Trimeresurus stejnegeri snake venom plasminogen activator - Site-directed mutagenesis and molecular modeling

The specific plasminogen activator from Trimeresurus stejnegeri venom (TSV-PA) is a serine proteinase presenting 23% sequence identity with the proteinase domain of tissue type plasminogen activator, and 63% with batroxobin, a fibrinogen clotting enzyme from Bothrops atrox venom that does not activate plasminogen. TSV-PA contains six disulfide bonds and has been successfully overexpressed in Escherichia coli (Zhang, Y., Wisner, A., Xiong, Y. L,, and Bon, C, (1995) J. Biol. Chem. 270, 10246-10255), To identify the functional domains of TSV-PA, we focused on three short peptide fragments of TSV-PA showing important sequence differences with batroxobin and other venom serine proteinases. Molecular modeling shows that these sequences are located in surface loop regions, one of which is next to the catalytic site, When these sequences were replaced in TSV-PA by the equivalent batroxobin residues none generated either fibrinogen-clotting or direct fibrinogenolytic activity, Two of the replacements had little effect in general and are not critical to the specificity of TSV-PA for plasminogen. Nevertheless, the third replacement, produced by the conversion of the sequence DDE 96a-98 to NVI, significantly increased the K-m for some tripeptide chromogenic substrates and resulted in undetectable plasminogen activation, indicating the key role that the sequence plays in substrate recognition by the enzyme.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Kinetic modeling of N incorporation in GaInNAs growth by plasma-assisted molecular-beam epitaxy

We have studied the growth of GaInNAs by a plasma-assisted molecular-beam epitaxy (MBE). It was found that the N-radicals were incorporated into the epitaxial layer like dopant atoms. In the range of 400-500 degrees C, the growth temperature (T-g) mainly affected the crystal quality of GaInNAs rather than the N concentration. The N concentration dropped rapidly when T-g exceeded 500 degrees C. Considering N desorption alone is insufficient to account for the strong falloff of the N concentration with T-g over 500 degrees C, the effect of thermally-activated N surface segregation must be taken into account. The N concentration was independent of the arsenic pressure and the In concentration in GaInNAs layers, but inversely proportional to the growth rate. Based on the experimental results, a kinetic model including N desorption and surface segregation was developed to analyze quantitatively the N incorporation in MBE growth. (C) 2000 American Institute of Physics. [S0003-6951(00)00928-1].

Effect of reflectivity at the interface of oxide layer on transverse mode control in oxide confined vertical-cavity surface-emitting lasers

The transverse mode control in oxide confined vertical-cavity surface-emitting lasers is discussed by modeling the dielectric aperture as a uniform waveguide and an extra reflectivity at the oxide layer. The phase of the extra reflectivity and the refractive index step can be adjusted to change the mode threshold gain. We calculate the lateral refractive index step from the mode wavelength difference between aperture and perimeter modes, and compare it with that obtained from the weighted average index. The mode reflectivity in terms of the lateral optical confinement factor at the oxide layer is considered in calculating the threshold gain for transverse modes. The numerical results show that higher transverse modes can be suppressed by adjusting the position of a thin AlAs-oxide layer inside a three-quarter-wave layer in the distributed Bragg reflector. (C) 1998 American Institute of Physics. [S0021-8979(98)04007-9].

Modeling of a coal-fired slagging combustor: Development of a slag submodel

In a slagging combustor or furnace, the high combustion temperature makes the molten slag layer cover the wall and capture the particles. If these particles contain combustible matter, they will continue to burn on the running slag. As a result, the total amount of ash deposition will be much greater than that in dry-wall combustors and the total heat flux through the deposition surface will change greatly. Considering the limitations of existing simulation methods for slagging combustion, this paper introduces a new wall burning model and slag flow model from the analysis; of particle deposition phenomena. Combined with a conventional combustion simulation program, the total computational frame is introduced. From comparisons of simulation results from several kinds of methods with experimental data, the conclusion is drawn that the conventional simulation methods are not very suitable for slagging combustion and the wall burning mechanism should be considered more thoroughly.

Modeling of Hillslope Runoff and Soil Erosion at Rainfall Events Using Cellular Automata Approach

National Science Fund for Distinguished Young Scholars of China [40225004]; National Natural Science Foundation of China [40471048]

Modeling All-sky Global Solar Radiation Using MODIS Atmospheric Products: A Case Study in Qinghai-Tibet Plateau

The surface solar radiation (SSR) is of great importance to bio-chemical cycle and life activities. However, it is impossible to observe SSR directly over large areas especially for rugged surfaces such as the Qinghai-Tibet Plateau. This paper presented an improved parameterized model for predicting all-sky global solar radiation on rugged surfaces using Moderate Resolution Imaging Spectroradiometer (MODIS) atmospheric products and Digital Elevation Model (DEM). The global solar radiation was validated using 11 observations within the plateau. The correlation coefficients of daily data vary between 0.67-0.86, while those of the averages of 10-day data are between 0.79-0.97. The model indicates that the attenuation of SSR is mainly caused by cloud under cloudy sky, and terrain is an important factor influencing SSR over rugged surfaces under clear sky. A positive relationship can also be inferred between the SSR and slope. Compared with horizontal surfaces, the south-facing slope receives more radiation, followed by the west- and east-facing slopes with less SSR, and the SSR of the north-facing slope is the least.

The effects of random surface waves on the steady Ekman current solutions

The response of near-surface current profiles to wind and random surface waves are studied based on the approach of Jenkins [1989. The use of a wave prediction model for driving a near surface current model. Dtsch. Hydrogr. Z. 42,134-149] and Tang et al. [2007. Observation and modeling of surface currents on the Grand Banks: a study of the wave effects on surface currents. J. Geophys. Res. 112, C10025, doi:10.1029/2006JC004028]. Analytic steady solutions are presented for wave-modified Ekman equations resulting from Stokes drift, wind input and wave dissipation for a depth-independent constant eddy viscosity coefficient and one that varies linearly with depth. The parameters involved in the solutions can be determined by the two-dimensional wavenumber spectrum of ocean waves, wind speed, the Coriolis parameter and the densities of air and water, and the solutions reduce to those of Lewis and Belcher [2004. Time-dependent, coupled, Ekman boundary layer solutions incorporating Stokes drift. Dyn. Atmos. Oceans. 37, 313-351] when only the effects of Stokes drift are included. As illustrative examples, for a fully developed wind-generated sea with different wind speeds, wave-modified current profiles are calculated and compared with the classical Ekman theory and Lewis and Belcher's [2004. Time-dependent, coupled, Ekman boundary layer solutions incorporating Stokes drift. Dyn. Atmos. Oceans 37, 313-351] modification by using the Donelan and Pierson [1987. Radar scattering and equilibrium ranges in wind-generated waves with application to scatterometry. J. Geophys. Res. 92, 4971-5029] wavenumber spectrum, the WAM wave model formulation for wind input energy to waves, and wave energy dissipation converted to currents. Illustrative examples for a fully developed sea and the comparisons between observations and the theoretical predictions demonstrate that the effects of the random surface waves on the classical Ekman current are important, as they change qualitatively the nature of the Ekman layer. But the effects of the wind input and wave dissipation on surface current are small, relative to the impact of the Stokes drift. (C) 2008 Elsevier Ltd. All rights reserved.

Numerical modeling of water wave interaction with a soft mud bed

A vertical 2-D numerical model is presented for simulating the interaction between water waves and a soft mud bed. Taking into account nonlinear rheology, a semi-empirical rheological model is applied to this water-mud model, reflecting the combined visco-elasto-plastic properties of soft mud under such oscillatory external forces as water waves. In order to increase the resolution of the flow in the neighborhood of both sides of the inter-surface, a logarithmic grid in the vertical direction is employed for numerical treatment. Model verifications are given through comparisons between the calculated and the measured mud mass transport velocities as well as wave height changes.

Modeling gross primary production of alpine ecosystems in the Tibetan Plateau using MODIS images and climate data

The eddy covariance technique provides measurements of net ecosystem exchange (NEE) Of CO2 between the atmosphere and terrestrial ecosystems, which is widely used to estimate ecosystem respiration and gross primary production (GPP) at a number Of CO2 eddy flux tower sites. In this paper, canopy-level maximum light use efficiency, a key parameter in the satellite-based Vegetation Photosynthesis Model (VPM), was estimated by using the observed CO2 flux data and photosynthetically active radiation (PAR) data from eddy flux tower sites in an alpine swamp ecosystem, an alpine shrub ecosystem and an alpine meadow ecosystem in Qinghai-Tibetan Plateau, China. The VPM model uses two improved vegetation indices (Enhanced Vegetation Index (EVI), Land Surface Water Index (LSWI)) derived from the Moderate Resolution Imaging Spectral radiometer (MODIS) data and climate data at the flux tower sites, and estimated the seasonal dynamics of GPP of the three alpine grassland ecosystems in Qinghai-Tibetan Plateau. The seasonal dynamics of GPP predicted by the VPM model agreed well with estimated GPP from eddy flux towers. These results demonstrated the potential of the satellite-driven VPM model for scaling-up GPP of alpine grassland ecosystems, a key component for the study of the carbon cycle at regional and global scales. (c) 2006 Elsevier Inc. All rights reserved.