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.

On the melting of the nascent state nylon 1010 with different molecular weights

The melting of the nascent state nylon 1010 samples melt condensation polymerized with different M(eta) have been studied by DSC. The relations of melting point, content of higher order crystal with M(eta) are similar, the plots like a peak, at M(eta)=1.48x10(4) have the maximum. The melting heat, melting entropy and crystallinity are decreased gradually with M(eta) increasing.

STATISTICAL THERMODYNAMICS OF POLYDISPERSE POLYMER MIXTURES

A statistical thermodynamics theory of polydisperse polymer blends based on a lattice model description of a fluid is formulated. Characterization of a binary polydisperse polymer mixture requires a knowledge of the pure polymer system and the interaction energy. It is assumed that the intrinsic and interactive properties of polymer (for example, T*, P*, rho*, and epsilon(ij)*) are independent of molecular size. Thermodynamic properties of ternary and higher order mixtures are completely defined in terms of the pure fluid polymer parameters and the binary interaction energies. Thermodynamic stability criteria for the phase transitions of a binary mixture are shown. The binodal and spinodal of general binary systems and of special binary systems are discussed.

Impact of difference accuracy on computational properties of vertical grids for a nonhydrostatic model

Starting from nonhydrostatic Boussinesq approximation equations, a general method is introduced to deduce the dispersion relationships. A comparative investigation is performed on inertia-gravity wave with horizontal lengths of 100, 10 and 1 km. These are examined using the second-order central difference scheme and the fourth-order compact difference scheme on vertical grids that are currently available from the perspectives of frequency, horizontal and vertical component of group velocity. These findings are compared to analytical solutions. The obtained results suggest that whether for the second-order central difference scheme or for the fourth-order compact difference scheme, Charny-Phillips and Lorenz ( L) grids are suitable for studying waves at the above-mentioned horizontal scales; the Lorenz time-staggered and Charny-Phillips time staggered (CPTS) grids are applicable only to the horizontal scales of less than 10 km, and N grid ( unstaggered grid) is unsuitable for simulating waves at any horizontal scale. Furthermore, by using fourth-order compact difference scheme with higher difference precision, the errors of frequency and group velocity in horizontal and vertical directions produced on all vertical grids in describing the waves with horizontal lengths of 1, 10 and 100 km cannot inevitably be decreased. So in developing a numerical model, the higher-order finite difference scheme, like fourth-order compact difference scheme, should be avoided as much as possible, typically on L and CPTS grids, since it will not only take many efforts to design program but also make the calculated group velocity in horizontal and vertical directions even worse in accuracy.

Fourier有限差分法深度偏移与正演模拟

With the development of seismic exploration, the target becomes more and more complex, which leads to a higher demand for the accuracy and efficiency in 3D exploration. Fourier finite-difference (FFD) method is one of the most valuable methods in complex structure exploration, which keeps the ability of finite-differenc method in dealing with laterally varing media and inherits the predominance of the phase-screen method in stablility and efficiency. In this thesis, the accuracy of the FFD operator is highly improved by using simulated annealing algorithm. This method takes the extrapolation step and band width into account, which is more suitable to various band width and discrete scale than the commonely-used optimized method based on velocity contrast alone. In this thesis, the FFD method is extended to viscoacoustic modeling. Based on one-way wave equation, the presented method is implemented in frequency domain; thus, it is more efficient than two-way methods, and is more convenient than time domain methods in handling attenuation and dispersion effects. The proposed method can handle large velocity contrast and has a high efficiency, which is helpful to further research on earth absorption and seismic resolution. Starting from the frequency dispersion of the acoustic VTI wave equation, this thesis extends the FFD migration method to the acoustic VTI media. Compared with the convetional FFD method, the presented method has a similar computational efficiency, and keeps the abilities of dealing with large velocity contrasts and steep dips. The numerical experiments based on the SEG salt model show that the presented method is a practical migration method for complex acoustical VTI media, because it can handle both large velocity contrasts and large anisotropy variations, and its accuracy is relatively high even in strong anisotropic media. In 3D case, the two-way splitting technique of FFD operator causes artificial azimuthal anisotropy. These artifacts become apparent with increasing dip angles and velocity contrasts, which prevent the application of the FFD method in 3D complex media. The current methods proposed to reduce the azimuthal anisotropy significantly increase the computational cost. In this thesis, the alternating-direction-implicit plus interpolation scheme is incorporated into the 3D FFD method to reduce the azimuthal anisotropy. By subtly utilizing the Fourier based scheme of the FFD method, the improved fast algorithm takes approximately no extra computation time. The resulting operator keeps both the accuracy and the efficiency of the FFD method, which is helpful to the inhancements of both the accuracy and the efficiency for prestack depth migration. The general comparison is presented between the FFD operator and the generalized-screen operator, which is valuable to choose the suitable method in practice. The percentage relative error curves and migration impulse responses show that the generalized-screen operator is much sensiutive to the velocity contrasts than the FFD operator. The FFD operator can handle various velocity contrasts, while the generalized-screen operator can only handle some range of the velocity contrasts. Both in large and weak velocity contrasts, the higher order term of the generalized-screen operator has little effect on improving accuracy. The FFD operator is more suitable to large velocity contrasts, while the generalized-screen operator is more suitable to middle velocity contrasts. Both the one-way implicit finite-difference migration and the two-way explicit finite-differenc modeling have been implemented, and then they are compared with the corresponding FFD methods respectively. This work gives a reference to the choosen of proper method. The FFD migration is illustrated to be more attractive in accuracy, efficiency and frequency dispertion than the widely-used implicit finite-difference migration. The FFD modeling can handle relatively coarse grids than the commonly-used explicit finite-differenc modeling, thus it is much faster in 3D modeling, especially for large-scale complex media.

全局优化的Fourier有限差分偏移方法研究

Seismic exploration is the main method of seeking oil and gas. With the development of seismic exploration, the target becomes more and more complex, which leads to a higher demand for the accuracy and efficiency in seismic exploration. Fourier finite-difference (FFD) method is one of the most valuable methods in complex structure exploration, which has obtained good effect. However, in complex media with wider angles, the effect of FFD method is not satisfactory. Based on the FFD operator, we extend the two coefficients to be optimized to four coefficients, then optimize them globally using simulated annealing algorithm. Our optimization method select the solution of one-way wave equation as the objective function. Except the velocity contrast, we consider the effects of both frequency and depth interval. The proposed method can improve the angle of FFD method without additional computation time, which can reach 75° in complex media with large lateral velocity contrasts and wider propagation angles. In this thesis, combinating the FFD method and alternative-direction-implicit plus interpolation(ADIPI） method, we obtain 3D FFD with higher accuracy. On the premise of keeping the efficiency of the FFD method, this method not only removes the azimuthal anisotropy but also optimizes the FFD mehod, which is helpful to 3D seismic exploration. We use the multi-parameter global optimization method to optimize the high order term of FFD method. Using lower-order equation to obtain the approximation effect of higher-order equation, not only decreases the computational cost result from higher-order term, but also obviously improves the accuracy of FFD method. We compare the FFD, SAFFD（multi-parameter simulated annealing globally optimized FFD）, PFFD, phase-shift method(PS）, globally optimized FFD （GOFFD）, and higher-order term optimized FFD method. The theoretical analyses and the impulse responses demonstrate that higher-order term optimized FFD method significantly extends the accurate propagation angle of the FFD method, which is useful to complex media with wider propagation angles.

各向异性与非线性介质中弹性波场传播特征研究

The topic of this study is about the propagation features of elastic waves in the anisotropic and nonlinear media by numerical methods with high accuracy and stability. The main achievements of this paper are as followings: Firstly, basing on the third order elastic energy formula, principle of energy conservation and circumvolved matrix method, we firstly reported the equations of non-linear elastic waves with two dimensions and three components in VTI media. Secondly, several conclusions about some numerical methods have been obtained in this paper. Namely, the minimum suitable sample stepth in space is about 1/8-1/12 of the main wavelength in order to distinctly reduce the numerical dispersion resulted from the numerical mehtod, at the same time, the higher order conventional finite difference (CFD) schemes will give little contribution to avoid the numerical solutions error accumulating with time. To get the similar accuracy with the fourth order center finite difference method, the half truncation length of SFFT should be no less than 7. The FDFCT method can present with the numerical solutions without obvious dispersion when the paprameters of FCT is suitable (we think they should be in the scope from 0.0001 to 0.07). Fortunately, the NADM method not only can reported us with the higher order accuracy solutions (higher than that of the fourth order finite difference method and lower than that of the sixth order finite difference method), but also can distinctly reduce the numerical dispersion. Thirdly, basing on the numerial and theoretical analysis, we reported such nonlinear response accumulating with time as waveform aberration, harmonic generation and resonant peak shift shown by the propagation of one- and two-dimensional non-linear elasticwaves in this paper. And then, we drew the conclusion that these nonlinear responses are controlled by the product between nonlinear strength (SN) and the amplitude of the source. At last, the modified FDFCT numerical method presented by this paper is used to model the two-dimensional non-linear elastic waves propagating in VTI media. Subsequently, the wavelet analysis and polarization are adopted to investigate and understand the numerical results. And then, we found the following principles (attention: the nonlinear strength presented by this paper is weak, the thickness of the -nonlinear media is thin (200m), the initial energy of the source is weak and the anisotropy of the media is weak too): The non-linear response shown by the elastic waves in VTI media is anisotropic too; The instantaneous main frequency sections of seismic records resulted from the media with a non-linear layer have about 1/4 to 1/2 changes of the initial main frequency of source with that resulted from the media without non-linear layer; The responses shown by the elasic waves about the anisotropy and nonlinearity have obvious mutual reformation, namely, the non-linear response will be stronger in some directions because of the anisotropy and the anisotropic strength shown by the elastic waves will be stronger when the media is nonlinear.

非言语学习不良青少年空间关系推理及其影响因素研究

It has reported that individuals with nonverbal learning disabilities (NLD) have deficits in visual-spatial organization and strengths in rote language abilities. At present, there are few studies on higher order cognitive abilities of adolescents with NLD, such as the reasoning about spatial relations. The study sampled three groups: a normal group (a control group, C), a nonverbal learning disabilities group (NLD), and a verbal learning disabilities group (VLD). The aim of this study was to examine spatial and nonspatial relation reasoning abilities in adolescents with NLD under figure and word conditions, and assessed the relative involvement of different working memory components in four types of reasoning tasks: reasoning about figure-spatial, figure-nonspatial, verbal-spatial, and verbal-nonspatial relations. Using the double-tasks methodology, visual, spatial, central-executive, and phonological loads were realized. We tried to find how working memory components impact on adolescents with NLD spatial and nonspatial reasoning. The main results of present research are as follows. (1) The NLD group didn’t differ from normal group on reasoning about figure-nonspatial relations. The NLD group scored lower than the C group in spatial problems. So, adolescents with NLD showed a dissociation between spatial and non-spatial relation reasoning. They scored higher in non-spatial problems than in spatial ones. Adolescents with VLD developed well in reasoning about figure-nonspatial relations, but showed deficits in other three tasks. (2) For each reasoning task, the difficult of four types of reasoning problem had different changing trend. For figure and verbal spatial problems, mental model approach can interpret performance of the four problems well. For verbal nonspatial problems, a logical rule approach can interpret performance of the four problems well. (3) Adolescents with NLD did not differ from adolescents with VLD and normal adolescents in phonological, central-executive, and visual dual tasks. But the NLD group had lower performance than the other two groups in spatial dual task. The results showed a dissociation between visual and spatial working memory in NLD group. The VLD group only experienced deficits in central-executive subsystem. (4) The studies found that spatial reasoning mainly loaded spatial working memory, whist the involvement of spatial resources in nonspatial reasoning was little. Visual working memory mainly involved in reasoning about spatial and figure-nonspatial relations, especially in figure-nonspatial problems, and had few impacts on verbal-nonspatial reasoning. Central executive system was involved in all reasoning tasks. The role of phonological loop in the reasoning tasks required further explored. (5) According to the findings, we concluded that the deficits in spatial working memory resulted in poor spatial reasoning abilities for teenagers with NLD, whist because of the limited central executive capability, teenagers with VLD showed poor reasoning abilities. (6) The three groups can used multiple strategies during the reasoning process. They didn’t differ from each other in reasoning strategies. They all used mental model strategy to solve figure and verbal spatial problems, and used logic rule strategy to solve verbal nonspatial problems.

Type-omega DPLs

Type-omega DPLs (Denotational Proof Languages) are languages for proof presentation and search that offer strong soundness guarantees. LCF-type systems such as HOL offer similar guarantees, but their soundness relies heavily on static type systems. By contrast, DPLs ensure soundness dynamically, through their evaluation semantics; no type system is necessary. This is possible owing to a novel two-tier syntax that separates deductions from computations, and to the abstraction of assumption bases, which is factored into the semantics of the language and allows for sound evaluation. Every type-omega DPL properly contains a type-alpha DPL, which can be used to present proofs in a lucid and detailed form, exclusively in terms of primitive inference rules. Derived inference rules are expressed as user-defined methods, which are "proof recipes" that take arguments and dynamically perform appropriate deductions. Methods arise naturally via parametric abstraction over type-alpha proofs. In that light, the evaluation of a method call can be viewed as a computation that carries out a type-alpha deduction. The type-alpha proof "unwound" by such a method call is called the "certificate" of the call. Certificates can be checked by exceptionally simple type-alpha interpreters, and thus they are useful whenever we wish to minimize our trusted base. Methods are statically closed over lexical environments, but dynamically scoped over assumption bases. They can take other methods as arguments, they can iterate, and they can branch conditionally. These capabilities, in tandem with the bifurcated syntax of type-omega DPLs and their dynamic assumption-base semantics, allow the user to define methods in a style that is disciplined enough to ensure soundness yet fluid enough to permit succinct and perspicuous expression of arbitrarily sophisticated derived inference rules. We demonstrate every major feature of type-omega DPLs by defining and studying NDL-omega, a higher-order, lexically scoped, call-by-value type-omega DPL for classical zero-order natural deduction---a simple choice that allows us to focus on type-omega syntax and semantics rather than on the subtleties of the underlying logic. We start by illustrating how type-alpha DPLs naturally lead to type-omega DPLs by way of abstraction; present the formal syntax and semantics of NDL-omega; prove several results about it, including soundness; give numerous examples of methods; point out connections to the lambda-phi calculus, a very general framework for type-omega DPLs; introduce a notion of computational and deductive cost; define several instrumented interpreters for computing such costs and for generating certificates; explore the use of type-omega DPLs as general programming languages; show that DPLs do not have to be type-less by formulating a static Hindley-Milner polymorphic type system for NDL-omega; discuss some idiosyncrasies of type-omega DPLs such as the potential divergence of proof checking; and compare type-omega DPLs to other approaches to proof presentation and discovery. Finally, a complete implementation of NDL-omega in SML-NJ is given for users who want to run the examples and experiment with the language.

Detecting Digital Forgeries Using Bispectral Analysis

With the rapid increase in low-cost and sophisticated digital technology the need for techniques to authenticate digital material will become more urgent. In this paper we address the problem of authenticating digital signals assuming no explicit prior knowledge of the original. The basic approach that we take is to assume that in the frequency domain a "natural" signal has weak higher-order statistical correlations. We then show that "un-natural" correlations are introduced if this signal is passed through a non-linearity (which would almost surely occur in the creation of a forgery). Techniques from polyspectral analysis are then used to detect the presence of these correlations. We review the basics of polyspectral analysis, show how and why these tools can be used in detecting forgeries and show their effectiveness in analyzing human speech.

Advanced Programming Language Features for Executable Design Patterns "Better Patterns Through Reflection

The Design Patterns book [GOF95] presents 24 time-tested patterns that consistently appear in well-designed software systems. Each pattern is presented with a description of the design problem the pattern addresses, as well as sample implementation code and design considerations. This paper explores how the patterns from the "Gang of Four'', or "GOF'' book, as it is often called, appear when similar problems are addressed using a dynamic, higher-order, object-oriented programming language. Some of the patterns disappear -- that is, they are supported directly by language features, some patterns are simpler or have a different focus, and some are essentially unchanged.

Revised Report on the Algorithmic Language Scheme

Data and procedures and the values they amass, Higher-order functions to combine and mix and match, Objects with their local state, the message they pass, A property, a package, the control of point for a catch- In the Lambda Order they are all first-class. One thing to name them all, one things to define them, one thing to place them in environments and bind them, in the Lambda Order they are all first-class. Keywords: Scheme, Lisp, functional programming, computer languages.

Asymptotics of Perturbations to the Wave Equation

M. Hieber, I. Wood: Asymptotics of perturbations to the wave equation. In: Evolution Equations, Lecture Notes in Pure and Appl. Math., 234, Marcel Dekker, (2003), 243-252.

Twierdzenia o punktach stałych pewnych klas operatorów nieliniowych wraz z ich zastosowaniami

Wydział Matematyki i Informatyki

Consciousness CLEARS the Mind

A full understanding of consciouness requires that we identify the brain processes from which conscious experiences emerge. What are these processes, and what is their utility in supporting successful adaptive behaviors? Adaptive Resonance Theory (ART) predicted a functional link between processes of Consciousness, Learning, Expectation, Attention, Resonance, and Synchrony (CLEARS), includes the prediction that "all conscious states are resonant states." This connection clarifies how brain dynamics enable a behaving individual to autonomously adapt in real time to a rapidly changing world. The present article reviews theoretical considerations that predicted these functional links, how they work, and some of the rapidly growing body of behavioral and brain data that have provided support for these predictions. The article also summarizes ART models that predict functional roles for identified cells in laminar thalamocortical circuits, including the six layered neocortical circuits and their interactions with specific primary and higher-order specific thalamic nuclei and nonspecific nuclei. These prediction include explanations of how slow perceptual learning can occur more frequently in superficial cortical layers. ART traces these properties to the existence of intracortical feedback loops, and to reset mechanisms whereby thalamocortical mismatches use circuits such as the one from specific thalamic nuclei to nonspecific thalamic nuclei and then to layer 4 of neocortical areas via layers 1-to-5-to-6-to-4.