Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the beta-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable ``tense'' state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin. (C) 2015 Elsevier Inc. All rights reserved.

Fully 3D refraction correction dosimetry system

The irradiation of selective regions in a polymer gel dosimeter results in an increase in optical density and refractive index (RI) at those regions. An optical tomography-based dosimeter depends on rayline path through the dosimeter to estimate and reconstruct the dose distribution. The refraction of light passing through a dose region results in artefacts in the reconstructed images. These refraction errors are dependant on the scanning geometry and collection optics. We developed a fully 3D image reconstruction algorithm, algebraic reconstruction technique-refraction correction (ART-rc) that corrects for the refractive index mismatches present in a gel dosimeter scanner not only at the boundary, but also for any rayline refraction due to multiple dose regions inside the dosimeter. In this study, simulation and experimental studies have been carried out to reconstruct a 3D dose volume using 2D CCD measurements taken for various views. The study also focuses on the effectiveness of using different refractive-index matching media surrounding the gel dosimeter. Since the optical density is assumed to be low for a dosimeter, the filtered backprojection is routinely used for reconstruction. We carry out the reconstructions using conventional algebraic reconstruction (ART) and refractive index corrected ART (ART-rc) algorithms. The reconstructions based on FDK algorithm for cone-beam tomography has also been carried out for comparison. Line scanners and point detectors, are used to obtain reconstructions plane by plane. The rays passing through dose region with a RI mismatch does not reach the detector in the same plane depending on the angle of incidence and RI. In the fully 3D scanning setup using 2D array detectors, light rays that undergo refraction are still collected and hence can still be accounted for in the reconstruction algorithm. It is found that, for the central region of the dosimeter, the usable radius using ART-rc algorithm with water as RI matched medium is 71.8%, an increase of 6.4% compared to that achieved using conventional ART algorithm. Smaller diameter dosimeters are scanned with dry air scanning by using a wide-angle lens that collects refracted light. The images reconstructed using cone beam geometry is seen to deteriorate in some planes as those regions are not scanned. Refraction correction is important and needs to be taken in to consideration to achieve quantitatively accurate dose reconstructions. Refraction modeling is crucial in array based scanners as it is not possible to identify refracted rays in the sinogram space.

Ellipse Fitting Using the Finite Rate of Innovation Sampling Principle

Standard approaches for ellipse fitting are based on the minimization of algebraic or geometric distance between the given data and a template ellipse. When the data are noisy and come from a partial ellipse, the state-of-the-art methods tend to produce biased ellipses. We rely on the sampling structure of the underlying signal and show that the x- and y-coordinate functions of an ellipse are finite-rate-of-innovation (FRI) signals, and that their parameters are estimable from partial data. We consider both uniform and nonuniform sampling scenarios in the presence of noise and show that the data can be modeled as a sum of random amplitude-modulated complex exponentials. A low-pass filter is used to suppress noise and approximate the data as a sum of weighted complex exponentials. The annihilating filter used in FRI approaches is applied to estimate the sampling interval in the closed form. We perform experiments on simulated and real data, and assess both objective and subjective performances in comparison with the state-of-the-art ellipse fitting methods. The proposed method produces ellipses with lesser bias. Furthermore, the mean-squared error is lesser by about 2 to 10 dB. We show the applications of ellipse fitting in iris images starting from partial edge contours, and to free-hand ellipses drawn on a touch-screen tablet.

A Nonlinear Guidance Law for Impact Time Control

This paper discusses the problem of impact time control of an interceptor against a stationary target. A nonlinear guidance law is proposed with the interceptor heading angle variation as a function of the range to target. Closed-form expressions for the design parameters are derived for an exact analysis of the impact time. A feedback form of the guidance law is presented for addressing realistic implementation in the presence of autopilot lag. Using the closed-form expressions of the impact time, a cooperative guidance scheme is presented for simultaneous impact in a salvo attack. Extensive simulation studies are presented validating the analytic findings.

Control of vortex shedding at moderate Reynolds numbers

The suppression method of vortex shedding from a circular cylinder has been studied experimentally in the Reynolds number range from 300 to 1600. The test is performed in a water channel. The model cylinder is 1 cm in diameter and 38 cm in length. A row of small rods of 0.18 cm in diameter and 1.5 cm in length are perpendicularly connected to the surface of the model cylinder and distributed along the meridian, The distance between the neighboring rods and the angle of attack of the rods can be changed so that the suppression effect on vortex shedding can be adjusted. The results show that vortex shedding can be suppressed effectively if the distance between the neighboring rods is smaller than 3 times and the cylinder diameter and the angle of attack is in the range of 30degreesless than or equal tobeta<90&DEG;.

Forebody Compressibility Research of Hypersonic Vehicle

Three kinds of forebody model of hypersonic vehicles were studied with numerical simulation method. It shows that the two- order compressive ramp model is the best selection among the three for its good evaluative parameters value at the cowl of the inlet . This model can provide higher value of flux coefficient and total pressure recovery coefficient and lower average Mach number compared with those of the other two models . Simultaneously different compressive angles may have different effects . The configuration which the firstorder of compressive angle is 4°and the second 5°is the optimum combination. Furthermore factors such as attack angle were concerned. Better result may be obtained with a range of attack angles . Based on the work above the integrated design for forebodyPinlet of a hypersonic vehicle was performed. The numerical result shows that this integrated model provides good flow field quality for inlet and engine work.

超声速大攻角旋成体迎风激波数值模拟

旋成弹体在大攻角超声速流动中其迎风面上有时会出现一种迎风激波.采用非定常雷诺平均的Navier-Stokes方程以及两方程kω-sst和代数B-L湍流模型成功地模拟了该现象,验证了该迎风激波是由于流场主旋涡导致超声速流动偏移造成的涡诱导激波的一部分的结论.

Elastic fields of interacting elliptic inhomogeneities

This paper presents a method for the calculation of two-dimensional elastic fields in a solid containing any number of inhomogeneities under arbitrary far field loadings. The method called 'pseudo-dislocations method', is illustrated for the solution of interacting elliptic inhomogeneities. It reduces the interacting inhomogeneities problem to a set of linear algebraic equations. Numerical results are presented for a variety of elliptic inhomogeneity arrangements, including the special cases of elliptic holes, cracks and circular inhomogeneities. All these complicated problems can be solved with high accuracy and efficiency.

The Effect of Conical Flowfields on the Performance of Waveriders at Mach 6

The performance of 23 kinds of waveriders, derived from different conical flowfields, is analyzed by the numerical computation under the conditions of fight speed of Mach 6, attack angle of 0° and flight altitude of 30 km. These results indicate that the performance is influenced by the shapes and the width to height ratios (W/H ) of generating cones. The geometrical parameter and the lift coefficient are proportional to W/H, while the drag coefficient and the lift to drag ratio (L/D ) have extreme values. Considering the base drag and the computation errors, the waverider with the highest L/D is cut from the elliptical cone’s flowfield (W/H = 1.5―1.618), and the configuration with the lowest drag can also be obtained at W/H = 1:1.5. Accordingly, good suggestions are proposed for practical design based on these computational results.

Modeling of Ammonothermal Growth of Nitrides

Bulk single crystals of GaN and AlN can be grown from supercritical fluids using the ammonothermal method, which utilizes ammonia as fluid rather than water as in the hydrothermal process. In this process, a mineralizer such as amide, imide or nitride is used to attack a bulk nitride feedstock at temperatures from 200°C to 500°C and pressures from 1 to 4 kbar. Ammonothermal systems have been modeled here using fluid dynamics, thermodynamics and heat transfer models. The nutrient is considered as a porous media bed and the fluid flow is simulated using the Darcy-Brinkman-Forchheimer model. The resulting governing equations are solved using the finite volume method. The effects of particle size on flow pattern and temperature distribution in an autoclave are analyzed.

Turbulence modeling for flows around convex features giving rapid eddy distortion

Reynolds averaged Navier-Stokes model performances in the stagnation and wake regions for turbulent flows with relatively large Lagrangian length scales (generally larger than the scale of geometrical features) approaching small cylinders (both square and circular) is explored. The effective cylinder (or wire) diameter based Reynolds number, ReW ≤ 2.5 × 103. The following turbulence models are considered: a mixing-length; standard Spalart and Allmaras (SA) and streamline curvature (and rotation) corrected SA (SARC); Secundov's νt-92; Secundov et al.'s two equation νt-L; Wolfshtein's k-l model; the Explicit Algebraic Stress Model (EASM) of Abid et al.; the cubic model of Craft et al.; various linear k-ε models including those with wall distance based damping functions; Menter SST, k-ω and Spalding's LVEL model. The use of differential equation distance functions (Poisson and Hamilton-Jacobi equation based) for palliative turbulence modeling purposes is explored. The performance of SA with these distance functions is also considered in the sharp convex geometry region of an airfoil trailing edge. For the cylinder, with ReW ≈ 2.5 × 103 the mixing length and k-l models give strong turbulence production in the wake region. However, in agreement with eddy viscosity estimates, the LVEL and Secundov νt-92 models show relatively little cylinder influence on turbulence. On the other hand, two equation models (as does the one equation SA) suggest the cylinder gives a strong turbulence deficit in the wake region. Also, for SA, an order or magnitude cylinder diameter decrease from ReW = 2500 to 250 surprisingly strengthens the cylinder's disruptive influence. Importantly, results for ReW ≪ 250 are virtually identical to those for ReW = 250 i.e. no matter how small the cylinder/wire its influence does not, as it should, vanish. Similar tests for the Launder-Sharma k-ε, Menter SST and k-ω show, in accordance with physical reality, the cylinder's influence diminishing albeit slowly with size. Results suggest distance functions palliate the SA model's erroneous trait and improve its predictive performance in wire wake regions. Also, results suggest that, along the stagnation line, such functions improve the SA, mixing length, k-l and LVEL results. For the airfoil, with SA, the larger Poisson distance function increases the wake region turbulence levels by just under 5%. © 2007 Elsevier Inc. All rights reserved.

Continuous spectrum growth and modal instability in swirling duct flow

We present results on the stability of compressible inviscid swirling flows in an annular duct. Such flows are present in aeroengines, for example in the by-pass duct, and there are also similar flows in many aeroacoustic or aeronautical applications. The linearised Euler equations have a ('critical layer') singularity associated with pure convection of the unsteady disturbance by the mean flow, and we focus our attention on this region of the spectrum. By considering the critical layer singularity, we identify the continuous spectrum of the problem and describe how it contributes to the unsteady field. We find a very generic family of instability modes near to the continuous spectrum, whose eigenvalue wavenumbers form an infinite set and accumulate to a point in the complex plane. We study this accumulation process asymptotically, and find conditions on the flow to support such instabilities. It is also found that the continuous spectrum can cause a new type of instability, leading to algebraic growth with an exponent determined by the mean flow, given in the analysis. The exponent of algebraic growth can be arbitrarily large. Numerical demonstrations of the continuous spectrum instability, and also the modal instabilities are presented.

Simulation of Coal Combustion by AUSM Turbulence-Chemistry Char Combustion Model and a Full Two-Fluid Model

An algebraic unified second-order moment (AUSM) turbulence-chemistry model of char combustion is introduced in this paper, to calculate the effect of particle temperature fluctuation on char combustion. The AUSM model is used to simulate gas-particle flows, in coal combustion in a pulverized coal combustor, together with a full two-fluid model for reacting gas-particle flows and coal combustion, including the sub-models as the k-epsilon-k(p) two-phase turbulence niodel, the EBU-Arrhenius volatile and CO combustion model, and the six-flux radiation model. A new method for calculating particle mass flow rate is also used in this model to correct particle outflow rate and mass flow rate for inside sections, which can obey the principle of mass conservation for the particle phase and can also speed up the iterating convergence of the computation procedure effectively. The simulation results indicate that, the AUSM char combustion model is more preferable to the old char combustion model, since the later totally eliminate the influence of particle temperature fluctuation on char combustion rate.

Weaknesses of Margulis and Ramanujan-Margulis low-density parity-check codes

We report weaknesses in two algebraic constructions of low-density parity-check codes based on expander graphs. The Margulis construction gives a code with near-codewords, which cause problems for the sum-product decoder; The Ramanujan-Margulis construction gives a code with low-weight codewords, which produce an error-floor. © 2004 Elsevier B.V.

Weaknesses of margulis and ramanujan-margulis low-density parity-check codes

We report weaknesses in two algebraic constructions of low-density parity-check codes based on expander graphs. The Margulis construction gives a code with near-codewords, which cause problems for the sum-product decoder; The Ramanujan-Margulis construction gives a code with low-weight codewords, which produce an error-floor. ©2003 Published by Elsevier Science B. V.