Quasi steady-state approximations in complex intracellular signal transduction networks – a word of caution

Enzyme reactions play a pivotal role in intracellular signal transduction. Many enzymes are known to possess Michaelis–Menten (MM) kinetics and the MM approximation is often used when modeling enzyme reactions. However, it is known that the MM approximation is only valid at low enzyme concentrations, a condition not fulfilled in many in vivo situations. Recently the total quasi steady-state approximation (tQSSA) has been developed for enzymes with MM kinetics. This new approximation is valid not only whenever the MM approximation is, but moreover in a greatly extended parameter range. Starting from a single reaction and arriving at the mitogen activated protein kinase (MAPK) cascade, we give several examples of biologically realistic scenarios where the MM approximation leads to quantitatively as well as qualitatively wrong conclusions, and show that the tQSSA improves the accuracy of the simulations greatly.      

基于梁平截面假设的复杂细长结构动力模型简化方法

针对纵向尺度显著大于横向的复杂细长结构,提出了一个基于梁平截面假设的模型简化方法,建立了具有物理意义的基向量。同时考虑这类结构截面变形的翘曲模式,增加了翘曲基向量,得到精度较高的简化动力模型。这样的简化模型可以用于原结构在不同边界条件的动力分析。结构频率计算的两个具体算例表明了简化方法的有效性。     

Memory and Markov Blankets

In theoretical biology, we are often interested in random dynamical systems—like the brain—that appear to model their environments. This can be formalized by appealing to the existence of a (possibly non-equilibrium) steady state, whose density preserves a conditional independence between a biological entity and its surroundings. From this perspective, the conditioning set, or Markov blanket, induces a form of vicarious synchrony between creature and world—as if one were modelling the other. However, this results in an apparent paradox. If all conditional dependencies between a system and its surroundings depend upon the blanket, how do we account for the mnemonic capacity of living systems? It might appear that any shared dependence upon past blanket states violates the independence condition, as the variables on either side of the blanket now share information not available from the current blanket state. This paper aims to resolve this paradox, and to demonstrate that conditional independence does not preclude memory. Our argument rests upon drawing a distinction between the dependencies implied by a steady state density, and the density dynamics of the system conditioned upon its configuration at a previous time. The interesting question then becomes: What determines the length of time required for a stochastic system to ‘forget’ its initial conditions? We explore this question for an example system, whose steady state density possesses a Markov blanket, through simple numerical analyses. We conclude with a discussion of the relevance for memory in cognitive systems like us.     

两个eCK模型下可证安全的密钥交换协议分析

基于eCK(extended Canetti-Krawczyk)模型的定义,针对eCK模型下证明安全的两个密钥交换协议进行了分析.结果显示两个密钥交换协议在eCK模型中都是不安全的,其中SAKA(secure authenticated key agree-ment)协议不能抵抗临时密钥泄露攻击也不能抵抗长期密钥泄露攻击,并且不具有前向安全性.另一个SHY(Shi-Huang-Yang)协议不能抵抗两方临时密钥同时泄露的攻击.     

Thermoelastoplastic deformation of noncircular cylindrical shells

A method to determine the nonstationary temperature fields and the thermoelastoplastic stress-strain state of noncircular cylindrical shells is developed. It is assumed that the physical and mechanical properties are dependent on temperature. The heat-conduction problem is solved using an explicit difference scheme. The temperature variation throughout the thickness is described by a power polynomial. For the other two coordinates, finite differences are used. The thermoplastic problem is solved using the geometrically nonlinear theory of shells based on the Kirchhoff-Love hypotheses. The theory of simple processes with deformation history taken into account is used. Its equations are linearized by a modified method of elastic solutions. The governing system of partial differential equations is derived. Variables are separated in the case where the curvilinear edges are hinged. The partial case where the stress-strain state does not change along the generatrix is examined. The systems of ordinary differential equations obtained in all these cases are solved using Godunov's discrete orthogonalization. The temperature field in a shell with elliptical cross-section is studied. The stress-strain state found by numerical integration along the generatrix is compared with that obtained using trigonometric Fourier series. The effect of a Winkler foundation on the stress-strain state is analyzed Translated from Prikladnaya Mekhanika, Vol. 44, No. 8, pp. 79–90, August 2008.     

热-力耦合原子-连续关联模型的框架及其算法

对热-力耦合的原子-连续关联模型进行了系统研究,给出了计及热-力耦合行为的金属微-纳米构件内材料的瞬态弹性常数,应力、应变、比热容等物理量的具体计算公式及其算法.利用原子运动中的“结构形变”部分来研究微-纳米尺度下多晶原子团簇的非均匀结构变形.将原子团簇晶格结构的变形与连续体的变形关联起来,在准简谐近似假设下,推导出依赖于微观结构变形和热振动的自由能密度、熵密度、内能密度表达式,从而给出了微-纳米尺度下的瞬态热-力学参数.     

Effect of polyradicals on gel formation in free radical polymer modification

The formation of polyradical chains is an important feature in free radical polymer modification with crosslinking. The effect of these polyradicals on the prediction of the gel point is theoretically investigated using the method of moments. The polyradical model derived gives a criterion for gelation, xr _W,0 = 1, which fully agrees with the Flory-Stockmayer classical theory. The validity of the widely used monoradical assumption and the stationary-state hypothesis in modeling of free radical gel formation is extensively examined by making comparisons to the polyradical model. It is found that both assumptions delay the prediction of the gel point. The magnitude of the discrepancies depends on the reaction conditions. Based on the calculations using a wide range of parameters, it is concluded that these two assumptions are acceptable provided R_in/K_haY_1,0Y_1,0 is smaller than 10^?7. However, this condition can be easily violated in a typical polymer modification system. Therefore, the use of polyradical models is suggested. © 1996 John Wiley & Sons, Inc.     

Secure authentication scheme for 10 Gbit/s Ethernet passive optical networks

With the development of access network, 10G EPON has gained more and more attention. As its topology structure is point-to-multi-point and the downstream data is broadcasted, it will suffer from eavesdropping and masquerading attack. To eliminate these safety threats, this paper proposes an integrated security scheme including a bilateral authentication method and an encryption algorithm combined with one-way hash function. The authentication method can verify OLT and ONU during the registration process, preventing illegal users joining the network, and safely establish a secret key used for encrypting as well. The proposed scheme's security is based on the computational Diffie–Hellman assumption and the target collision resistant hash functions. The simulation results indicate that this mechanism is more suitable for practical use.     

Breaking of Global Gauge Symmetries on a Spatial-temporal Subdomain

It is generally considered that global gauge symmetry of an action integral over a finite spatial-temporal domain as a whole holds in any subdomain of this domain. However, in this paper we demonstrate that when the so-called localized assumption is no longer valid, the global gauge symmetry will break in the subdomain of this spatial-temporal domain, due to occurrence of a new source called the nonlocal residual. The nonlocal residual is correlated with a gauge field and satisfies the zero mean condition with respect to whole spatial-temporal domain. An example is given to support this conclusion.     

Hamiltonian formulation of nonlinear water waves in a two-fluid system

ＩｎｔｒｏｄｕｃｔｉｏｎＴｈｅｇｅｏｍｅｔｒｉｚａｔｉｏｎｏｆｍｅｃｈａｎｉｃｓｉｓａｔｅｎｄｅｎｃｙｏｆｔｈｅｄｅｖｅｌｏｐｍｅｎｔｏｆｃｏｎｔｉｎｕｕｍｍｅｃｈａｎｉｃｓａｎｄｄｒａｗｓｅｘｔｅｎｓｉｖｅａｔｅｎｔｉｏｎｏｆｒｅｓｅａｒｃｈｅｒｓ...