Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

Four-level decay model of P-6(7/2) excited state of Eu2+ ion in KMgF3

A four-level model of P-6(7/2) excited state of Eu2+ ion in KMgF3: Eu2+ has been proposed. The decay profiles of the P-6(7/2) excited sstate of Eu2+ are two exponential and the physical implication of each term in the fit equation responsible for the model is interpreted. The data obtained spectroscopically are in good agreement with the fit results.

Study of energy transfer in KMgF3 : Eu-X (X = Gd, Cr, Ce) by the decay model of P-6(7/2) exited state of Eu2+

Energy transfer processes between Eu2+ and Gd3+, Cr3+, Ce3+ ions in KMgF3, which are difficult to study spectroscopically, have been investigated by using the proposed four-level decay model of the P-6(7/2) excited state of the Eu2+ ion. Gd3+ and Ce3+ transfer its energy to the vibronic transition of the P-6(7/2) --> S-8(7/2) transition of Eu2+, whereas Cr3+ receive energy from Eu2+ via the d-d interaction. The energy transfer from the Eu2+ 4f(6)5d level to the Ce3+ 4f5d state is observed spectroscopically, and the energy transfer mechanism is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.

A new model of phycobilisome in Spirulina platensis

Phycobilisomes (PBS) were isolated from blue-green alga Spirulina platensis. Scanning tunneling microscope was used to investigate the three-dimensional structure of PBS deposited on freshly cleaved highly oriented pyrolytic graphite (HOPG) in ambient condition at room temperature. The results showed that the rods of PBS radiated from the core to different directions in the space other than arrayed in one plane, which was different from the typical hemi-discoidal model structure. The diameter of PBS was up to 70 nm, and the rod was approximately 50 nm in length. Similar results were observed in Langmuir-Blodgett (LB) film of PBS. The dissociated PBS could reaggregate into rod-like structures and easily form two-dimensional membrane while being absorbed on HOPG, however, no intact PBS was observed. The filling-space model structure of PBS in Spirulina platensis with STM from three-dimensional real space at nanometer scale was found, which showed that this new structural model of PBS surely exists in blue-green algae and red algae. The function of this structural model of PBS was also discussed.

Genetic model of the hydrate system in the fine grain sediments in the northern continental slope of South China Sea

Gas hydrate samples were obtained firstly in China by drilling on the northern margin of South China Sea (SCS). To understand the formation mechanism of this unique accumulation system, this paper discusses the factors controlling the formation of the system by accurate geophysical interpretation and geological analysis, based on the high precision 2-D and 3-D multichannel seismic data in the drilling area. There are three key factors controlling the accumulation of the gas hydrate system in fine grain sediment: (1) large volume of fluid bearing methane gas Joins the formation of gas hydrate. Active fluid flow in the northern South China Sea makes both thermal gas and/or biogenic gas migrate into shallow strata and form hydrate in the gas hydrate stability zone (GHSZ). The fluid flow includes mud diapir and gas chimney structure. They are commonly characterized by positive topographic relief, acoustic turbidity and push-down, and low reflection intensity on seismic profiles. The gas chimneys can reach to GHSZ, which favors the development of BSRs. It means that the active fluid flow has a close relationship with the formation and accumulation of gas hydrate. (2) The episodic process of fracture plays an important role in the generation of gas hydrate. It may provide the passage along which thermogenic or biogenic gas migrated into gas hydrate stability zone (GHSZ) upward. And it increases the pore space for the growth of hydrate crystal. (3) Submarine landslide induced the anomalous overpressure activity and development of fracture in the GHSZ. The formation model of high concentration gas hydrate in the drilling sea area was proposed on the basis of above analysis.

Origin, development and evolutionary model of shelf desertization environment in late stage of Upper Pleistocene

Based on the study of palaeo-environmental evolution in the shelves of the Eastern China Seas, the concept of ''shelf desertization'' in the late stage of Upper Pleistocene is defined; the environmental background and evolutionary process of shelf desertization are analysed. Study on the records of subbottom profiling and the data of core samples from shelf areas revealed that during low sea-level stages, the sedimentary environment in the exposed shelf plains was dominated by aeolian depositional process under cold and dry climatic conditions, i.e. under the action of strong winter-monsoon winds. Parts of the exposed marine strata were disintegrated, and aeolian sand dunes were formed on the disintegrated marine deposits, from which the finer sediment grains were blown away by wind and deposited in the downwind areas to form the derivative loess deposits. Thus a desertization environmental system was formed in the exposed shelf plains of the Eastern China Seas.

A microwave emissivity model of sea surface under wave breaking

With the effective medium approximation theory of composites, a remedial model is proposed for estimating the microwave emissivity of sea surface under wave breaking driven by strong wind on the basis of an empirical model given by Pandey and Kakar. In our model, the effects of the shapes of seawater droplets and the thickness of whitecap layer (i.e. a composite layer of air and sea water droplets) over the sea surface on the microwave emissivity are investigated by calculating the effective dielectric constant of whitecaps layer. The wind speed is included in our model, and the responses of water droplets shapes, such as sphere and ellipsoid, to the emissivity are also discussed at different microwave frequencies. The model is in good agreement with the experimental data of microwave emissivity of sea surface at microwave frequencies of 6.6, 10.7 and 37GHz.

A mechanistic model of algal photoinhibition induced by photodamage to Photosystem-II

Photoinhibition is a central problem for the understanding of plasticity in photosynthesis vs. irradiance response. It effectively reduces the photosynthetic rate. In this contribution, we present a mechanistic model of algal photoinhibition induced by photodamage to photosystem-II. Photosystem-IIs (PSIIs) are assumed to exist in three states: open, closed and inhibited. Photosynthesis is closely associated with the transitions between the three states. The present model is defined by four parameters: effective cross section of PSII, number of PSIIs, turnover time of electron transfer chains and the ratio of rate constant of damage to that of repair of D1 proteins in PSIIs. It gives a photosynthetic response curve of phytoplankton to irradiance (PI-curve). Without photoinhibition, the PI-curve is in hyperbola with the first three parameters. The PI-curve with photoinhibition can be simplified to the same form as the hyperbola by replacing either the number of PSIIs with the number of functional PSIIs or the turnover time of electron transfer chains with the average turnover time.