Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.

Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We found that the first passage-time (FPT) distribution undergoes a dynamic transition at a temperature below which the FPT distribution develops a power-law tail, a signature of the intermittent nonexponential kinetic phenomena for the folding dynamics. Possible applications to single-molecule dynamics experiments are discussed.

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.

Theoretical estimation of thermodynamic properties of the system PS/PPO on the basis of modified combining rule of Sanchez-Lacombe lattice fluid model

The three scaling parameters described in Sanchez-Lacombe lattice fluid theory (SLLFT), T*, P* and rho* of pure polystyrene (PS), pure poly(2,6-dimethyl-1,4-phenylene oxide) (PPO) and their mixtures are obtained by fitting corresponding experimental pressure volume-temperature data with equation-of-state of SLLFT. A modified combining rule in SLLFT used to match the volume per mer, v* of the PS/PPO mixtures was advanced and the enthalpy of mixing and Flory-Huggins (FH) interaction parameter were calculated using the new rule. It is found that the difference between the new rule and the old one presented by Sanchez and Lacombe is quite small in the calculation of the enthalpy of mixing and FH interaction parameter and the effect of volume-combining rule on the calculation of thermodynamic properties is much smaller than that of energy-combining rule. But the relative value of interaction parameter changes much due to the new volume-based combining rule. This effect can affect the position of phase diagram very much, which is reported elsewhere [Macromolecules 34 (2001) 6291]

P-6(7/2)-excited-state decay mechanism and energy-transfer processes in KMgF3 : Eu2+ and KMgF3 : EuX (X = Gd, Ce, Cr)

A four-level decay model in KMgF3:Eu2+ is proposed. The decay profiles of the P-6(7/2) excited state of Eu2+ are biexponential, and the physical implication of each term in the fit equation responsible for the model is interpreted. The evidence obtained spectroscopically for supporting the model is presented. A new method to study energy transfer between Eu2+ and X3+ in KMgF3:Eu-X (X = Gd, Ce, Cr) is established on the basis of the proposed model.

PREDICTION OF THE GIBBS ENERGY OF ION TRANSFER ACROSS THE WATER NITROBENZENE INTERFACE USING 3 NEW TOPOLOGICAL INDEXES

Correlation analysis of the standard Gibbs energy for a series of tetraalkylammonium ions, protonated substituted ethylenediamine derivatives and protonated aromatic amine derivatives using three new topological indices Ax1, Ax2 and Ax has been studied. T

STATISTICAL THERMODYNAMICS IN THE FRAMEWORK OF THE LATTICE FLUID MODEL .2. BINARY MIXTURE OF POLYDISPERSE POLYMERS OF SPECIAL DISTRIBUTION

In this paper, the Gibbs free energy, the equation of state and the chemical potentials of polydisperse multicomponent polymer mixtures are derived. For general binary mixtures of polydisperse polymers, we also give the Gibbs free energy, the equation of

STATISTICAL THERMODYNAMICS IN THE FRAMEWORK OF THE LATTICE FLUID MODEL .3. BINARY MIXTURE OF POLYDISPERSE POLYMERS OF SPECIAL DISTRIBUTION WITH STRONG-INTERACTIONS

For a binary mixture of polydisperse polymers with strong interactions, the free energy, the equation of state, the chemical potentials and the spinodal are formulated on the basis of the lattice fluid model. Further, the spinodal curves for the system wi

Annual cycle of stratification and tidal fronts in the Bohai Sea: A model study

In general, competition between buoyancy mechanisms and mixing dynamics largely determines the water column structure in a shelf sea. A three dimensional baroclinic ocean model forced by surface heat fluxes and the 2.5 order Mellor-Yamada turbulence scheme is used to simulate the annual cycle of the temperature in the Bohai Sea. The difference between the sea surface temperature (SST) and sea bottom temperature (SBT) is used to examine the evolution of its vertical stratification. It is found that the water column is well-mixed from October to March and that the seasonal thermocline appears in April, peaks in July and then weakens afterwards, closely following the heat budget. In addition, the Loder parameter based on the topography and tidal current amplitude is also computed in order to examine tidal fronts in the BS, which are evident in summer months when the wind stirring mechanism is weak.

Submesoscale activity over the shelf of the northern South China Sea in summer: simulation with an embedded model

We applied a primitive equation ocean model to simulate submesoscale activities and processes over the shelf of the northern South China Sea (NSCS) with a one-way nesting technology for downscaling. The temperature and density fields showed that submesoscale activities were ubiquitous in the NSCS shelf. The vertical velocity was considerably enhanced in submesoscale processes and could reach an average of 58 m per day in the subsurface. At this point, the mixed layer depth also was deepened along the front, and the surface kinetic energy also increased with the intense vertical movement induced by submesoscale activity. Thus, submesoscale stirring/mixing is important for tracers, such as temperature, salinity, nutrients, dissolved organic, and inorganic carbon. This result may have implication for climate and biogeochemical investigations.

A stable carbon isotopic approach for understanding the CO2 flux at the Haibei Alpine Meadow Ecosystem - A simple model

Although respiration of organisms and biomass as well as fossil fuel burning industrial production are identified as the major sources, the CO2 flux is still unclear due to the lack of proper measurements. A mass-balance approach that exploits differences in the carbon isotopic signature (delta(13)C) of CO2 Sources and sinks was introduced and may provide a means of reducing uncertainties in the atmospheric budget. delta(13)C measurements of atmospheric CO2 yielded an average of - 10.3 parts per thousand relative to the Peedee Belemnite standard; soil and plants had a narrow range from -25.09 parts per thousand to -26.51 parts per thousand and averaged at -25.80 parts per thousand. Based on the fact of steady fractionation and enrichment during respiration of mitochondria, we obtained the emission Of CO2 of 35.451 mol m(-2) a(-1) and CO2 flux of 0.2149 mu mol m(-2) s(-)1. The positive CO2 flux indicated the Haibei Alpine Meadow Ecosystem a source rather than a sink. The mass-balance model can be applied for other ecosystem even global carbon cycles because it neglects the complicated process of carbon metabolism, however just focuses on stable carbon isotopic compositions in any of compartments of carbon sources and sinks. (C) 2005 Elsevier B.V. All rights reserved.

中高层大气对低层大气声重波响应的分析

Acoustic Gravity waves (AGW) play an important role in balancing the atmospheric energy and momentum budget. Propagation of gravity wave in the atmosphere is one of the important factors of changing middle and upper atmosphere and ionosphere. The purpose of this dissertation is to study the propagation of gravity wave in a compression atmosphere whit means of numerical simulation and to analyze the response of middle and upper atmosphere to pulse disturbance from lower atmosphere. This work begins with the establishment of 2-D fully nonlinear compressible atmospheric dynamic model in polar coordinate, which is used ton numerically study gravity wave propagation. Then the propagation characteristics of acoustic gravity wave packets are investigated and discussed. We also simulate the response of middle and upper atmosphere to pulse disturbance of lower atmosphere in background winds or without background winds by using this model and analyze the data we obtained by using Fourier Transform (FT), Short-time Fourier Transform (STFT) and Empirical Mode Decomposition (EMD) method which is an important part of Hilbert-Huang Transform (HHT). The research content is summarized in the following: 1. By using a two-dimensional full-implicit-continuous-Eulerian (FICE) scheme and taking the atmospheric basic motion equations as the governing equations, a numerical model for nonlinear propagation of acoustic gravity wave disturbance in two-dimensional polar coordinates is solved. 2. Then the propagation characteristics of acoustic gravity wave packets are investigated and discussed. Results of numerical simulation show that the acoustic gravity wave packets propagate steadily upward and keep its shape well after several periods. 3. We simulate the response of middle and upper atmosphere to pulse disturbance of lower atmosphere in background winds or without background winds by using this model, and obtain the distribution of a certain physical quantity in time and space from earth’s surface to 300km above. The results reveal that the response of ionosphere occurs at a large horizontal distance from the source and the disturbance becomes greater with increasing of height. The situation when the direction of the background wind is opposite to or the same as the direction of disturbed velocity of gravity-wave is studied. The results show that gravity wave propagating against winds is easier than those propagating along winds and the background wind can accelerate gravity wave propagation. Just upon the source, an acoustic wave component with period of 6 min can be found. These images of simulation are similar to observations of the total electron content (TEC) disturbances caused by the great Sumatra-Andaman earthquake on December 26 in 2004. 4. Using the EMD method the disturbed velocity data of a certain physical quantity in time and space can be decomposed into a series of intrinsic mode function (IMF) and a trend mode respectively. The results of EMD reveal impact of the gravity wave frequency under the background winds.

Dynamic Model and Control of an Artificial Muscle Based on Contractile Polymers

A dynamic model and control system of an artificial muscle is presented. The artificial muscle is based on a contractile polymer gel which undergoes abrupt volume changes in response to variations in external conditions. The device uses an acid-base reaction to directly convert chemical to mechanical energy. A nonlinear sliding mode control system is proposed to track desired joint trajectories of a single link controlled by two antagonist muscles. Both the model and controller were implemented and produced acceptable tracking performance at 2Hz.