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Bin Wang

Publications and source records attributed to Bin Wang.

At least 1,099 records · Page 61Linked to original sources
arXiv2000

Correlation property of length sequences based on global structure of complete genome

This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences. The values of the exponents from these methods of these three kinds of length sequences of bacteria indicate that the long-range correlations exist in most of these sequences. The correlation have a rich variety of behaviours including the presence of anti-correlations. Further more, using the exponent $γ$, it is found that these correlations are all linear ($γ=1.0\pm 0.03$). It is also found that these sequences exhibit $1/f$ noise in some interval of frequency ($f>1$). The length of this interval of frequency depends on the length of the sequence. The shape of the periodogram in $f>1$ exhibits some periodicity. The period seems to depend on the length and the complexity of the length sequence.

physics.bio-ph↗
arXiv2000

One way to Characterize the compact structures of lattice protein model

On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact structure. The Partnum is compared with the concept Designability of protein structures emerged recently. It is shown that the highly designable structures have, on average, an atypical number of local degree of freedom. The statistical property of Partnum and its dependence on sequence length is also studied.

physics.bio-ph↗
arXiv2000

Statistically Significant Strings are Related to Regulatory Elements in the Promoter Regions of Saccharomyces cerevisiae

Finding out statistically significant words in DNA and protein sequences forms the basis for many genetic studies. By applying the maximal entropy principle, we give one systematic way to study the nonrandom occurrence of words in DNA or protein sequences. Through comparison with experimental results, it was shown that patterns of regulatory binding sites in Saccharomyces cerevisiae(yeast) genomes tend to occur significantly in the promoter regions. We studied two correlated gene family of yeast. The method successfully extracts the binding sites varified by experiments in each family. Many putative regulatory sites in the upstream regions are proposed. The study also suggested that some regulatory sites are a ctive in both directions, while others show directional preference.

physics.bio-ph↗
arXiv2000

Minimum Entropy Aproach to Word Segmentation Problems

Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at revealing the nonrandomness of the sequence as strongly as possible, by applying maximum likelihood method, we find a quantity called Segmentation Entropy that can be used to fulfill the duty. Contrary to commonplace where maximum entropy principle was applied to obtain good solution, we choose to {\em minimize} the segmentation entropy to obtain good segmentation. The concept developed in this letter can be used to study the noncoding DNA sequences, e.g., for regulatory elements prediction, in eukaryote genomes.

physics.bio-ph↗
arXiv2000

A time series model of CDS sequences in complete genome

A time series model of CDS sequences in complete genome is proposed. A map of DNA sequence to integer sequence is given. The correlation dimensions and Hurst exponents of CDS sequences in complete genome of bacteria are calculated. Using the average of correlation dimensions, some interesting results are obtained.

physics.bio-ph↗
arXiv2000

Entropy and holography constraints for inhomogeneous universes

We calculated the entropy of a class of inhomogeneous dust universes. Allowing spherical symmetry, we proposed a holographic principle by reflecting all physical freedoms on the surface of the apparent horizon. In contrast to flat homogeneous counterparts, the principle may break down in some models, though these models are not quite realistic. We refined fractal parabolic solutions to have a reasonable entropy value for the present observable universe and found that the holographic principle always holds in the realistic cases.

astro-ph↗
arXiv2000

Extreme black hole entropy obtained in an operational approach

The entropy of anti-de Sitter Reissner-Nordstrom black hole is found to be stored in the material which gathers to form it and equals to $A/4$ regardless of material states. Extending the study to two kinds of extreme black holes, we find different entropy results for the first kind of extreme black hole due to different material states. However for the second kind of extreme black hole the results of entropy are uniform independently of the material states. Relations between these results and the stability of two kinds of extreme black holes have been addressed.

hep-th↗
arXiv2000

Quasinormal modes of Reissner-Nordstr$\ddot{o}$m Anti-de Sitter Black Holes

Complex frequencies associated with quasinormal modes for large Reissner-Nordstr$\ddot{o}$m Anti-de Sitter black holes have been computed. These frequencies have close relation to the black hole charge and do not linearly scale with the black hole temperature as in Schwarzschild Anti-de Sitter case. In terms of AdS/CFT correspondence, we found that the bigger the black hole charge is, the quicker for the approach to thermal equilibrium in the CFT. The properties of quasinormal modes for $l>0$ have also been studied.

hep-th↗
arXiv2000

Entropy bound for a rotating system from Anti de Sitter black holes

General geodesic equations of the motion of spinning systems around the (3+1)-dimensional and (2+1)-dimensional rotating anti-de Sitter black holes have been obtained. Based upon these equations, we derived the entropy bound for a rotating system from Kerr-Anti de Sitter black holes and BTZ black holes, respectively. Our result coincides with that of Hod's derived from Kerr black hole, which shows that the entropy bound of the rotating system is neither dependent on the black hole parameters, nor on spacetime dimensions. It is a universal entropy bound.

gr-qc↗
arXiv1999

Holography and the generalized second law of thermodynamics in (2+1)-dimensional cosmology

The Fischler-Susskind entropy bound has been studied in (2+1)-dimensional universes with negative cosmological constant. As in all contracting universes, that bound is not satisfied. Furthermore, we found that the Fischler-Susskind bound is not compatible with a generalized second law of thermodynamics in (2+1)-dimensional cosmology, neither the classical nor the quantum version. On the other hand, the Hubble entropy bound has been constructed in (2+1)-dimensional cosmology and it is shown compatible with the generalized second law of thermodynamics.

hep-th↗
arXiv1999

Entropy of extreme three-dimensional charged black holes

It is shown that three-dimensional charged black holes can approach the extreme state at nonzero temperature. Unlike even dimensional cases, the entropy for the extreme three-dimensional charged black hole is uniquely described by the Bekenstein-Hawking formula, regardless of different treatments of preparing the extreme black hole, namely, Hawking's treatment and Zaslavskii's treatment.

hep-th↗
arXiv1999

Holography in (2+1)-dimensional cosmological models

The cosmic holographic principle suggested by Fischler and Susskind has been examined in (2+1)-dimensional cosmological models. Analogously to the (3+1)-dimensional counterpart, the holographic principle is satisfied in all flat and open universes. For (2+1)-dimensional closed universes the holographic principle cannot be realized in general. The principle cannot be maintained, neither introducing negative pressure matter nor matter with highly unconventional equation of state.

hep-th↗
arXiv1999

Conservative Currents of Boundary Charges in $AdS_{2+1}$ Gravity

The boundary charges which constitute the Virasoro algebra in 2+1 dimensional anti-de Sitter gravity are derived by way of Noether theorem and diffeomorphic invariance. It shows that the boundary charges under discussion recently exhaust all the independent nontrivial charges available. Therefore, the state counting via the Virasoro algebra is complete.

hep-th↗
arXiv1999

Superalgebra and Conservative Quantities in N=1 Self-dual Supergravity

The N=1 self-dual supergravity has SL(2,C) and the left-handed and right -handed local supersymmetries. These symmetries result in SU(2) charges as the angular-momentum and the supercharges. The model possesses also the invariance under the general translation transforms and this invariance leads to the energy-momentum. All the definitions are generally covariant . As the SU(2) charges and the energy-momentum we obtained previously constituting the 3-Poincare algebra in the Ashtekar's complex gravity, the SU(2) charges, the supercharges and the energy-momentum here also restore the super-Poincare algebra, and this serves to support the reasonableness of their interpretations.

hep-th↗
arXiv1999

Entropy, topology of two-dimensional extreme black holes

Through direct thermodynamic calculations we have shown that different classical entropies of two-dimensional extreme black holes appear due to two different treatments, namely Hawking's treatment and Zaslavskii's treatment. Geometrical and topological properties corresponding to these different treatments are investigated. Quantum entropies of the scalar fields on the backgrounds of these black holes concerning different treatments are also exhibited. Different results of entropy and geometry lead us to argue that there are two kinds of extreme black holes in the nature. Explanation of black hole phase transition has also been given from the quantum point of view.

gr-qc↗
arXiv1999

Primordial Black Hole Formation from Inflaton

Measurements of the distances to SNe Ia have produced strong evidence that the Universe is really accelarating, implying the existence of a nearly uniform component of dark energy with the simplest explanation as a cosmological constant. In this paper a small changing cosmological term is proposed, which is a function of a slow-rolling scalar field, by which the de Sitter primordial black holes' properties, for both charged and uncharged cases, are carefully examined and the relationship between the black hole formation and the energy transfer of the inflaton within this cosmological term is eluciated

hep-ph↗
arXiv1998

Quantum entropy of two-dimensional extreme charged dilaton black hole

By using Hawking's treatment as well as Zaslavskii's treatment respectively and the brick wall model, two different values of classical entropy and quantum entropy of scalar fields in the two-dimensional extreme charged dilaton black hole backgrounds have been obtained. A new divergent term emerges in the quantum entropy under the extreme limit for Zaslavskii's treatment and its connection with the phase transition has been addressed.

gr-qc↗