Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

Elasticity, stability, and ideal strength of beta-SiC in plane-wave-based ab initio calculations

On the basis of the pseudopotential plane-wave method and the local-density-functional theory, this paper studies energetics, stress-strain relation, stability, and ideal strength of beta-SiC under various loading modes, where uniform uniaxial extension and tension and biaxial proportional extension are considered along directions [001] and [111]. The lattice constant, elastic constants, and moduli of equilibrium state are calculated and the results agree well with the experimental data. As the four SI-C bonds along directions [111], [(1) over bar 11], [11(1) over bar] and [111] are not the same under the loading along [111], internal relaxation and the corresponding internal displacements must be considered. We find that, at the beginning of loading, the effect of internal displacement through the shuffle and glide plane diminishes the difference among the four Si-C bonds lengths, but will increase the difference at the subsequent loading, which will result in a crack nucleated on the {111} shuffle plane and a subsequently cleavage fracture. Thus the corresponding theoretical strength is 50.8 GPa, which agrees well with the recent experiment value, 53.4 GPa. However, with the loading along [001], internal relaxation is not important for tetragonal symmetry. Elastic constants during the uniaxial tension along [001] are calculated. Based on the stability analysis with stiffness coefficients, we find that the spinodal and Born instabilities are triggered almost at the same strain, which agrees with the previous molecular-dynamics simulation. During biaxial proportional extension, stress and strength vary proportionally with the biaxial loading ratio at the same longitudinal strain.

Formation, Thermal Stability and Deformation Behavior of Graphite-Flakes Reinforced Cu-based Bulk Metallic Glass Matrix Composites

Graphite-flake reinforced Cu47Ti34Zr11 Ni-8 bulk metallic glass matrix composite was fabricated by water-cooled copper mould cast. Most of the graphite flakes still keep unreacted and distribute uniformly in the amorphous matrix except that some reactive wetting occurs by the formation of TiC particles around the flakes. It reveals that the presence of graphite flakes does not affect the onset of the glass transition temperature, crystallization reaction and liquidus of the metallic glass. The resulting material shows obvious serrated flow and higher fracture strength under room temperature compressive load, comparing with the monolithic bulk metallic glass (BMG). Three types of interaction between the shear bands and graphite flakes, namely, shear band termination, shear bands branching and new shear bands formation near the graphite flakes can be observed by quasi-static uniaxial compression test and bonded interface technique through Vickers indentation.

Stability and Liqueafaction Analysis of Seabed to Wave Loading

波浪作用下海床的稳定性与液化分析是海底管线、防波堤和海洋平台设计中必须仔细考虑的问题。推荐了一个循环荷载作用下土体的弹塑性实用本构模型,并给出了一种粉土的模型参数。该模型直接根据初始应力状态和循环应力的大小与作用时间计算土体的塑性应变增量,在有限元计算中不需要引入弹塑性矩阵。采用Biot理论和有限单元法,计算了粉土海床在波浪作用下的孔隙水压力和有效应力的变化过程,并对海床的稳定性和液化进行了分析。计算结果与波浪槽实验反映的规律是相符的。

Stability and Bifurcation Bahaviour of Electrostatic Torsional NEMS Varactor Influenced by Dispersion Forces

The influences of Casimir and van der Waals forces on the nano-electromechanical systems (NEMS) electrostatic torsional varactor are studied. A one degree of freedom, the torsional angle, is adopted, and the bifurcation behaviour of the NEMS torsional varactor is investigated. There are two bifurcation points, one of which is a Hopf bifurcation point and the other is an unstable saddle point. The phase portraits are also drawn, in which periodic orbits are around the Hopf bifurcation point, but the periodic orbit will break into a homoclinic orbit when meeting the unstable saddle point.

Effect of Fe content on the thermal stability and dynamic mechanical behavior of NdAlNiCu bulk metallic glasses

The dependence of microstructure and thermal stability on Fe content of bulk Nd60Al10Ni10Cu20-xFex (0 less than or equal to x less than or equal to 20) metallic glasses is investigated by means of differential scanning calorimetry (DSC), X-ray diffraction (XRD) and high-resolution transmission electron micrograph (HRTEM). All samples exhibit typical amorphous feature under the detect limit of XRD, however, HRTEM results show that the microstructure of Nd60Al10Ni10Cu20-xFex alloys changes from a homogeneous amorphous phase to a composite structure consisting of clusters dispersed in amorphous matrix by increasing Fe content. Dynamic mechanical properties of these alloys with controllable microstructure are studied, expressed via storage modulus, the loss modulus and the mechanical damping. The results reveal that the storage modulus of the alloy without Fe added shows a distinct decrease due to the main a relaxation. This decrease weakens and begins at a higher temperature with increasing Fe content. The mechanism of the effect of Fe addition on the microstructure and thermal stability in this system is discussed in terms of thermodynamics viewpoints. (C) 2004 Elsevier B.V. All rights reserved.

Stability and bifurcation behaviour of electrostatic torsional NEMS varactor influenced by dispersion forces

The influences of Casimir and van der Waals forces on the nano-electromechanical systems (NEMS) electrostatic torsional varactor are studied. A one degree of freedom, the torsional angle, is adopted, and the bifurcation behaviour of the NEMS torsional varactor is investigated. There are two bifurcation points, one of which is a Hopf bifurcation point and the other is an unstable saddle point. The phase portraits are also drawn, in which periodic orbits are around the Hopf bifurcation point, but the periodic orbit will break into a homoclinic orbit when meeting the unstable saddle point.

Thermal stability and spectroscopic properties of Er3+-doped niobium tellurite glasses for broadband amplifiers

Three Er3+-doped tellurite glasses with compositions of 70TeO(2)-30ZnO, 70TeO(2)-20ZnO-10Nb(2)O(5) and 70TeO(2)-20ZnO-5BaO-5Nb(2)O(5) have been investigated for developing fiber and planar broadband amplifiers and lasers. The optical spectroscopic properties and thermal stability of Er3+-doped tellurite glasses have been discussed. The results show that the incorporation of Nb2O5 increases the thermal stability of Er3+-doped tellurite glasses significantly, Er3+-doped niobium tellurite glasses 70TeO(2)-20ZnO-10Nb(2)O(5) and 70TeO(2)-20ZnO-5BaO-5Nb(2)O(5) exhibit the good thermal stability (DeltaT > 150degreesC), the large emission cross-section (>10 x 10(-21) cm(2)) and broad full width at half maximum (similar to65 nm), will be preferable for broadband Er3+-doped fiber amplifiers. (C) 2004 Elsevier B.V. All rights reserved.

Effect of bismuth oxide on the thermal stability and Judd-Ofelt parameters of Er 3(+)/Yb3(+) co-doped aluminophosphate glasses

The Er3+/Yb3+ co-doped glasses with compositions of xBi(2)O(3)-(65-x)P2O5-4Yb(2)O(3)-11Al(2)O(3)-5BaO-15Na(2)O (where x = 0, 2.5, 5, 7.5 and 10 mol%) were prepared using the normal melt quench technique. The optical absorption spectra of the glasses were recorded in the wavelength range 300-1700 nm. The effect of Bi2O3 content on the thermal stability and absorption spectra of glasses was investigated. In addition, the Judd-Ofelt parameters and oscillator strengths were calculated by employing Judd-Ofelt theory. It was observed that the positions of the fundamental absorption edge and cut-off wavelength shifted towards red as the content of Bi2O3 increased. However, there were no red shifts found both in the peak wavelength and in the center of mass wavelength of all absorption bands with Bi2O3 content increasing. The results of Judd-Ofelt theory analysis showed that Judd-Ofelt parameters Omega(t), (t = 2, 4, 6) changed sharply when Bi2O3 concentration exceeded 5 mol%. The variation trends of experimental oscillator strength were similar with those of Judd-Ofelt parameters as function of Bi2O3 concentrations. Moreover, differential scanning calorimetry experiments showed that the increases of Bi2O3 content weakened the network structure and then lowered the thermal stability of the glasses. The spontaneous emission probability A(rad), branching ratio beta and the radiative lifetime tau(rad) were also calculated and analyzed. The stimulated emission cross-section of Er3+ was calculated according to the McCumber theory. It was found that the stimulated emission cross-section of Er3+ was monotonically increases with Bi2O3 content increasing. (C) 2006 Elsevier B.V. All rights reserved.

Effect of oxygen substitution by halide ions on structure, thermal stability and upconversion fluorescence in Er3(+)/Yb3(+)-codoped germanium-bismuth glasses

For the first time. effect of halide ions (F-, Cl-, Br-, and I-) introduction on structure, thermal stability, and upconversion fluorescence in Er3+/Yb3+-codoped oxide-halide germanium-bismuth glasses has been systematically investigated. The results show that halide ions modified germanium-bismuth glasses have lower maximum phonon energy and phonon density, worse thermal stability. longer measured lifetimes of I-4(l1/2) level, and stronger upconversion emission than germanium-bismuth glass. All these results indicate that halide ions play an important role in the formation of glass network, and have an important influence on the upconversion luminescence. The possible upconversion mechanisms of Er3+ ion are also evaluated. © 2005 Elsevier Ltd. All rights reserved.

Host dependent thermal stability and frequency upconversion of Er3+-doped heavy metal oxyfluoride germanate glasses

The upconversion properties of Er3+-doped heavy metal oxyfluoride germanate glasses under 975 nm excitation have been investigated. The intense green (551 and 529 nm) and relatively weak red (657 nm) emissions corresponding to the transitions S-4(3/2) -> I-4(15/2), H-2(11/2) -> I-4(15/2) and F-4(9/2) -> I-4(15/2), respectively, were simultaneously observed at room temperature. The content of PbF2 has an important influence on the upconversion luminescence emission. With increasing content of PbF2, the intensities of green (529 nm) and red (657 nm) emissions increase slightly, while the green emission (551 nm) increases markedly. These results suggest that PbF2 has an influence on the green (551 nm) emission more than on the green (529 nm) and red (657 nm) emissions.

Effect of chloride ions' introduction on structural, thermal stability, and spectroscopic properties in Yb3+Er3+-codoped germanate-bismuth-lead glasses

Yb3+Er3+-codoped chloride-modified germanate-bismuth-lead glasses have been synthesized by the conventional melting and quenching method. Structural and thermal stability properties have been obtained on the basis of the Raman spectra and differential thermal analysis, which indicate that the PbCl2 addition has an important influence on the phonon density of states, maximum phonon energy, and thermal stability of host glasses. The Judd-Ofelt intensity parameters and quantum efficiencies were calculated on the basis of the Judd-Ofelt theory and lifetime measurements. For the 1.53 mu m emission band, the full widths at the half-maximum increase and peak wavelengths are blueshifted with increasing PbCl2 content. Moreover, the effect of the PbCl2 addition on the phonon density of states, OH- content, and upconversion luminescence has been discussed and evaluated. Our results reveal that, with increasing PbCl2 content, the decrease of phonon density and OH- content contributes more to the enhanced upconversion emissions than that of maximum phonon energy. (c) 2005 Optical Society of America

Effect of alkali and alkaline earth fluoride introduction on thermal stability and structure of fluorophosphate glasses

The thermal stability and structure of RF-RF2-AIF(3)-Al(PO3)(3) fluorophosphate glasses were investigated. Analyses of infrared absorbance spectra and Raman spectra reveal that with increasing number of alkali and alkaline earth fluoride components, the sum of P-O-P bond and O-P-O bond increases and glass network is strengthened. Consequently, the inhibition to nucleation and crystallization processes is improved, which is proved by the increment of thermal stability factors AT and S determined by differential scanning calorimetry. In addition, it was found that LiF has poor ability to form glass in univalent alkali fluorides and MgF2 has comparative strong ability to form glass in bivalent alkaline earth fluorides. (c) 2006 Published by Elsevier B.V.

Effect of CdF2 addition on thermal stability and upconversion luminescence properties in Tm3+-Yb3+ codoped oxyfluoride silicate glasses

Tm3+-Yb3+ codoped oxyfluoride silicate glasses suitable for upconversion laser has been fabricated. In this paper, effect of CdF2 addition on thermal stability and upconversion luminescence properties in Tm3+-Yb3+ codoped oxyfluoride silicate glasses have been systematically investigated. The experimental results indicate that, with the substitution CdF2 for PbF2, the glass thermal stability increases and the UV cutoff edge moves to short-wave band slightly. With increasing CdF2 content, the blue and red upconversion luminescence intensity increases slightly at first, and then increases rapidly. While the near infrared (NIR) upconversion emission intensity increases notably at first and then increases slightly. However, the blue and NIR luminescence intensity are much stronger than that of red, indicating these oxyfluoride silicate glasses are more preferable for blue and NIR emissions than red emission. The possible upconversion mechanisms for the blue, red and NIR fluorescence are also estimated and evaluated. (c) 2006 Elsevier B.V. All rights reserved.