Hepatitis C virus NS3 protease requires its NS4A cofactor peptide for optimal binding of a boronic acid inhibitor as shown by NMR

NMR spectroscopy was used to characterize the hepatitis C virus (HCV) NS3 protease in a complex with the 24 residue peptide cofactor from NS4A and a boronic acid inhibitor, Ac-Asp-Glu-Val-Val-Pro-boroAlg-OH. Secondary-structure information, NOE constraints between protease and cofactor, and hydrogen-deuterium exchange rates revealed that the cofactor was an integral strand in the N-terminal beta-sheet of the complex as observed in X-ray crystal structures. Based upon chemical-shift perturbations, inhibitor-protein NOEs, and the protonation state of the catalytic histidine, the boronic acid inhibitor was bound in the substrate binding site as a transition state mimic. In the absence of cofactor, the inhibitor had a lower affinity for the protease. Although the inhibitor binds in the same location, differences were observed at the catalytic site of the protease.     

Finite-dimensional quantum mechanics of a particle. III. The Weylian quantum mechanics of confined quarks

A finite-dimensional analog of Weyl's formulation of quantum kinematics of a physical system through irreducible Abelian groups of unitary ray rotations in system space offers many possibilities for the quantum mechanics of confined particles. This paper is devoted to the expansion of the recently developed framework of such Weylian finite-dimensional quantum mechanics which may provide a new way of thinking about the characteristics of quark physics.     

A numerical investigation of the resonance of gas-filled microbubbles: resonance dependence on acoustic pressure amplitude

The general Keller-Herring equation for free gas bubbles is augmented by specific terms to describe the elasticity, viscosity and thickness of the encapsulating shell in ultrasound contrast agent microbubbles. A numerical investigation that analyses the acoustic backscatter from bubbles is employed to identify resonance frequencies that can be compared, for increasing driving pressure amplitude, with linear approximations obtained via analytical considerations. Calculations for bubbles of the size employed in diagnostic ultrasound, between 2 and 6 mum diameter, that are immersed in water and blood and exposed to monochromatic insonation, causing the bubbles to undergo stable cavitation, reveal that the resonance frequency diverges from the linear approximation as the pressure amplitude is increased. The shift in resonance, to lower frequency values, is found to be more pronounced for larger bubbles with the calculated value differing by up to 40% from the linear approximation. The results of this simulation might be potentially useful in preparation of formulations of ultrasound contrast agents with the specifically desired features, such as for instance resonance frequency.     

On the hopf structure of U p,q (gl(1∣1)) and the universal T-matrix of fun p,q (GL(1∣1))

The dually conjugate Hopf superalgebras Fun _p,q (GL(11)) and U _p,q (gl(11)) are studied using the Frønsdal-Galindo approach and the full Hopf structure of U _p,q (gl(11)) is extracted. A finite expression for the universal T-matrix, identified with the dual form and expressing the generalization of the exponential map of the classical groups, is obtained for Fun _p,q (GL(11)). In a representation with a colour index, the T-matrix assumes a form that satisfies a coloured graded Yang-Baxter equation.     

Modification of plasma-etched profiles by sputtering

Two-dimensional etch profiles are modeled for plasma etching. The etch rate dependence on the angle of incidence of the bombarding ions on the etched surface has a sputtering-type yield. The etch profile is advanced in time by an evolution equation for an etch rate proportional to the modified ion energy flux. Approximate analytical expressions for the etch rates are derived as a product of the etch rates in the absence of the sputtering-type yield and a weighting factor that depends on the angle the ion drift velocity makes with the normal to the wafer surface. The weighting factor is determined from experimental measurements of the angular dependence of ion beam etching by sputtering. These etch rates are valid when the ratio of the ion drift speed to the ion thermal speed is large compared to one. The etching is modeled in the ion flux-limited regime for simplicity. The modifications of the shape of etch profiles of a long rectangular trench and a waveguide structure or strip are treated     

A trial phase function method for a class of λ-ω reaction-diffusion systems: Reduction to a Schrödinger type problem in an eigen sub-domain

The perturbed central force problem $\text{γ}{}_{\mathrm{xx}}\text{? ?}{}^2\text{γ}\text{a}\text{?}{}^2\text{+ γλ(γ) = 0, γ}\text{a}\text{?}{}_{\mathrm{x}}\text{+ 2}\text{a}\text{?}\text{γ}{}_{\mathrm{x}}\text{+ γ[}\text{}\text{?}\text{gw(γ}{}^1\text{) ?}\text{}\text{?}\text{gw(γ)] = 0}$ arising from the λ-ω system

$\text{α}\text{αt}\text{C}{}_1\text{C}{}_2\text{=}\text{λ}\text{?ω}\text{ω}\text{λ}\text{C}{}_1\text{C}{}_2\text{+}\text{α}\text{αt}\text{C}{}_1\text{C}{}_2$

where $\text{c}{}_1\text{=}\text{γ}\text{(x)cosθ(x,t), c}{}_2\text{=}\text{γ}\text{(x)sinθ(x,t), θ = σt ? ?∝}{}^{\mathrm{x}}\text{a}\text{?}\text{(x′)dx′}\text{and}\text{ω = ?}\text{}\text{?}\text{gw(}\text{γ}\text{)}$ is considered for the class $\text{λ}\text{=}\text{}\text{?}\text{gw}\text{= 1 ? g(}\text{γ}\text{)}$. The resulting linear equation in $\text{γ(x), γ}{}_{\mathrm{xx}}\text{+ 2}\text{a}\text{?}\text{γ}{}_{\mathrm{x}}\text{+}\text{γ[α}{}^2\text{+}\text{a}\text{?}{}_{\mathrm{x}}\text{?}\text{?}{}^2\text{a}\text{?}{}^2\text{] = 0}$ is solved with the aid of a class of trial phase functions $\text{a}\text{?}{}_{\mathrm{T}}\text{(x)}$ generated by the unperturbed central force problem for the case g(γ) = γ². An application of the Liouville-Green approximation procedure reduces the system to a Schrödinger type boundary value problem in an eigen sub-domain. The analytical estimates for α are in reasonable agreement with the results of numerical integration of the nonlinear system. The eigenfunctions γ(x) display expected oscillatory behaviour inside an eigen sub-domain. The higher modes and the span of the most extended centre structure are estimated and interpreted in the context of WKBJ connection formula.     

The eight-fold way for optical quasicrystals

Network theory is increasingly employed to study the structure and behaviour of social, physical and technological systems — including civil infrastructure. Many of these systems are interconnected and the interdependencies between them allow disruptive events to propagate across networks, enabling damage to spread far beyond the immediate footprint of disturbance. In this research we experiment with a model to characterise the configuration of interdependencies in terms of direction, redundancy, and extent, and we analyse the performance of interdependent systems with a wide range of possible coupling modes. We demonstrate that networks with directed dependencies are less robust than those with undirected dependencies, and that the degree of redundancy in inter-network dependencies can have a differential effect on robustness depending on the directionality of the dependencies. As interdependencies between many real-world systems exhibit these characteristics, it is likely that many such systems operate near their critical thresholds. The vulnerability of an interdependent network is shown to be reducible in a cost effective way, either by optimising inter-network connections, or by hardening high degree nodes. The results improve understanding of the influence of interdependencies on system performance and provide insight into how to mitigate associated risks.     

A Mössbauer study of amorphous Fe40Ni40B20

Amorphous Fe₄₀Ni₄₀B₂₀ (VITROVAC 0040) alloy has been investigated using ⁵⁷Fe Mössbauer Spectroscopy. The Curie temperature T_c is found to be well defined and is 695 ± 1 K. The quadrupole splitting just above T_c is 0.64 mm sec^?1. The crystallization temperature is 698 ± 2 K, close to but definitely above T_c. The average hyperfine field H_eff(T) of the glassy state shows a temperature dependence of $\text{H}{}_{\mathrm{<mtext>eff</mtext>}}\text{(0)[1 ? B}{}_{\mathrm{<mtext>3</mtext><mtext>2</mtext>}}\text{(T/T}{}_{\mathrm{c}}\text{)}{}^{\mathrm{<mtext>3</mtext><mtext>2</mtext>}}\text{? C}{}_{\mathrm{<mtext>5</mtext><mtext>2</mtext>}}\text{(T/T}{}_{\mathrm{c}}\text{)}{}^{\mathrm{<mtext>5</mtext><mtext>2</mtext>}}\text{? …]}$ indicative of the existence of spin wave excitations. The values of $\text{B}{}_{\mathrm{<mtext>3</mtext><mtext>2</mtext>}}$ and $\text{C}{}_{\mathrm{<mtext>5</mtext><mtext>2</mtext>}}$ are found to be 0.40 and 0.06, respectively, for T/T_c ? 0.72. At temperatures close to T_c, H_eff(T) varies as (1 ? T/T_c)^β where β is one of the critical exponents and its value is found to be 0.29 ± 0.02.     

A Mössbauer study of FeC2O4·2D2O below the néel temperature

From low-temperature Mössbauer measurement on FeC₂O₄·2D₂O the reported difference in quadrupole splitting from the simple dihydrate is inferred to be due to lattice effects. The Zeeman split spectrum has been analyzed taking into account the ambiguity problem and the hyperfine parameters were determined to be I.S.=1.22 mm/sec; Q.S.=1.93 mm/sec; =0.65 to 0.72; =90 to 83.1^o and =0 to 11.8^o. The principal electric field gradient axis lies along the crystal a-axis with V_YY and lying along the crystal b-axis. The crystal field parameters 10Dq, Ds and Dt have been determined to be 10500, 185 and 211 cm^–1, respectively.