Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach

Reconstruction of biochemical reaction networks (BRN) and genetic regulatory networks (GRN) in particular is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and rational functions are typically used to model biochemical reaction networks. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data quite difficult. In this paper, we present a network reconstruction algorithm that can deal with ODE model descriptions containing polynomial and rational functions. Rather than identifying the parameters of linear or nonlinear ODEs characterised by pre-defined equation structures, our methodology allows us to determine the nonlinear ODEs structure together with their associated parameters. To solve the network reconstruction problem, we cast it as a compressive sensing (CS) problem and use sparse Bayesian learning (SBL) algorithms as a computationally efficient and robust way to obtain its solution. © 2012 IEEE.

Enlarging regions of stable running with segmented legs

In human and animal running spring-like leg behavior is found, and similar concepts have been demonstrated by various robotic systems in the past. In general, a spring-mass model provides self-stabilizing characteristics against external perturbations originated in leg-ground interactions and motor control. Although most of these systems made use of linear spring-like legs. The question addressed in this paper is the influence of leg segmentation (i.e. the use of rotational joint and two limb-segments) to the self-stability of running, as it appears to be a common design principle in nature. This paper shows that, with the leg segmentation, the system is able to perform self-stable running behavior in significantly broader ranges of running speed and control parameters (e.g. control of angle of attack at touchdown, and adjustment of spring stiffness) by exploiting a nonlinear relationship between leg force and leg compression. The concept is investigated by using a two-segment leg model and a robotic platform, which demonstrate the plausibility in the real world. ©2008 IEEE.

Numerical and theoretical analysis of the crosstalk in linear optical amplifiers

The dynamic characteristics, including the crosstalk and relaxation oscillation, of linear optical amplifiers (LOAs) are investigated by small-signal analysis under an averaging carrier density approximation and compared with the results of numerical simulation. The good agreement between the numerical simulation and the small-signal analysis indicated the averaging carrier density is an appropriate approximation for analyzing LOAs. Theoretical analyzes also show that the dynamic properties of the vertical laser fields dominate the dynamic performance of LOAs. Based on the small-signal analysis, a concise equation for the crosstalk under high bit rate was derived, which can be applied to measure the differential gain of LOAs.

Electronic structure of ZnO wurtzite quantum wires

The electronic structure and optical properties of ZnO wurtzite quantum wires with radius R >= 3 nm are studied in the framework of six-band effective-mass envelope function theory. The hole effective-mass parameters of ZnO wurtzite material are calculated by the empirical pseudopotential method. It is found that the electron states are either two-fold or four-fold degenerate. There is a dark exciton effect when the radius R of the ZnO quantum wires is in the range of [3,19.1] nm (dark range in our model). The dark ranges of other wurtzite semiconductor quantum wires are calculated for comparison. The dark range becomes smaller when the |Delta(so)| is larger, which also happens in the quantum-dot systems. The linear polarization factor of ZnO quantum wires is larger when the temperature is higher.

Linear spatio-temporal instability analysis of ice growth under a falling water film

A linear spatio-temporal stability analysis is conducted for the ice growth under a falling water film along an inclined ice plane. The full system of linear stability equations is solved by using the Chebyshev collocation method. By plotting the boundary curve between the linear absolute and convective instabilities (AI/CI) of the ice mode in the parameter plane of the Reynolds number and incline angle, it is found that the linear absolute instability exists and occurs above a minimum Reynolds number and below a maximum inclined angle. Furthermore, by plotting the critical Reynolds number curves with respect to the inclined angle for the downstream and upstream branches, the convectively unstable region is determined and divided into three parts, one of which has both downstream and upstream convectively unstable wavepackets and the other two have only downstream or upstream convectively unstable wavepacket. Finally, the effect of the Stefan number and the thickness of the ice layer on the AI/CI boundary curve is investigated.

Melting of Au and Al in nanometer Fe/Au and Fe/Al multilayers under swift heavy ions: A thermal spike study

Knowing that Fe is sensitive to swift heavy ion irradiations whereas Au and Al are not, the behavior of nanometric metallic multilayer systems, like [Fe(3 nm)/Au(x)](y) and [Fe(3 nm)/Al(x)](y) with x ranging between 1 and 10 mn, were studied within the inelastic thermal spike model. In addition to the usual cylindrical geometry of energy dissipation perpendicular to the ion projectile direction, the heat transport along the ion path was implemented in the electronic and atomic sub-systems. The simulations were performed using three different values of linear energy transfer corresponding to 3 MeV/u of Pb-208, Xe-132 and Kr-84 ions. For the Fe/Au system, evidence of appearance of a molten phase was found in the entire Au layer, provided the Au thickness is less than 7 nm and 3 nm for Pb and Xe ions, respectively. For the Fe/Al(x) system irradiated with Pb ions, the Al layers with a thickness less than 4 nm melt along the entire ion track. Surprisingly, the Fe layer does not melt if the Al thickness is larger than 2 nm, although the deposited energy surpasses the electronic stopping power threshold of track formation in Fe. For Kr ions melting does not occur in any of the multilayer systems.

Preparation and properties of a reactive type nonionic surfactant grafted linear low density polyethylene

A reactive type nonionic surfactant, monostearic acid monomaleic acid glycerol diester (MMGD) was synthesized in our laboratory. Grafting-copolymerization of linear low density polyethylene ( LLDPE) with MMGD was carried out by using beta ray irradiation in air in a twin-screw extruder. Evidence of the grafting of MMGD as well as its extent was determined by Fourier-transformed infrared (FT-IR) spectroscopy. The effects of monomer concentration, reaction temperature and screw run speed on degree of grafting were studied systematically. The thermal behavior of LLDPE-g-MMGD was investigated by using differential scanning calorimety ( DSC). Compared with neat LLDPE, the crystallization temperature ( Tc) of LLDPE-g-MMGD increased about 3 degrees C, and the melting enthalpy (Delta H-m) decreased with increase of MMGD content. It showed that the grafted MMGD monomer onto LLDPE acted as a nucleating agent. The tensile properties and light transmission of blown films were determined. Comparing with neat LLDPE film, no obvious changes could be found for the tensile strength, elongation at break and right angle tearing strength of LLDPE-g-MMGD film. The wettability is expressed by the water contact angle. With an increasing percentage of MMGD, the contact angles of water on film surface of LLDPE- g-MMGD decrease monotonically.

Preparation and properties of a novel nonionic surfactant grafted linear low density polyethylene

A novel nonionic surfactant, glycerol monostearic acid monomaleic acid diester (GMMD) was synthesized in our laboratory. Grafting-copolymerization of linear low density polyethylene (LLDPE) with GMMD was carried out by using P-ray irradiation in a twin-screw extruder. Evidence of the grafting of GMMD, as well as its extent, was determined by FT-IR. The effects of monomer concentration, reaction temperature and screw run speed on degree of grafting were studied systematically. The thermal behavior of LLDPE-g-GMMD was investigated by using differential scanning calorimety (DSC). Compared with neat LLDPE, the crystallization temperature (T,) of LLDPE-g-GMMD increased about 3 degrees C, and the melting enthalpy (Delta H-m) decreased with increase of GMMD content. It showed that the arafted GMMD monomer onto LLDPE acted as a nucleating agent. The tensile properties and light transmission of blown films were determined. Comparing with neat LLDPE film, no obvious changes could be found for the tensile strength, elongation at break and right angle tearing strength of LLDPE-g-GMMD film. Accelerated dripping property of film samples was investigated. The dripping duration of LLDPE-g-GMMD film and commercial anti-fog dripping film at 60 degrees C were 52 days and 17 days, respectively.

Electrochemiluminescent determination of peroxydisulfate with Cr(bpy)(3)(3+) in purely aqueous solution

A novel method for the sensitive and selective determination of peroxydisulfate was proposed. It was based on an electrochemiluminescent method with Cr(bpy)(3)(3+). The applied potential was set at -0.5 V in Cr(bpy)(3)(3+) system which was much more positive than those in Ru(bpz)(3)(2+) and Ru(bpy)(3)(2+) systems. A linear calibration was obtained over the range of 7-100 mu mol l(-1) with a correlation coefficient of 0.993. The relative standard deviation was 2% for 10 replicate injections of 0.01 mol l(-1) S2O82- solution. The detection limit (S/N=3) was 1 mu mol l(-1). The method was successfully applied to determination of peroxydisulfate in phase transfer catalysis. (C) 2000 Elsevier Science B.V. All rights reserved.

Crystallization behavior of blends of high-density polyethylene with novel linear low-density polyethylene

Blends of high-density polyethylene (HDPE) with novel linear low-density polyethylene (LLDPE) samples in the whole range of compositions were investigated by means of differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD). The LLDPEs are ethylene/octene-1 copolymers prepared with a single-site catalyst, with a narrower distribution of branches compared to Ziegler-Natta type polymers. It was found that cocrystallization or separate crystallization in the blends profoundly depends on the content of branches in the LLDPE, while the critical branch content of the novel LLDPE for separate crystallization is much lower than that of commercial LLDPE (prepared with Ziegler-Natta catalysts). This implies that the miscibility of linear and branched polyethylene is also affected by the distribution of branches. The marked expansion of the unit cell in cocrystals, which are formed by HDPE with the novel LLDPE, indicates that the branches are included in the crystal lattice during the cocrystallization process. The result is very helpful to understand the phenomenon that the unit cell dimensions of commercial branched polyethylene are larger than those of linear polyethylene.

SYNTHESIS OF A POLYETHYLENE-GRAFT-POLYSTYRENE COPOLYMER AND ITS COMPATIBILIZATION FOR LINEAR LOW-DENSITY POLYETHYLENE/POLY(PHENYLENE OXIDE) BLENDS

Based on unsteady diffusion kinetics, polyethylene(PE)-graft-polystyrene (PS) copolymers were designed and synthesized with a heterogeneous high yield titanium-based catalyst by copolymerization of ethylene with a PS-macromonomer using 1-hexene as a short chain agent to promote the incorporation of the PS-macromonomer. The presence of 1-hexene facilitated the diffusion of the PS-macromonomer, giving rise to the significantly increased incorporation of the PS-macromonomer. Compatibilization of blends of linear low density polyethylene (LLDPE)/poly(phenylene oxide) (PPO) with the PE-g-PS copolymer were investigated using scanning electron microscopy (SEM) and dynamic mechanical analysis (DMA).

COMPARISON OF THE BEHAVIOR OF CYCLIC AND LINEAR POLYSTYRENE IN DILUTE-SOLUTION

Using a low angle laser light scattering photometer, the second virial coefficients (A2) of both cyclic and linear polystyrene were determined in cyclohexane, toluene and methyl ethyl ketone (MEK) solutions. From the data obtained in cyclohexane solution the theta-temperature of cyclic polystyrene was determined to be 30-degrees-C. In toluene solution A2 of cyclic polystyrene is smaller than that of linear polystyrene with the same molecular weight, but in MEK the values are similar.

ELECTROCHEMICAL INVESTIGATION OF LIQUID/LIQUID SYSTEMS USING VARIOUS ORGANIC SOLVENTS

The potential windows of the system water/pure solvent (W/P) and water/solvent mixtures(W/S) have been investigated by cyclic voltammetry with solvents whose dielectric constants lie between 5.87 and 34.82. In the presence of LiCI in the aqueous phase and tetrabutytammoniumtetraphenylborate(TBATPB) in the organic phase, the systems water/allyl iso-thiocyanate (W/AIT) and water/nitrobensene (W/NB) show a same wide epotential window. thermodynamic parameters of ion transfer W/AIT interface were determined. In systems of W/P and V/S the influence solvent effect on the standard gibbs energies of transfer of was discussed.

KINETICS OF ION TRANSFER ACROSS LIQUID LIQUID INTERFACE BY CHRONOPOTENTIOMETRY WITH LINEAR CURRENT SCANNING

The equation of the potential-current curve for the ion transfer across the liquid/liquid interface during the linear current scanning has been derived theoretically. A method to calculate the kinetics parameters for the ion transfer by the way of linear current scanning is presented. The transfer of TPAs~+ ions, which is a typical basic electrolyte ion usually used in liquld/liquid interface electrochemistry, was practically investigated at the water/nitrobenzene interface.

Linear solvation energy relationships regarding sorption and retention properties of hydrophobic organic compounds in soil leaching column chromatography

The capacity factors of a series of hydrophobic organic compounds (HOCs) were measured in soil leaching column chromatography (SLCC) on a soil column, and in reversed-phase liquid chromatography on a C-18 column with different volumetric fractions (phi) of methanol in methanol-water mixtures. A general equation of linear solvation energy relationships, log(XYZ) = XYZ(0) + mV(1)/100 + spi* + bbeta(m) + aalpha(m), was applied to analyze capacity factors (k'), soil organic partition coefficients (K-oc) and octanol-water partition coefficients (P). The analyses exhibited high accuracy. The chief solute factors that control log K-oc, log P, and log k' (on soil and on C-18) are the solute size (V-1/100) and hydrogen-bond basicity (beta(m)). Less important solute factors are the dipolarity/polarizability (pi*) and hydrogen-bond acidity (alpha(m)). Log k' on soil and log K-oc have similar signs in four fitting coefficients (m, s, b and a) and similar ratios (m:s:b:a), while log k' on C-18 and log P have similar signs in coefficients (m, s, b and a) and similar ratios (m:s:b:a). Consequently, log k' values on C-18 have good correlations with log P (r > 0.97), while log k' values on soil have good correlations with log K-oc (r > 0.98). Two K-oc estimation methods were developed, one through solute solvatochromic parameters, and the other through correlations with k' on soil. For HOCs, a linear relationship between logarithmic capacity factor and methanol composition in methanol-water mixtures could also be derived in SLCC. (C) 2002 Elsevier Science Ltd. All rights reserved.