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.

Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Nonlinear fatigue damage model based on the residual strength degradation law

In this paper, a logarithmic expression to describe the residual strength degradation process is developed in order to fatigue test results for normalized carbon steel. The definition and expression of fatigue damage due to symmetrical stress with a constant amplitude are also given. The expression of fatigue damage can also explain the nonlinear properties of fatigue damage. Furthermore, the fatigue damage of structures under random stress is analyzed, and an iterative formula to describe the fatigue damage process is deduced. Finally, an approximate method for evaluating the fatigue life of structures under repeated random stress blocking is presented through various calculation examples.

Degradation failure features of chromium-plated gun barrels with a laser-discrete-quenched substrate

The effect of substrate laser-discrete quenching on the degradation failure of chromium-plated gun barrels was metallurgically investigated. The results show that substrate laser-discrete quenching changes the failure patterns of chromium coatings during firing, and some periodic through-thickness cracks in the fired chromium coatings are justly located at original substrate zones between two adjacent laser-quenched tracks. Moreover, chromium coatings and the laser-quenched zones on the substrate are simultaneously degraded in microstructure and property during firing. Furthermore, the periodic structure of the laser-discrete-quenched steel (LDQS) substrate near the breech remains after firing, and the hardness of the fired laser-quenched zones is still higher than that of original substrates. The specific failure features were utilized to illustrate the mechanism of the extended service life of chromium-plated gun barrels with the LDQS substrate. (c) 2007 Elsevier B.V All rights reserved.

Post-cyclic Strength Degradation of Undisturbed and Remolded Marine Silty Clay

A series of static and cyclic-static tri-axial compression tests under consolidated-undrained conditions are carried out to study the characteristics of post-cyclic strength of the undisturbed and the remolded samples of marine silty clay. It is found that the post-cyclic monotonic strength decreases if the cyclic strain or pore pressure is over a certain value. The maximum degradation is 10% for undisturbed samples while 70% for remolded ones. The relationship between normalized undrained shear strength and apparent overconsolidation ratio, which is determined by the excess pore pressure induced by cyclic loading, is also established. Static consolidated-undrained tests on overconsolidated remolded samples are also performed. It is proposed that the static consolidated-undrained tests may be substituted for the cyclic-static consolidated-undrained tests if the post-cyclic strength degradation of remolded silty clay is needed to be evaluated simply.

Study on the Capacity Degradation of Bucket Foundation in Liquefied Sand Layer under Cyclic Loads

The capacity degradation of bucket foundation in liquefied sand layer under cyclic loads such as equivalent dynamic ice-induced loads is studied. A simplified numerical model of liquefied sand layer has been presented based on the dynamic centrifuge experiment results. The ice-induced dynamic loads are modeled as equivalent sine cyclic loads, the liquefaction degree in different position of sand layer and effects of main factors are investigated. Subsequently, the sand resistance is represented by uncoupled, non-linear sand springs which describe the sub-failure behavior of the local sand resistance as well as the peak capacity of bucket foundation under some failure criterion. The capacity of bucket foundation is determined in liquefied sand layer and the rule of capacity degradation is analyzed. The capacity degradation in liquefied sand layer is analyzed comparing with that in non-liquefied sand layer. The results show that the liquefaction degree is 0.9 at the top and is only 0.06 at the bottom of liquefied sand layer. The numerical results are agreement well with the centrifugal experimental results. The value of the degradation of bucket capacity is 12% in numerical simulating whereas it is 17% in centrifugal experiments.

Reduced deep-tissue image degradation in three-dimensional multiphoton microscopy with concentric two-color two-photon fluorescence excitation

We theoretically demonstrate that enhanced penetration depth in three-dimensional multiphoton microscopy can be achieved using concentric two-color two-photon (C2C2P) fluorescence excitation in which the two excitation beams are separated in space before reaching their common focal spot. Monte Carlo simulation shows that, in comparison with the one-color two-photon excitation scheme, the C2C2P fluorescence microscopy provides a significantly greater penetration depth for imaging into a highly scattering medium. (C) 2008 Optical Society of America.

Analysis of beam-quality degradation in nonlinear frequency conversion

Based on the ripple transfers of electric-field amplitude and phase in frequency tripling, simple formulas are derived for the harmonic laser's beam-quality factor M-3omega(2), with an arbitrary fundamental incidence to ideal nonlinear crystals. Whereas the harmonic beam's quality is generally degraded, the beam's divergence is similar to that of the fundamental after nonlinear frequency conversion. For practical crystals with periodic surface ripples that are caused by their machining, a multiorder diffractive model is presented with which the focusing properties of harmonic beams can be studied. Predictions of the theories are shown to be in excellent agreement with full numerical simulations. (C) 2002 Optical Society of America.