First-passage time distribution and non-Markovian diffusion dynamics of protein folding

We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described in terms of an order parameter given by the fraction of native conformations. The non-Markovian diffusion dynamics is analyzed in detail and an expression for the mean first-passage time (MFPT) from non-native unfolded states to native folded state is obtained. It was found that the MFPT has a V-shaped dependence on the temperature. We also find that the MFPT is shortened as one increases the gap between the energy of the native and average non-native folded states relative to the fluctuations of the energy landscape. The second- and higher-order moments are studied to infer the first-passage time distribution. At high temperature, the distribution becomes close to a Poisson distribution, while at low temperatures the distribution becomes a Levy-type distribution with power-law tails, indicating a nonself-averaging intermittent behavior of folding dynamics. We note the likely relevance of this result to single-molecule dynamics experiments, where a power law (Levy) distribution of the relaxation time of the underlined protein energy landscape is observed.

Physical diffusion and electron-transfer dynamics of electroactive solutes in polymer electrolytes .2. Effect of the ionic size of supporting electrolytes

The diffusion coefficients(D-app) and the heterogeneous electron-transfer rate constants(k(s)) for ferrocene in MPEG/salt electrolytes were determined by using steady-state voltammetry. The temperature dependence of the two parameters obeys the Arrhenius equation. The effect of the ionic size of six supporting electrolytes on diffusion and electron transfer dynamics of ferrocene was discussed.

Physical diffusion and electron-transfer dynamics of electroactive solutes in polymer electrolytes .3. Effect of the polymer solvents

The diffusion coefficients(D-app) and the heterogeneous electron transfer rate constants(k(s)) for ferrocene in several polymer solvents were determined by using steady-state voltammetry. The temperature dependence of the two parameters indicates Arrhenius behavior, The polymer solvent effects on diffusion and electron transfer dynamics of ferrocene were discussed.

Physical diffusion and electron-transfer dynamics of electroactive solutes in polymer electrolytes .1. Effect of the nature of electroactive solutes

The diffusion coefficients(D-app) and the heterogeneous electron-transfer rate constants(k(s)) for ferrocene and its seven derivatives in MPEG/LiClO4 electrolyte were determined by using steady-state voltammetry. The two parameters increase with increasing temperature, indicating Arrhenius behavior. The effects of the nature of electroactive solute molecules on D-app, k(s), and the half-wave potentials(E-1/2) are discussed.

LOCAL MAIN-CHAIN DYNAMICS OF PHENOLPHTHALEIN POLYETHERSULFONE

Local main chain dynamics of dissolved phenolphthalein polyethersulfone (PES-C) in solution with chloroform-d(1) were examined through C-13 NMR relaxation measurements. Spin-lattice relaxation times and NOE (nuclear Overhauser effects) factors were measured as a function of temperature. The relaxation data were interpreted in terms of main chain segmental motion by using the damped orientational diffusion model (DAMP) and the conformation jump model (VJGM) derived by Valeur, Jarry, Geny, and Monnerie. The simulation method used is N-SIMPLEX, which gives, in this study, a result of the object function less than 10(-4). Correlation times were obtained for the main chain motion of PES-C with these models and the results indicate that the main chain of PES-C are flexible. The comparison between PES-C and 1,2-polybutadiene is proposed. The distribution of the correlation time for the main chain motion by using VJGM model is discussed. The temperature dependence of correlation times for PES-C indicating the dynamical rigidity of its chains is obtained.

MISCIBILITY, MICROSTRUCTURE, AND DYNAMICS OF BLENDS CONTAINING BLOCK-COPOLYMER .1. MISCIBILITY OF BLENDS OF HOMOPOLYSTYRENE WITH STYRENE-BUTADIENE BLOCK-COPOLYMERS

The miscibilities of blends of homopolystyrene/styrene-butadiene/styrene (PS/SBS) and PS/SB-4A (4-arm star block copolymer) have been studied by dynamic mechanical analysis (DMA) and C-13 CPMAS NMR techniques. The results indicate that the miscibilities o

MISCIBILITY, MICROSTRUCTURE, AND DYNAMICS OF BLENDS CONTAINING BLOCK-COPOLYMER .2. MICROSTRUCTURE OF BLENDS OF HOMOPOLYSTYRENE WITH STYRENE-BUTADIENE BLOCK-COPOLYMERS

The microstructures of styrene-butadiene triblock (SBS) and styrene-butadiene four-arm star block (SB-4A) copolymers and their blends with homopolystyrene (PS) of different molecular weights, MPS, have been investigated by means of small-angle X-ray scatt

MISCIBILITY, MICROSTRUCTURE, AND DYNAMICS OF BLENDS CONTAINING BLOCK-COPOLYMER .3. MOLECULAR-MOTION IN HOMOPOLYSTYRENE AND POLYSTYRENE 4-ARM STYRENE-BUTADIENE STAR BLOCK-COPOLYMER BLENDS

The proton spin-spin relaxation times (T-2(H)) at different temperatures (from 160 to 390 K) have been determined for polystyrene (PS) and four-arm star styrene-butadiene block copolymer (SB-4A) and its blends with PS of different molecular weights (M(PS)

Tectonic Evolution and Dynamics of Deepwater Area of Pearl River Mouth Basin, Northern South China Sea

Quantitative studies on the evolution and dynamics of the deepwater area of Pearl River Mouth basin (PRMB) were carried out based on the latest geological and seismic data. The study area is generally in an extensional state during the Cenozoic. The major extension happened in the earlier syn-rift stages before 23 Ma and the extension after 23 Ma is negligible. Two rapid subsidence periods, 32-23 Ma and 5.3-2.6 Ma, are identified, which are related to the abrupt heat decay during margin breakup and the collision between the Philippine Sea plate and the Eurasian plate, respectively. The strongest crustal thinning in the Baiyun (sic) sag may trigger the syn-rift volcanism along the weak faulted belt around the sag. The Cenozoic tectonic evolution of the study area could be divided into five stages: rifting (similar to 50-40 Ma), rift-drift transition (similar to 40-32 Ma), early post-breakup (similar to 32-23 Ma), thermal subsidence (similar to 23-5.3 Ma) and neotectonic movement (similar to 5.3-0 Ma).

Dynamics of intraseasonal sea level and thermocline variability in the equatorial Atlantic during 2002-03

Satellite and in situ observations in the equatorial Atlantic Ocean during 2002-03 show dominant spectral peaks at 40-60 days and secondary peaks at 10-40 days in sea level and thermocline within the intraseasonal period band (10-80 days). A detailed investigation of the dynamics of the intraseasonal variations is carried out using an ocean general circulation model, namely, the Hybrid Coordinate Ocean Model (HYCOM). Two parallel experiments are performed in the tropical Atlantic Ocean basin for the period 2000-03: one is forced by daily scatterometer winds from the Quick Scatterometer (QuikSCAT) satellite together with other forcing fields, and the other is forced by the low-passed 80-day version of the above fields. To help in understanding the role played by the wind-driven equatorial waves, a linear continuously stratified ocean model is also used. Within 3 degrees S-3 degrees N of the equatorial region, the strong 40-60-day sea surface height anomaly (SSHA) and thermocline variability result mainly from the first and second baroclinic modes equatorial Kelvin waves that are forced by intraseasonal zonal winds, with the second baroclinic mode playing a more important role. Sharp 40-50-day peaks of zonal and meridional winds appear in both the QuikSCAT and Pilot Research Moored Array in the Tropical Atlantic (PIRATA) data for the period 2002-03, and they are especially strong in 2002. Zonal wind anomaly in the central-western equatorial basin for the period 2000-06 is significantly correlated with SSHA across the equatorial basin, with simultaneous/ lag correlation ranging from-0.62 to 0.74 above 95% significance. Away from the equator (3 degrees-5 degrees N), however, sea level and thermocline variations in the 40-60-day band are caused largely by tropical instability waves (TIWs). On 10-40-day time scales and west of 10 degrees W, the spectral power of sea level and thermocline appears to be dominated by TIWs within 5 degrees S-5 degrees N of the equatorial region. The wind-driven circulation, however, also provides a significant contribution. Interestingly, east of 10 W, SSHA and thermocline variations at 10 40- day periods result almost entirely from wind-driven equatorial waves. During the boreal spring of 2002 when TIWs are weak, Kelvin waves dominate the SSHA across the equatorial basin (2 degrees S-2 degrees N). The observed quasi-biweekly Yanai waves are excited mainly by the quasi-biweekly meridional winds, and they contribute significantly to the SSHA and thermocline variations in 1 degrees-5 degrees N and 1 degrees-5 degrees S regions.

Long-Wave Dynamics of Sea Level Variations during Indian Ocean Dipole Events

Long-wave dynamics of the interannual variations of the equatorial Indian Ocean circulation are studied using an ocean general circulation model forced by the assimilated surface winds and heat flux of the European Centre for Medium-Range Weather Forecasts. The simulation has reproduced the sea level anomalies of the Ocean Topography Experiment (TOPEX)/Poseidon altimeter observations well. The equatorial Kelvin and Rossby waves decomposed from the model simulation show that western boundary reflections provide important negative feedbacks to the evolution of the upwelling currents off the Java coast during Indian Ocean dipole (IOD) events. Two downwelling Kelvin wave pulses are generated at the western boundary during IOD events: the first is reflected from the equatorial Rossby waves and the second from the off-equatorial Rossby waves in the southern Indian Ocean. The upwelling in the eastern basin during the 1997-98 IOD event is weakened by the first Kelvin wave pulse and terminated by the second. In comparison, the upwelling during the 1994 IOD event is terminated by the first Kelvin wave pulse because the southeasterly winds off the Java coast are weak at the end of 1994. The atmospheric intraseasonal forcing, which plays an important role in inducing Java upwelling during the early stage of an IOD event, is found to play a minor role in terminating the upwelling off the Java coast because the intraseasonal winds are either weak or absent during the IOD mature phase. The equatorial wave analyses suggest that the upwelling off the Java coast during IOD events is terminated primarily by western boundary reflections.

Dynamics of the buoyant plume off the Pearl River Estuary in summer

Field measurements of salinity, wind and river discharge and numerical simulations of hydrodynamics from 1978 to 1984 are used to investigate the dynamics of the buoyant plume off the Pearl River Estuary (PRE), China during summer. The studies have shown that there are four major horizontal buoyant plume types in summer: Offshore Bulge Spreading (Type I), West Alongshore Spreading (Type II), East Offshore Spreading (Type III), and Symmetrical Alongshore Spreading (Type IV). River mouth conditions, winds and ambient coastal currents have inter-influences to the transport processes of the buoyant plume. It is found that all of the four types are surface-advected plumes by analysing the vertical characteristic of the plumes, and the monthly variations of the river discharge affect the plume size dominantly. The correlation coefficient between the PRE plume size and the river discharge reaches 0.85 during the high river discharge season. A wind strength index has been introduced to examine the wind effect. It is confirmed that winds play a significant role in forming the plume morphology. The alongshore wind stress and the coastal currents determine the alongshore plume spreading. The impact of the ambient currents such as Dongsha Current and South China Sea (SCS) Warm Current on the plume off the shelf has also assessed. The present study has demonstrated that both the river discharge and wind conditions affect the plume evolution.

Dynamics of nonlinear error growth and season-dependent predictability of El Nino events in the Zebiak-Cane model

With the intermediate-complexity Zebiak-Cane model, we investigate the 'spring predictability barrier' (SPB) problem for El Nino events by tracing the evolution of conditional nonlinear optimal perturbation (CNOP), where CNOP is superimposed on the El Nino events and acts as the initial error with the biggest negative effect on the El Nino prediction. We show that the evolution of CNOP-type errors has obvious seasonal dependence and yields a significant SPB, with the most severe occurring in predictions made before the boreal spring in the growth phase of El Nino. The CNOP-type errors can be classified into two types: one possessing a sea-surface-temperature anomaly pattern with negative anomalies in the equatorial central-western Pacific, positive anomalies in the equatorial eastern Pacific, and a thermocline depth anomaly pattern with positive anomalies along the Equator, and another with patterns almost opposite to those of the former type. In predictions through the spring in the growth phase of El Nino, the initial error with the worst effect on the prediction tends to be the latter type of CNOP error, whereas in predictions through the spring in the decaying phase, the initial error with the biggest negative effect on the prediction is inclined to be the former type of CNOP error. Although the linear singular vector (LSV)-type errors also have patterns similar to the CNOP-type errors, they cover a more localized area than the CNOP-type errors and cause a much smaller prediction error, yielding a less significant SPB. Random errors in the initial conditions are also superimposed on El Nino events to investigate the SPB. We find that, whenever the predictions start, the random errors neither exhibit an obvious season-dependent evolution nor yield a large prediction error, and thus may not be responsible for the SPB phenomenon for El Nino events. These results suggest that the occurrence of the SPB is closely related to particular initial error patterns. The two kinds of CNOP-type error are most likely to cause a significant SPB. They have opposite signs and, consequently, opposite growth behaviours, a result which may demonstrate two dynamical mechanisms of error growth related to SPB: in one case, the errors grow in a manner similar to El Nino; in the other, the errors develop with a tendency opposite to El Nino. The two types of CNOP error may be most likely to provide the information regarding the 'sensitive area' of El Nino-Southern Oscillation (ENSO) predictions. If these types of initial error exist in realistic ENSO predictions and if a target method or a data assimilation approach can filter them, the ENSO forecast skill may be improved. Copyright (C) 2009 Royal Meteorological Society

Dynamics of the cold-water event off the southeast coast of the United States in the summer of 2003

The cold-water event along the southeast coast of the United States in the summer of 2003 is studied using satellite data combined with in situ observations. The analysis suggests that the cooling is produced by wind-driven coastal upwelling, which breaks the thermocline barrier in the summer of 2003. The strong and persistent southwesterly winds in the summer of 2003 play an important role of lifting the bottom isotherms up to the surface and away from the coast, generating persistent surface cooling in July-August 2003. Once the thermocline barrier is broken, the stratification in the nearshore region is weakened substantially, allowing further coastal cooling of large magnitudes by episodic southerly wind bursts or passage of coastally trapped waves at periods of a few days. These short-period winds or waves would otherwise have no effects on the surface temperature because of the strong thermocline barrier in summer if not for the low-frequency cooling produced by the persistent southwesterly winds.