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.

Kinetics of atomic force microscope-based scanned probe oxidation on an octadecylated silicon(111) surface

Atomic force microscope (AFM)-based scanned probe oxidation (SPO) nanolithography has been carried out on an octadecyl-terminated Si(111) surface to create dot-array patterns under ambient conditions in contact mode. The kinetics investigations indicate that this SPO process involves three stages. Within the steadily growing stage, the height of oxide dots increases logarithmically with pulse duration and linearly with pulse voltage. The lateral size of oxide dots tends to vary in a similar way. Our experiments show that a direct-log kinetic model is more applicable than a power-of-time law model for the SPO process on an alkylated silicon in demonstrating the dependence of oxide thickness on voltage exposure time within a relatively wide range. In contrast with the SPO on the octodecysilated SiO2/silicon surface, this process can be realized by a lower voltage with a shorter exposure time, which will be of great benefit to the fabrication of integrated nanometer-sized electronic devices on silicon-based substrates. This study demonstrates that the alkylated silicon is a new promising substrate material for silicon-based nanolithography.

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.

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

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.

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.

空间电流体系地磁反演及理论研究

The space currents definitely take effects on electromagnetic environment and also are scientific highlight in the space research. Space currents as a momentum and energy provider to Geospace Storm, disturb the varied part of geomagnetic field, distort magnetospheric configuration and furthermore take control of the coupling between magnetosphere and ionosphere. Due to both academic and commercial objectives above, we carry on geomagnetic inverse and theoretical studies about the space currents by using geomagnetic data from INTERMAGNET. At first, we apply a method of Natural Orthogonal Components (NOC) to decomposition the solar daily variation, especially for (solar quiet variation). NOC is just one of eign mode analysis, the most advantage of this method is that the basic functions (BFs) were not previously designated, but naturally came from the original data so that there are several BFs usually corresponding to the process really happened and have more physical meaning than the traditional spectrum analysis with the fixed BFs like Fourier trigonometric functions. The first two eign modes are corresponding to the and daily variation and their amplitudes both have the seasonal and day-to-day trend, that will be useful for evaluating geomagnetic activity indices. Because of the too strict constraints of orthogonality, we try to extend orthogonal contraints to the non-orthogonal ones in order to give more suitable and appropriate decomposition of the real processes when the most components did not satisfy orthogonality. We introduce a mapping matrix which can transform the real physical space to a new mathematical space, after that process, the modified components which associated with the physical processes have satisfied the orthogonality in the new mathematical space, furthermore, we can continue to use the NOC decomposition in the new mathematical space, and then all the components inversely transform back to original physical space, so that we would have finished the non-orthogonal decomposition which more generally in the real world. Secondly, geomagnetic inverse of the ring current’s topology is conducted. Configurational changes of the ring current in the magnetosphere lead to different patterns of disturbed ground field, so that the global configuration of ring current can be inferred from its geomagnetic perturbations. We took advantages of worldwide geomagnetic observatories network to investigate the disturbed geomagnetic field which produced by ring current. It was found that the ring current was not always centered at geomagnetic equator, and significantly deviated off the equator during several intense magnetic storms. The deviation owing to the tilting and latitudinal shifting of the ring current with respect to the earth’s dipole can be estimated from global geomagnetic survey. Furthermore those two configurational factors which gave a quantitative description of the ring current configuration, will be helpful to improve the Dst calibration and understand the dependence of ring current’s configuration on the plasma sheet location relative to the equator when magnetotail field warped. Thirdly, the energization and physical acceleration process of ring current during magnetic storm has been proposed. When IMF Bz component increase, the enhanced convection electric field drive the plasma injection into the inner magnetosphere. During the transport process, a dynamic heating is happened which make the particles more ‘hot’ when the injection is more deeply inward. The energy gradient along the injection path is equivalent to a kind of force, which resist the plasma more earthward injection, as a diamagnetic effect of the magnetosphere anti and repellent action to the exotically injected plasma. The acceleration efficiency has a power law form. We use analytical way to quantitatively describe the dynamical process by introducing a physical parameter: energization index, which will be useful to understand how the particle is heated. At the end, we give a scheme of how to get the from storm time geomagnetic data. During intense magnetic storms, the lognormal trend of geomagnetic Dst decreases depend on the heating dynamic of magnetosphere controlling ring current. The descending pattern of main phase is governed by the magnetospheric configuration, which can be describled by the energization index. The amplitude of Dst correlated with convection electric field or south component of the solar wind. Finally, the Dst index is predicted by upstream solar wind parameter. As we known space weather have posed many chanllenges and impacts on techinal system, the geomagnetic index for evaluating the activity space weather. We review the most popular Dst prediction method and repeat the Dst forecasting model works. A concise and convnient Key Points model of the polar region is also introduced to space weather. In summary, this paper contains some new quantitative and physical description of the space currents with special focus on the ring current. Whatever we do is just to gain a better understanding of the natural world, particularly the space environment around Earth through analytical deduction, algorithm designing and physical analysis, to quantitative interpretation. Applications of theoretical physics in conjunction with data analysis help us to understand the basic physical process govering the universe.

Load-Unload Response Ratio and Accelerating Moment/Energy Release Critical Region Scaling and Earthquake Prediction

The main idea of the Load-Unload Response Ratio (LURR) is that when a system is stable, its response to loading corresponds to its response to unloading, whereas when the system is approaching an unstable state, the response to loading and unloading becomes quite different. High LURR values and observations of Accelerating Moment/Energy Release (AMR/AER) prior to large earthquakes have led different research groups to suggest intermediate-term earthquake prediction is possible and imply that the LURR and AMR/AER observations may have a similar physical origin. To study this possibility, we conducted a retrospective examination of several Australian and Chinese earthquakes with magnitudes ranging from 5.0 to 7.9, including Australia's deadly Newcastle earthquake and the devastating Tangshan earthquake. Both LURR values and best-fit power-law time-to-failure functions were computed using data within a range of distances from the epicenter. Like the best-fit power-law fits in AMR/AER, the LURR value was optimal using data within a certain epicentral distance implying a critical region for LURR. Furthermore, LURR critical region size scales with mainshock magnitude and is similar to the AMR/AER critical region size. These results suggest a common physical origin for both the AMR/AER and LURR observations. Further research may provide clues that yield an understanding of this mechanism and help lead to a solid foundation for intermediate-term earthquake prediction.

Similarity consideration of structural bifurcation buckling

Many structural bifurcation buckling problems exhibit a scaling or power law property. Dimensional analysis is used to analyze the general scaling property. The concept of a new dimensionless number, the response number-Rn, suggested by the present author for the dynamic plastic response and failure of beams, plates and so on, subjected to large dynamic loading, is generalized in this paper to study the elastic, plastic, dynamic elastic as well as dynamic plastic buckling problems of columns, plates as well as shells. Structural bifurcation buckling can be considered when Rn(n) reaches a critical value.

Finite Element Solutions for Plane Strain Mode I Crack with Strain Grading Effect

In this paper, a new phenomenological theory with strain gradient effects is proposed to account for the size dependence of plastic deformation at micro- and submicro-length scales. The theory fits within the framework of general couple stress theory and three rotational degrees of freedom omega(i) are introduced in addition to the conventional three translational degrees of freedom mu(i). omega(i) is called micro-rotation and is the sum of material rotation plus the particles' relative rotation. While the new theory is used to analyze the crack tip field or the indentation problems, the stretch gradient is considered through a new hardening law. The key features of the theory are that the rotation gradient influences the material character through the interaction between the Cauchy stresses and the couple stresses; the term of stretch gradient is represented as an internal variable to increase the tangent modulus. In fact the present new strain gradient theory is the combination of the strain gradient theory proposed by Chen and Wang (Int. J. Plast., in press) and the hardening law given by Chen and Wang (Acta Mater. 48 (2000a) 3997). In this paper we focus on the finite element method to investigate material fracture for an elastic-power law hardening solid. With remotely imposed classical K fields, the full field solutions are obtained numerically. It is found that the size of the strain gradient dominance zone is characterized by the intrinsic material length l(1). Outside the strain gradient dominance zone, the computed stress field tends to be a classical plasticity field and then K field. The singularity of stresses ahead of the crack tip is higher than that of the classical field and tends to the square root singularity, which has important consequences for crack growth in materials by decohesion at the atomic scale. (C) 2002 Elsevier Science Ltd. All rights reserved.

What is indentation hardness?

Using dimensional analysis and finite element calculations, we derive simple scaling relationships for loading and unloading curve, contact depth, and hardness. The relationship between hardness and the basic mechanical properties of solids, such as Young's modulus, initial yield strength, and work-hardening exponent, is then obtained. The conditions for 'piling-up' and 'sinking-in' of surface profiles during indentation are determined. A method for estimating contact depth from initial unloading slope is examined. The work done during indentation is also studied. A relationship between the ratio of hardness to elastic modulus and the ratio of irreversible work to total work is discovered. This relationship offers a new method for obtaining hardness and elastic modulus. Finally, a scaling theory for indentation in power-law creep solids using self-similar indenters is developed. A connection between creep and 'indentation size effect' is established.