a dense, ad hoc wireless network confined to a small region, such that direct communication is possible between any pair of nodes. The physical communication model is that a receiver decodes the signal from a single transmitter, while treating all other signals as interference. Data packets are sent between source-destination pairs by multihop relaying. We assume that nodes self-organise into a multihop network such that all hops are of length d meters, where d is a design parameter. There is a contention based multiaccess scheme, and it is assumed that every node always has data to send, either originated from it or a transit packet (saturation assumption). In this scenario, we seek to maximize a measure of the transport capacity of the network (measured in bit-meters per second) over power controls (in a fading environment) and over the hop distance d, subject to an average power constraint. We first argue that for a dense collection of nodes confined to a small region, single cell operation is efficient for single user decoding transceivers. Then, operating the dense ad hoc network (described above) as a single cell, we study the optimal hop length and power control that maximizes the transport capacity for a given network power constraint. More specifically, for a fading channel and for a fixed transmission time strategy (akin to the IEEE 802.11 TXOP), we find that there exists an intrinsic aggregate bit rate (Theta(opt) bits per second, depending on the contention mechanism and the channel fading characteristics) carried by the network, when operating at the optimal hop length and power control. The optimal transport capacity is of the form d(opt)((P) over bar (t)) x Theta(opt) with d(opt) scaling as (P) over bar (1/eta)(t), where (P) over bar (t) is the available time average transmit power and eta is the path loss exponent. Under certain conditions on the fading distribution, we then provide a simple characterisation of the optimal operating point.