Generalized binomial and negative binomial distributions of order<Emphasis Type="Italic">k</Emphasis> by the<Emphasis Type="Italic">l</Emphasis>-overlapping enumeration scheme

In this paper, we investigate the exact distribution of the waiting time for ther-th ℓ-overlapping occurrence of success-runs of a specified length in a sequence of two state Markov dependent trials. The probability generating functions are derived explicitly, and as asymptotic results, relationships of a negative binomial distribution of orderk and an extended Poisson distribution of orderk are discussed. We provide further insights into the run-related problems from the viewpoint of the ℓ-overlapping enumeration scheme. We also study the exact distribution of the number of ℓ-overlapping occurrences of success-runs in a fixed number of trials and derive the probability generating functions. The present work extends several properties of distributions of orderk and leads us a new type of geneses of the discrete distributions.     

Stability and vibrational spectra of toroidal isomers of C 240

To study the thermodynamic and mechanical stability of toroidal isomers of C ₂₄₀, we use a semi-empirical tight-binding theory and calculate their electronic structure, cohesive energy and vibrational spectra within the harmonic approximation. From these, we deduce their free energy at temperatures up to 1500K. The results are also compared to the isomer with icosahedral symmetry. Finally, we discuss within this approach, their stability and abundance.     

Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.     

Waiting time problems for a sequence of discrete random variables

Let X ₁, X ₂,... be a sequence of nonnegative integer valued random variables.For each nonnegative integer i, we are given a positive integer k _i . For every i = 0, 1, 2,..., E _i denotes the event that a run of i of length k _i occurs in the sequence X ₁, X ₂,.... For the sequence X ₁, X ₂,..., the generalized pgf's of the distributions of the waiting times until the r-th occurrence among the events % MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXafv3ySLgzGmvETj2BSbqefm0B1jxALjhiov2D% aebbfv3ySLgzGueE0jxyaibaiiYdd9qrFfea0dXdf9vqai-hEir8Ve% ea0de9qq-hbrpepeea0db9q8as0-LqLs-Jirpepeea0-as0Fb9pgea% 0lrP0xe9Fve9Fve9qapdbaqaaeGacaGaaiaabeqaamaabaabcaGcba% WaaiWabeaacaWGfbWaaSbaaSqaaiaadMgaaeqaaaGccaGL7bGaayzF% aaWaa0baaSqaaiaadMgacqGH9aqpcaaIWaaabaGaeyOhIukaaaaa!43D8!\[\left\{ {E_i } \right\}_{i = 0}^\infty\]are obtained. Though our situations are general, the results are very simple. For the special cases that X's are i.i.d. and {0, 1}-valued, the corresponding results are consistent with previously published results.This research was partially supported by the ISM Cooperative Research Program (90-ISM-CRP-11) of the Institute of Statistical Mathematics.     

Stress-induced nonlinear structural transition in DNA

DNA undergoes structural transition between right-handed B form and left-handed Z form upon twisting. We describe this phenomenon as a stress-induced nonlinear excitation, and show that the twisting of a circular DNA leads to a domain wall type excitation, in which a certain length of Z domain appears with a pair of domain walls. Detailed examination of the nonlinear stress-strain relationship shows that there is an attractive interaction between the domain walls with exponential distance dependence.     

Crystal structure of copper(II) complex with N,N-bis(2-benzimidazolylmethyl)benzylamine

The copper(II) complex with N,N-bis(2-benzimidazolylmethyl)benzylamine has been synthesized and its crystal structure was determined by X-ray diffraction methods.     

Lifetime distribution and estimation problems of consecutive-k-out-of-n:F systems

Explicit formula is given for the lifetime distribution of a consecutive-k-out-of-n:F system. It is given as a linear combination of distributions of order statistics of the lifetimes of n components. We assume that the lifetimes are independent and identically distributed. The results should make it possible to treat the parametric estimation problems based on the observations of the lifetimes of the system. In fact, we take up, as some examples, the cases where the lifetimes of the components follow the exponential, the Weibull, and the Pareto distributions, and obtain feasible estimators by moment method. In particular, it is shown that the moment estimator is quite good for the exponential case in the sense that the asymptotic efficiency is close to one.This research was partially supported by the ISM Cooperative Research Program (94-ISM-CRP-5).     

Joint distributions of numbers of occurrences of a discrete pattern and weak convergence of an empirical process for the pattern

For a {0, 1}-pattern of finite length, an empirical process is introduced in order to describe the number of overlapping occurrences of the pattern at each level t[0,1] in a sequence of the corresponding indicators of i.i.d. [0, 1]-valued observations of length n. A method for obtaining the exact finite-dimensional distributions of the empirical process is given. The weak convergence of the process to a Gaussian process in D[0,1] as n tends to infinity is also established. The limiting process depends on the given pattern. The exact covariance function is compared with the asymptotic covariance function in a numerical example.     

Properties of phosphorothioate DNA analogs. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion

Ab initio HF and MP2 calculations on prototype model linkages of phosphorothioate DNA backbones illuminate the effects of phosphorothioation on electronic and structural properties of DNA backbone. The replacement of a bridging oxygen atom by sulfur in the phosphodiester linkage is energetically favored over that of replacement of a non-bridging oxygen atom. In phosphorothioate derivatives containing the P(OS)_nb moiety, the non-bridging oxygen atom always bears a higher negative charge than the non-bridging sulfur. Additional calculations on protonated (neutral) adducts suggest that phosphorothioation of the phosphodiester linkage lowers its proton affinity. Moreover, protonation of the non-bridging oxygen atom at phosphorous is favored over the protonation of the non-bridging sulfur atom for linkages containing the P(OS)_nb moiety. The ab initio calculated structural parameters are compared to the available crystallographic data of small phosphorothioate molecules and phosphorothioate oligodeoxynucleotides. These results have implications upon the biological activity of phosphorothioate DNA analogs.