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.

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.

Nanometer scale mechanical study on well defined nanostructured chain aggregation of polyethylene

Two kinds of polyethylene chain aggregation with chain axis perpendicular and parallel to the supported substrate were designed and successfully obtained from melt under an electric field and by melt-drawn method

Branched crystal morphology of linear polyethylene crystallized in a two-dimensional diffusion-controlled growth field

The branched crystal morphology of linear polyethylene formed at various temperatures from thin films has been studied by atomic-force microscopy (AFM), transmission electron microscopy (TEM), electron diffraction (ED) pattern and polymer decoration technique. Two types of branched patterns, i.e. dendrite and seaweed patterns, have been visualized. The fractal dimension d(f) = 1.65 of both dendrite and some of seaweed patterns was obtained by using the box-counting method, although most of the seaweed patterns are compact. Selected-area ED patterns indicate that the fold stems tilt about 34.5degrees around the b-axis and polymer decoration patterns show that the chain folding direction and regularity in two (200). regions are quite different from each other. Because of chain tilting, branched crystals show three striking features: 1) the lamella-like branches show two (200) regions with different thickness; 2) the crystals usually bend towards the thin region; 3) the thick region grows faster by developing branches, thus branches usually occur outside the thick region. The branched patterns show a characteristic width w, which gives a linear relationship with the crystallization temperature on a semilogarithmic plot.

Sol-gel derived carbon ceramic electrode containing methylene blue-intercalted alpha-zirconium phosphate micro particles

Methylene blue-intercalated a-zirconium phosphate (MBZrP) micro particles in deionized water were deposited onto the surface of graphite powder to prepare graphite powder-supported MBZrP, which was subsequently dispersed into methyltrimethoxysilane-derived gels to yield a conductive composite. The composite was used as electrode material to fabricate a surface-renewable, rigid, leak-free carbon ceramic composite electrode, bulk-modified with methylene blue (MB). In the configuration, alpha-zirconium phosphate was employed as a solid host for MB, which acted as a catalyst. Graphite powder ensured conductivity by percolation, the silicate provided a rigid porous backbone and the methyl groups endowed hydrophobicity and thus limited the wetting section of the modified electrode. Peak currents of the MBZrP-modified electrode were surface-confined at low scan rates but diffusion-controlled at high scan rates. Square-wave voltammetric study revealed that MBZrP immobilized in carbon ceramic matrix presented a two-electron, three-proton redox process in acidic aqueous solution with pH ranged from 0.44 to 2.94. In addition, the chemically modified electrode showed an electrocatalytic activity toward nitrite reduction at +0.15 V (vs. Ag/AgCl) in acidic aqueous solution (pH=0.44). The linear range and detection limit are 1 x 10(-6)-4 x 10(-3) mol L-1 and 1.5 x 10(-7) mol L-1, respectively.

Aggregation behavior of amphiphilic D-pi-A molecules bearing recognition group

Aggregation behavior of two amphiphilic D-pi -A molecules bearing barbituric acid as both recogniton group and electron-drawing substituent, 5-(4-dodecyl oxybenzylidene)-(1H, 3H)-2,4,6-pyrimidine trione (PB12) and 5-(4-N,N-didodecyl aminobenzylidene)-(1H,3H)-2,4,6-pyrimidine trione (AB(12)) was studied by UV-visible, fluorescence, and surface voltaic spectroscopies (SPS). The experimental results indicate that PB12 tends to form J-aggregate and AB(12) tends to form H-aggregate under increasing concentration. An intramolecular twisted charge transfer (TICT) emission around 500 nm is observed when J-aggregate is formed between PB12 molecules, and an excimer emission around 600 nm is observed when H-aggregate is formed between AB(12) molecules.

Tuning the aggregation of polyimide thin films by modification of their molecular interactions

Thin films of an organo-soluble polyimide based on 1,4-(3,4-dicarboxyphenoxy)benzene dianhydride (HQDPA) and 2,2'-dimethyl-4,4'-methylene dianiline (DMMDA) have been studied. A prism coupler was used to measure the refractive indices. The average refractive indices of thin films prepared by annealing at different temperatures and times were chosen to characterize the condensation states of thin films. Thin films annealed at 200 degrees C show irreversible changes in physical properties, eg solubility. FTIR spectroscopy showed that the chain structures of the above thin films remained unchanged. It is proposed that specific molecular interactions induce the irreversible changes revealed by fluorescence spectroscopy. (C) 2000 Society of Chemical Industry.

Determination of electron mobility in a blue-emitting alternating block copolymer by space-charge-limited current measurements

In this communication we analyse current versus voltage data obtained using one carrier injection at metal/polymer/metal structures, The used polymer is a soluble blue-emitting alternating block copolymer, Our experimental results demonstrate that the electron current is limited by a large amount of traps with exponential energy distribution in the copolymer. The electron ;mobility of 5.1 x 10(-10) cm(2)/V s is directly determined by space-charge-limited current measurements. The electron mobility is at least three orders of magnitude smaller than that for holes in the copolymer. (C) 1999 Elsevier Science Ltd. All rights reserved.

Isotope effect in proton-transfer and association-dissociation reactions for butylamine by ultrasonic relaxation methods

Ultrasonic absorption coefficients were measured for butylamine in heavy water (D2O) in the frequency range from 0.8 to 220 MHz and at concentrations from 0.0278 to 2.5170 mol dm(-3) at 25 degrees C; two kinds of relaxation processes were observed. One was found in relatively dilute solutions (up to 0.5 mol dm(-3)), which was attributed to the hydrolysis of butylamine. In order to compare the results, absorption measurements were also carried out in light water (H2O). The rate and thermodynamic parameters were determined from the concentration dependence of the relaxation frequency and the maximum absorption per wavelength. The isotope effects on the diffusion-controlled reaction were estimated and the stability of the intermediate of the hydrolysis was considered while comparing it with the results for propylamine in H2O and D2O. Another relaxation process was observed at concentrations greater than 1 mol dm(-3) in D2O. In order to examine the solution characteristics, proton NMR measurements for butylamine were also carried out in D2O. The chemical shifts for the gamma- and delta-proton in butylamine molecule indicate the existence of an aggregate. From profiles of the concentration dependence of the relaxation frequency and the maximum absorption per wavelength of sound absorption, the source of the relaxation was attributed to an association-dissociation reaction, perhaps, associated with a hydrophobic interaction. The aggregation number, the forward and reverse rate constants and the standard volume change of the reaction were determined. It was concluded from a comparison with the results in H2O that the hydrophobic interaction of butylamine in D2O is stronger than that in H2O. Also, the isotope effect on this reaction was interpreted in terms of the solvent structure.

Preparation of the phosphor BaMgAl10O17 : Eu2+ by the surface diffusion method

A surface diffusion method was proposed and applied to prepare blue phosphor BaMgAl10O17:Eu2+. The results show that, compared with the direct synthesis method by common high temperature solid state, the concentration of Eu2+ in the phosphor BaMgAl10O17:Eu2+ prepared by the surface diffusion method can be greatly reduced owing to the activator Eu2+ ions distributed mainly over the surface of the phosphor. It is possible to reduce the cost of this kind of the luminescent materials with the aid of the surface diffusion method.

Fluorescence and aggregation behavior of a polyimide in solutions

The UV-visible absorption and fluorescence spectra of a soluble polyimide, YS-30, in several organic solvents were measured over a wide range of concentration. The experimental results show that there exist both intramolecular and intermolecular electron donor acceptor interactions for YS-30 molecules. The fluorescence behavior of YS-30 in N,N-dimethylacetamide and in chloroform solutions is similar in general, except that its ground-state intermolecular charge transfer emission is more obvious in N,N-dimethylacetamide solution. This difference is attributed to the greater extent of disruption of the chain packing by solvent or/and the more efficient radiationless energy dissipation process from the excited state complexes to chloroform. The intensity ratio of intermolecular charge transfer emission to intramolecular charge transfer emission is used to characterize the state of aggregation of YS-30 molecules in solutions. The plot of this ratio versus concentration indicates the existence of two critical concentrations. It is also found from the same plot that the decrease of coil size is very pronounced during the initial stage of shrinkage.

A study of dimethylferrocene diffusion and electrode kinetics using microelectrode voltammetry in poly(ethylene glycol) solvent

The heterogeneous electron transfer rate constant (k(s)) of dimethylferrocene (DMFc) was estimated using cyclic voltammetric peak potential separations taken typically in a mixed diffusion geometry regime in a polyelectrolyte, and the diffusion coefficient (D) of DMFc was obtained using a steady-state voltammogram. The heterogeneous electron transfer rate constant and diffusion coefficient are both smaller by about 100-fold in the polymeric solvent than in the monomeric solvent. The results are in agreement with the difference of longitudinal dielectric relaxation time (tau(L)) in the two kinds of solvents, poly(ethylene glycol) (PEG) and CH3CN, indicating that k(s) varies inversely with tau(L); k(s), is proportional to D of DMFc. Both D and k(s) of DMFc in PEG containing different supporting electrolytes and at different temperatures have been estimated. These results show that D and k(s) of DMFc increase with increasing temperature in the polyelectrolyte, whereas they vary only slightly with changing the supporting electrolyte.

Synchronous fluorescence spectra of hemoglobin: A study of aggregation states in aqueous solutions

The synchronous fluorescence spectra of hemoglobin solutions are reported for the first rime. The main fluorescence peaks observed in the spectra are assigned. The effect of the concentration of hemoglobin solution on the spectra is studied. Characteristic fluorescence peaks due to the dimer and tetramer of hemoglobin molecules are recognized. (C) 1998 Academic Press.

A novel electrochemical method for simultaneously measuring diffusion coefficient and ion transference number

This paper introduces a new method to estimate the diffusion coefficient and transference number of a salt or an electroactive ion in a solution with little or no supporting electrolyte. The above two parameters can be obtained from a single potential step experiment without previous knowledge of either one. It would appear that the method could also be used in the study of ion transport in a high viscosity solvent or a solid electrolyte. (C) 1998 Elsevier Science S.A.

A study on the diffusion of quinhydrone in polymer electrolyte

The diffusion coefficients (D) of quinhydrone were estimated in polymer electrolytes by using non-steady-state chronoamperometry and steady-state current voltammetry. The D values have been estimated in polyethylene glycol (PEG) containing different concentrations, and cations of supporting electrolytes, and in different solvents over a range of temperatures. The dependencies of electroactive probe diffusion coefficients on temperature, supporting electrolyte concentration and polymer chain length are discussed. The results show that D increases with increasing temperature and decreasing concentration of supporting electrolyte. The diffusion coefficient depends strongly on the length of polymer chain and decreases sharply with increasing polymer chain length. The contribution of electron self-exchange has been explored and it seems to be negligible here. (C) 1998 Elsevier Science S.A.