Functional Analysis of DNA Replication Fork Reversal Catalyzed by Mycobacterium tuberculosis RuvAB Proteins

Initially discovered in Escherichia coli, RuvAB proteins are ubiquitous in bacteria and play a dual role as molecular motor proteins responsible for branch migration of the Holliday junction(s) and reversal of stalled replication forks. Despite mounting genetic evidence for a crucial role of RuvA and RuvB proteins in reversal of stalled replication forks, the mechanistic aspects of this process are still not fully understood. Here, we elucidate the ability of Mycobacterium tuberculosis RuvAB (MtRuvAB) complex to catalyze the reversal of replication forks using a range of DNA replication fork substrates. Our studies show that MtRuvAB, unlike E. coli RuvAB, is able to drive replication fork reversal via the formation of Holliday junction intermediates, suggesting that RuvAB-catalyzed fork reversal involves concerted unwinding and annealing of nascent leading and lagging strands. We also demonstrate the reversal of replication forks carrying hemi-replicated DNA, indicating that MtRuvAB complex-catalyzed fork reversal is independent of symmetry at the fork junction. The fork reversal reaction catalyzed by MtRuvAB is coupled to ATP hydrolysis, is processive, and culminates in the formation of an extended reverse DNA arm. Notably, we found that sequence heterology failed to impede the fork reversal activity of MtRuvAB. We discuss the implications of these results in the context of recognition and processing of varied types of replication fork structures by RuvAB proteins.

Selective synthesis of metallic and semiconducting single-walled carbon nanotubes

As-prepared single-walled carbon nanotubes (SWNTs) are generally mixtures of semiconducting and metallic species, the proportion of the former being around 67%. Since most applications of SWNTs are best served by semiconducting or metallic nanotubes, rather than by mixtures of the two, methods which would directly yield semiconducting and metallic SWNTs in pure form are desirable. In this article, we present the available methods for the direct synthesis of such SWNTs along with the methods available to separate semiconducting and metallic SWNTs from mixtures. We also discuss the synthesis of Y-junction carbon nanotubes.

Tractable theories for the synthesis of neural networks

The Radius of Direct attraction of a discrete neural network is a measure of stability of the network. it is known that Hopfield networks designed using Hebb's Rule have a radius of direct attraction of Omega(n/p) where n is the size of the input patterns and p is the number of them. This lower bound is tight if p is no larger than 4. We construct a family of such networks with radius of direct attraction Omega(n/root plog p), for any p greater than or equal to 5. The techniques used to prove the result led us to the first polynomial-time algorithm for designing a neural network with maximum radius of direct attraction around arbitrary input patterns. The optimal synaptic matrix is computed using the ellipsoid method of linear programming in conjunction with an efficient separation oracle. Restrictions of symmetry and non-negative diagonal entries in the synaptic matrix can be accommodated within this scheme.

New Insights into Optimal Discrete Rate Adaptation for Average Power Constrained Single and Multi-Node Systems

The throughput-optimal discrete-rate adaptation policy, when nodes are subject to constraints on the average power and bit error rate, is governed by a power control parameter, for which a closed-form characterization has remained an open problem. The parameter is essential in determining the rate adaptation thresholds and the transmit rate and power at any time, and ensuring adherence to the power constraint. We derive novel insightful bounds and approximations that characterize the power control parameter and the throughput in closed-form. The results are comprehensive as they apply to the general class of Nakagami-m (m >= 1) fading channels, which includes Rayleigh fading, uncoded and coded modulation, and single and multi-node systems with selection. The results are appealing as they are provably tight in the asymptotic large average power regime, and are designed and verified to be accurate even for smaller average powers.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Quenching across quantum critical points in periodic systems: Dependence of scaling laws on periodicity

We study the quenching dynamics of a many-body system in one dimension described by a Hamiltonian that has spatial periodicity. Specifically, we consider a spin-1/2 chain with equal xx and yy couplings and subject to a periodically varying magnetic field in the (z) over cap direction or, equivalently, a tight-binding model of spinless fermions with a periodic local chemical potential, having period 2q, where q is a positive integer. For a linear quench of the strength of the magnetic field (or chemical potential) at a rate 1/tau across a quantum critical point, we find that the density of defects thereby produced scales as 1/tau(q/(q+1)), deviating from the 1/root tau scaling that is ubiquitous in a range of systems. We analyze this behavior by mapping the low-energy physics of the system to a set of fermionic two-level systems labeled by the lattice momentum k undergoing a nonlinear quench as well as by performing numerical simulations. We also show that if the magnetic field is a superposition of different periods, the power law depends only on the smallest period for very large values of tau, although it may exhibit a crossover at intermediate values of tau. Finally, for the case where a zz coupling is also present in the spin chain, or equivalently, where interactions are present in the fermionic system, we argue that the power associated with the scaling law depends on a combination of q and the interaction strength.

Bose-Hubbard model in a strong effective magnetic field: Emergence of a chiral Mott insulator ground state

Motivated by experiments on Josephson junction arrays, and cold atoms in an optical lattice in a synthetic magnetic field, we study the ``fully frustrated'' Bose-Hubbard model with half a magnetic flux quantum per plaquette. We obtain the phase diagram of this model on a two-leg ladder at integer filling via the density matrix renormalization group approach, complemented by Monte Carlo simulations on an effective classical XY model. The ground state at intermediate correlations is consistently shown to be a chiral Mott insulator (CMI) with a gap to all excitations and staggered loop currents which spontaneously break time-reversal symmetry. We characterize the CMI state as a vortex supersolid or an indirect exciton condensate, and discuss various experimental implications.

Incremental Cycle Detection, Topological Ordering, and Strong Component Maintenance

We present two online algorithms for maintaining a topological order of a directed n-vertex acyclic graph as arcs are added, and detecting a cycle when one is created. Our first algorithm handles m arc additions in O(m(3/2)) time. For sparse graphs (m/n = O(1)), this bound improves the best previous bound by a logarithmic factor, and is tight to within a constant factor among algorithms satisfying a natural locality property. Our second algorithm handles an arbitrary sequence of arc additions in O(n(5/2)) time. For sufficiently dense graphs, this bound improves the best previous bound by a polynomial factor. Our bound may be far from tight: we show that the algorithm can take Omega(n(2)2 root(2lgn)) time by relating its performance to a generalization of the k-levels problem of combinatorial geometry. A completely different algorithm running in Theta (n(2) log n) time was given recently by Bender, Fineman, and Gilbert. We extend both of our algorithms to the maintenance of strong components, without affecting the asymptotic time bounds.

Pricing Defaultable Bonds in a Markov Modulated Market

We address the problem of pricing defaultable bonds in a Markov modulated market. Using Merton's structural approach we show that various types of defaultable bonds are combination of European type contingent claims. Thus pricing a defaultable bond is tantamount to pricing a contingent claim in a Markov modulated market. Since the market is incomplete, we use the method of quadratic hedging and minimal martingale measure to derive locally risk minimizing derivative prices, hedging strategies and the corresponding residual risks. The price of defaultable bonds are obtained as solutions to a system of PDEs with weak coupling subject to appropriate terminal and boundary conditions. We solve the system of PDEs numerically and carry out a numerical investigation for the defaultable bond prices. We compare their credit spreads with some of the existing models. We observe higher spreads in the Markov modulated market. We show how business cycles can be easily incorporated in the proposed framework. We demonstrate the impact on spreads of the inclusion of rare states that attempt to capture a tight liquidity situation. These states are characterized by low risk-free interest rate, high payout rate and high volatility.

Study of n-ZnO/p-Si (100) thin film heterojunctions by pulsed laser deposition without buffer layer

ZnO/Si heterojunctions were fabricated by growing ZnO thin films on p-type Si (100) substrate by pulsed laser deposition without buffer layers. The crystallinity of the heterojunction was analyzed by high resolution X-ray diffraction and atomic force microscopy. The optical quality of the film was analyzed by room temperature (RT) photoluminescence measurements. The high intense band to band emission confirmed the high quality of the ZnO thin films on Si. The electrical properties of the junction were studied by temperature dependent current-voltage measurements and RT capacitance-voltage (C-V) analysis. The charge carrier concentration and the barrier height (BH) were calculated, to be 5.6x10(19) cm(-3) and 0.6 eV respectively from the C-V plot. The BH and ideality factor, calculated using the thermionic emission (TE) model, were found to be highly temperature dependent. We observed a much lower value in Richardson constant, 5.19x10(-7)A/cm(2) K-2 than the theoretical value (32 A/cm(2) K-2) for ZnO. This analysis revealed the existence of a Gaussian distribution (GD) with a standard deviation of sigma(2)=0.035 V. By implementing the GD to the TE, the values of BH and Richardson constant were obtained as 1.3 eV and 39.97 A/cm(2) K-2 respectively from the modified Richardson plot. The obtained Richardson constant value is close to the theoretical value for n-ZnO. These high quality heterojunctions can be used for solar cell applications. (C) 2012 Elsevier B.V. All rights reserved.

Analysis of current voltage characteristics of MWIR homojunction photodiodes for uncooled operation

Dark currents n(+)/v/p(+) Hg0.69Cd0.Te-31 mid wave infrared photodiodes were measured at room temperature. The diodes exhibited negative differential resistance at room-temperature, but with increasing leakage currents as a function of reverse bias. The current-voltage characteristics were simulated and fitted by incorporating trap assisted tunneling via traps and Shockley-Read-Hall generation recombination process due to dislocations in the carrier transport equations. The thermal suppression of carriers was simulated by taking energy level of trap (E-t), trap density (N-t) and the doping concentrations of n(+) and v regions as fitting parameters. Values of E-t and N-t were 0.78E(g) and similar to 6-9 x 10(14) cm(-3) respectively for most of the diodes. Variable temperature current voltage measurements on variable area diode array (VADA) structures confirmed the fact that variation in zero bias resistance area product (R(0)A) is related to g-r processes originating from variation in concentration and kind of defects that intersect a junction area. (C) 2012 Elsevier B.V. All rights reserved.

Carbon dioxide detection by boron nitride nanotubes

The effect of gas molecule adsorption is investigated on the density of states of (9,0) zigzag boron nitride nanotube within a random tight-binding Hamiltonian model. The Green function approach and coherent potential approximation have been implemented. The results show that the adsorption of carbon dioxide gas molecules by boron atoms only leads to a donor type semiconductor while the adsorption by nitrogen atoms only leads to an acceptor. Since the gas molecules are adsorbed by both boron and nitrogen atoms, a reduction of the band gap is found. In all cases, increasing the gas concentration causes an increase in the height of the peaks in the band gap. This is due to an increasing charge carrier concentration induced by adsorbed gas molecules.

The Hinge Region of Human Thyroid-Stimulating Hormone (TSH) Receptor Operates as a Tunable Switch between Hormone Binding and Receptor Activation

The mechanism by which the hinge regions of glycoprotein hormone receptors couple hormone binding to activation of downstream effecters is not clearly understood. In the present study, agonistic (311.62) and antagonistic (311.87) monoclonal antibodies (MAbs) directed against the TSH receptor extracellular domain were used to elucidate role of the hinge region in receptor activation. MAb 311.62 which identifies the LRR/Cb-2 junction (aa 265-275), increased the affinity of TSHR for the hormone while concomitantly decreasing its efficacy, whereas MAb 311.87 recognizing LRR 7-9 (aa 201-259) acted as a non-competitive inhibitor of Thyroid stimulating hormone (TSH) binding. Binding of MAbs was sensitive to the conformational changes caused by the activating and inactivating mutations and exhibited differential effects on hormone binding and response of these mutants. By studying the effects of these MAbs on truncation and chimeric mutants of thyroid stimulating hormone receptor (TSHR), this study confirms the tethered inverse agonistic role played by the hinge region and maps the interactions between TSHR hinge region and exoloops responsible for maintenance of the receptor in its basal state. Mechanistic studies on the antibody-receptor interactions suggest that MAb 311.87 is an allosteric insurmountable antagonist and inhibits initiation of the hormone induced conformational changes in the hinge region, whereas MAb 311.62 acts as a partial agonist that recognizes a conformational epitope critical for coupling of hormone binding to receptor activation. The hinge region, probably in close proximity with the alpha-subunit in the hormone-receptor complex, acts as a tunable switch between hormone binding and receptor activation.

Rainbow connection number and connected dominating sets

The rainbow connection number of a connected graph is the minimum number of colors needed to color its edges, so that every pair of its vertices is connected by at least one path in which no two edges are colored the same. In this article we show that for every connected graph on n vertices with minimum degree delta, the rainbow connection number is upper bounded by 3n/(delta + 1) + 3. This solves an open problem from Schiermeyer (Combinatorial Algorithms, Springer, Berlin/Hiedelberg, 2009, pp. 432437), improving the previously best known bound of 20n/delta (J Graph Theory 63 (2010), 185191). This bound is tight up to additive factors by a construction mentioned in Caro et al. (Electr J Combin 15(R57) (2008), 1). As an intermediate step we obtain an upper bound of 3n/(delta + 1) - 2 on the size of a connected two-step dominating set in a connected graph of order n and minimum degree d. This bound is tight up to an additive constant of 2. This result may be of independent interest. We also show that for every connected graph G with minimum degree at least 2, the rainbow connection number, rc(G), is upper bounded by Gc(G) + 2, where Gc(G) is the connected domination number of G. Bounds of the form diameter(G)?rc(G)?diameter(G) + c, 1?c?4, for many special graph classes follow as easy corollaries from this result. This includes interval graphs, asteroidal triple-free graphs, circular arc graphs, threshold graphs, and chain graphs all with minimum degree delta at least 2 and connected. We also show that every bridge-less chordal graph G has rc(G)?3.radius(G). In most of these cases, we also demonstrate the tightness of the bounds.

Continuum theory of edge states of topological insulators: variational principle and boundary conditions

We develop a continuum theory to model low energy excitations of a generic four-band time reversal invariant electronic system with boundaries. We propose a variational energy functional for the wavefunctions which allows us to derive natural boundary conditions valid for such systems. Our formulation is particularly suited for developing a continuum theory of the protected edge/surface excitations of topological insulators both in two and three dimensions. By a detailed comparison of our analytical formulation with tight binding calculations of ribbons of topological insulators modelled by the Bernevig-Hughes-Zhang (BHZ) Hamiltonian, we show that the continuum theory with a natural boundary condition provides an appropriate description of the low energy physics.