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.

Dielectric response of spherically anisotropic graded piezoelectric composites

A graded piezoelectric composite consisting of a spherically anisotropic graded piezoelectric inclusion imbedded in an infinite nonpiezoelectric matrix, with the physical properties of the graded spherical inclusion having a power-law profile with respect to the radial variable r, is studied theoretically. Under an external uniform electric field, the electric displacement field and the elastic stress tensor field of this spherically anisotropic graded piezoelectric composite are derived exactly by means of displacement separation technique, based on the governing equations in the dilute limit. A piezoelectric response mechanism, in which the effective piezoelectric response vanishes along the z direction (or x,y directions), is revealed in this kind of graded piezoelectric composites. Furthermore, it is found that the effective dielectric constant decreases (or increases) with the volume fraction p of the inclusions if the exponent parameter k of the grading profile is larger (or smaller) than a critical value. (C) 2007 American Institute of Physics.

Dielectric responses of anisotropic graded granular composites having arbitrary inclusion shapes

The transformation field method (TFM) originated from Eshelby's transformation field theory is developed to estimate the effective permittivity of an anisotropic graded granular composite having inclusions of arbitrary shape and arbitrary anisotropic grading profile. The complicated boundary-value problem of the anisotropic graded composite is solved by introducing an appropriate transformation field within the whole composite region. As an example, the effective dielectric response for an anisotropic graded composite with inclusions having arbitrary geometrical shape and arbitrary grading profile is formulated. The validity of TFM is tested by comparing our results with the exact solution of an isotropic graded composite having inclusions with a power-law dielectric grading profile and good agreement is achieved in the dilute limit. Furthermore, it is found that the inclusion shape and the parameters of the grading profile can have profound effect on the effective permittivity at high concentrations of the inclusions. It is pointed out that TFM used in this paper can be further extended to investigate the effective elastic, thermal, and electroelastic properties of anisotropic graded granular composite materials.

Transformation field method for calculating the effective properties of isotropic graded composites having arbitrary shapes

A method of transformation field is developed to estimate the effective properties of graded composites whose inclusions have arbitrary shapes and gradient profiles by means of a periodic cell model. The boundary-value problem of graded composites having arbitrary inclusion shapes is solved by introducing the transformation field into the inclusion region. As an example, the effective dielectric response of isotropic graded composites having arbitrary shapes and gradient profiles is handled by the transformation field method (TFM). Moreover, TFM results are validated by the exact solutions of isotropic graded spherical inclusions having a power-law profile and good agreement is obtained in the dilute limit. Furthermore, it is found that the inclusion shapes and the parameters of the gradient profiles can have profound effect on the effective properties of composite systems at high concentration of inclusions.