Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

The complex kinetics of protein folding in wide temperature ranges

The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T-0 is found to be smaller than the folding transition temperature T-f. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal behavior, from high-temperature exponential Poissonian kinetics to the relatively low-temperature highly nonexponential kinetics. The transition temperature is at T-k and T-0, T-k, T-f. In certain low-temperature regimes, a power law behavior at long time emerges. At very low temperatures ( lower than trapping transition temperature T< T-0/(4&SIM;6)), the kinetics is an exponential Poissonian process again.

Electrical conductivity of a single Au/polyaniline microfiber

We report the measurements of conductivity, I-V curve, and magnetoresistance of a single Au/polyaniline microfiber with a core-shell structure, on which a pair of platinum microleads was attached by focused ion beam. The Au/polyaniline microfiber shows a much higher conductivity (similar to 110 S/cm at 300 K) and a much weaker temperature dependence of resistance [R(4 K)/R(300 K)=5.1] as compared with those of a single polyaniline microtube [sigma(RT)=30-40 S/cm and R(4 K)/R(300 K)=16.2]. The power-law dependence of R(T)proportional to T-beta, with beta=0.38, indicates that the measured Au/polyaniline microfiber is lying in the critical regime of the metal-insulator transition. In addition, the microfiber shows a H-2 dependent positive magnetoresistance at 2, 4, and 6 K.

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.

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.

SURFACE FRACTALS IN BLOCK-COPOLYMERS

A surface fractal model was presented to describe the interface in block copolymers. It gives a simple power-law relationship between the scattering intensity I(q) and the wave vector q in a relatively wide range as qxi >> 1, I(q) is-proportional-to q(D-6

DETERMINATION OF INITIATION VALUE OF MODE-I INTERLAMINAR FRACTURE-TOUGHNESS OF UNIDIRECTIONAL POLYMER COMPOSITES

The use of interlaminar fracture tests to measure the delamination resistance of unidirectional composite laminates is now widespread. However, because of the frequent occurrence of fiber bridging and multiple cracking during the tests, it leads to artificially high values of delamination resistance, which will not represent the behavior of the laminates. Initiation fracture from the crack starter, on the other hand, does not involve bridging, and should be more representative of the delamination resistance of the composite laminates. Since there is some uncertainty involved in determining the initiation value of delamination resistance in mode I tests in the literature, a power law of the form G(IC) = A.DELTA alpha(b) (where G(IC) is mode I interlaminar fracture toughness and DELTA alpha is delamination growth) is presented in this paper to determine initiation value of mode I interlaminar fracture toughness. It is found that initiation values of the mode I interlaminar fracture toughness, G(IC)(ini), can be defined as the G(IC) value at which 1 mm of delamination from the crack starter has occurred. Examples of initiation values determined by this method are given for both carbon fiber reinforced thermoplastic and thermosetting polymers.

Self-organized Criticality Model for Ocean Internal Waves

In this paper, we present a simple spring-block model for ocean internal waves based on the self-organized criticality (SOC). The oscillations of the water blocks in the model display power-law behavior with an exponent of -2 in the frequency domain, which is similar to the current and sea water temperature spectra in the actual ocean and the universal Garrett and Munk deep ocean internal wave model [Geophysical Fluid Dynamics 2(1972) 225; J. Geophys. REs. 80 (1975) 291]. The influence of the ratio of the driving force to the spring coefficient to SOC behaviors in the model is also discussed.

Dielectric responses of graded cylindrical composites

The effective dielectric responses of linear composites with graded cylindrical particles are investigated under an external uniform electric field. As an example, with the Kummer function, we have obtained the analytical solutions of electric potentials of graded composites with a cylindrical inclusion particle of dielectric function profile epsilon(i) = cr(k)e(betar), where r is the inside distance of a point in cylindrical particle from the original point of cylindrical coordinates. In the dilute limit, the effective dielectric response is derived by means of the mean field method. For larger volume fraction, we have estimated the dielectric response of the graded composites with an effective medium approximation. Furthermore, from our results, we have discussed the effective responses of graded composites for power-law and exponential dielectric function profiles, respectively. (C) 2004 Elsevier B.V. All rights reserved.

The nonlinear effective dielectric response of graded composites

The perturbation method is developed to deal with the effective nonlinear dielectric responses of weakly nonlinear graded composites, which consist of the graded inclusion with a linear dielectric function of spatial variables of inclusion material. For Kerr-like nonlinear graded composites, as an example in two dimensions, we have used the perturbation method to solve the boundary value problems of potentials, and studied the effective responses of nonlinear graded composites, where a cylindrical inclusion with linear dielectric function and nonlinear dielectric constant is randomly embedded in a homogeneous host with linear and nonlinear dielectric constants. For the exponential function and the power-law dielectric profiles of cylindrical inclusions, in the dilute limit, we have derived the formulae of effective nonlinear responses of both graded nonlinear composites.

Dielectric response of composites with graded cylindrical particles

Effective dielectric responses of graded cylindrical composites are investigated when an external uniform field is applied to the composites. Considering linear random composites of cylindrical particles with a specific dielectric function, which varies along the radial direction of the particles, we have studied three cases of dielectric profiles: exponential function, linear and power-law profiles. For each case, the effective dielectric response of graded composites is given on the basis of exact solutions of the local potentials of composites in the dilute limit. For a larger volume fraction, we have proposed an effective medium approximation to estimate the effective dielectric response.

Effective properties of graded elliptical cylindrical composites

The effective property has been investigated theoretically in graded elliptical cylindrical composite's consisting of inhomogeneous graded elliptical cylinders and an isotropic matrix under external uniform electric field. As a theoretical model, the dielectric gradient profile in the elliptical cylinder is modeled by a power-law function of short semi-axis variable parameter (xi(2) - 1) in the elliptical cylindrical coordinates, namely epsilon(i)(xi) = c(k) (xi(2) - 1)(k), where c(k) and k are the parameters, and xi is the long semi-axis space variable in an elliptical cylindrical inclusion region. In the dilute limit, the local analytical potentials in inclusion and matrix regions are derived exactly by means of the hyper-geometric function, and the formulas are given for estimating the effective dielectric responses under the external lfield along (x) over cap- and (y) over cap -directions, respectively. Furthermore, we have demonstrated that our effective response formulas can be reduced to the well-known results of homogeneous isotropic elliptical cylindrical composites if we take the limit k -> 0 in graded elliptical cylindrical composites. (c) 2006 Elsevier B.V. All rights reserved.

Effective ac dielectric response of graded cylindrical composites

Under an external alternating current (ac) field, the effective ac dielectric response of graded composites consisting of the graded cylindrical inclusion having complex permittivity profiles has been investigated theoretically. A model that the dielectric function is assumed to be a constant while the conductivity has a power-law dependence on the radial variable r, namely epsilon(i)(r) = A + cr(k)/i omega. is studied and the local analytical potentials of the inclusion and the host regions are derived in terms of hyper-geometric function. In the dilute limit, the effective ac dielectric response is predicted. Meanwhile, we have given the exact proof of the differential effective dipole approximation (DEDA) method, which is suitable to arbitrary graded profiles. Furthermore, we have given the analytical potentials and the effective ac dielectric responses of coated graded cylindrical composites for two cases, case (a) graded core and case (b) graded coated layer, having the graded dielectric profiles, respectively. (c) 2005 Elsevier B.V. All rights reserved.

Effective thermal conductivity of graded nonlinear composites with heat contact resistance

The perturbation expansion method is used to find the effective thermal conductivity of graded nonlinear composites having thermal contact resistance on the inclusion surface. As an example, we have studied the graded composites with cylindrical inclusions immersed in a homogeneous matrix. The thermal conductivity of the cylindrical inclusion is assumed to have a power-law profile of the radial distance r measured from its origin. For weakly nonlinear constitutive relations between the heat flow density q and the temperature field T, namely, q = -mu del T - chi vertical bar del T vertical bar(2) del T, in both the inclusion and the matrix regions, we have derived the temperature distributions using the perturbation expansion method. A nonlinear effective medium approximation of graded composites is proposed to estimate the effective linear and nonlinear thermal conductivities. by considering the temperature singularity on the inclusion surface due to the heat contact resistance. (c) 2006 Elsevier B.V. All rights reserved.