Potential Landscape and Flux Framework of Nonequilibrium Networks: Robustness, Dissipation, and Coherence of Biochemical Oscillations

We established a theoretical framework for studying nonequilibrium networks with two distinct natures essential for characterizing the global probabilistic dynamics: the underlying potential landscape and the corresponding curl flux. We applied the idea to a biochemical oscillation network and found that the underlying potential landscape for the oscillation limit cycle has a distinct closed ring valley (Mexican hat-like) shape when the fluctuations are small. This global landscape structure leads to attractions of the system to the ring valley.

Robustness and dissipation of mitogen-activated protein kinases signal transduction network: Underlying funneled landscape against stochastic fluctuations

We uncovered the underlying energy landscape of the mitogen-activated protein kinases signal transduction cellular network by exploring the statistical natures of the Brownian dynamical trajectories. We introduce a dimensionless quantity: The robustness ratio of energy gap versus local roughness to measure the global topography of the underlying landscape. A high robustness ratio implies funneled landscape. The landscape is quite robust against environmental fluctuations and variants of the intrinsic chemical reaction rates.

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.

Ac voltammetric and square wave voltammetric study of the self-assembled monolayers of thiol-functionalized viologen derivative

Electroactive self-assembled monolayers (SAMs) containing viologen group are formed through the adsorption of thiol-functionalized viologen compound CH3(CH2)(9)V2+(CH2)(8)SH, where V2+ is N,N'-dialkylbipyridinium (i.e. a viologen group), onto gold electrodes from methanol/water solution and its electrochemical behavior is investigated ty Ac voltammetry and square wave voltammetry, which have the high sensitivity against background charging. The viologen SAM formed is a sub-monolayer and the normal potentials corresponding to the two successive one-electron transfer processes of the active centers (viologen) are -360 mV and -750 mV (vs. Ag/AgCl) in 0.1 mol/L phosphate buffer solutions (pH 6.96) respectively, and the standard electron transfer rate constant is 9.0 s(-1). The electrochemical behavior of this SAM in various solutions has been preliminarily discussed.

STRUCTURE-PROPERTY RELATIONSHIP BETWEEN HALF-WAVE POTENTIALS OF ORGANIC-COMPOUNDS AND THEIR TOPOLOGY

A significant correlation was found between half-wave potentials of organic compounds and their topological indices, A(x1), A(x2), and A(x3). The simplicity of calculation of the index from the connectivity in the molecular skeleton, together with the significant correlation, indicates its practical value. Good results have been obtained by using them to predict the half-wave potentials of some organic compounds.

P wave velocity of the pumice from the Okinawa Trough at high temperature and high pressure.

P wave velocity of the pumice sample from the middle Okinawa Trough and andesite sample from vicinity Yingdao volcanic island, Kyushu Japan were measured at temperature (from room temperature to 1500 C) and pressure (from room pressure to 2.4GPa) using a multi-anvil pressure apparatus called the YJ-3000 press. The measured data shows that at low temperature and low pressure (<1GPa, <800degreesC), the P wave velocity of pumice is lower than that of andesite, while at high temperature and high pressure (>1GPa, >800degreesC) the P wave velocity of pumice and andesite. becomes consistent (5.9km/s). The paper points out that 1GPa/800degreesC is the point of thermodynamic phase transformation Okinawa Trough pumice and vicinity andesite, and the point is deeper than 18km.

The change of characteristics of tidal wave in the Changjiang River mouth area since the post-glacial transgression maximum

During the period of the post-glacial transgression maximum (PGTM), there was a huge trumpet estuary in the modern Changjiang River Delta area. The location and the shape of the Paleo-Changjiang River Estuary (PCRE) were much different from those of the present Changjiang River Estuary. The study on the change of characteristics of tidal wave in the Changjiang River mouth area since the PGTM can help to understand better the dynamic development of the Changjiang River Delta. The course curves of tidal level and tidal current velocity during a single tidal cycle for 35 points are calculated, and characteristics of tidal waves in the PCRE and its adjacent area are compared with those of tidal waves in the modern Changjiang River mouth area. The results show that the tidal waves within the PCRE and in its adjacent area during the period of the PGTM belonged to standing wave or a mixture of standing wave and progressive wave. Since then, the tidal wave in the Changjiang River mouth become gradually to be progressive wave with the PCRE being filled and the Changjiang River mouth shifting southeastwards.