Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Molecular dynamics simulation of entropy and surface tension for grain boundary of α-Fe

The grain boundary is an interface and the surface tension is one of its important thermodynamic properties. In this paper, the surface tension of the ∑9 grain boundary for α-Fe at various temperatures and pressures is calculated by means of Computer Molecular Dynamics (CMD). The results agree satisfactorily with the experimental data. It is shown that the contribution of entropy to surface tension of grain boundary can be ignored.

Energy and entropy radiated by a black hole embedded in a de Sitter braneworld

We study the Hawking radiation of a (4+n)-dimensional Schwarzschild black hole imbedded in space-time with a positive cosmological constant. The greybody and energy emission rates of scalars, fermions, bosons, and gravitons are calculated in the full range of energy. Valuable information on the dimensions and curvature of space-time is revealed. Furthermore, we investigate the entropy radiated and lost by black holes. We find their ratio near 1 in favor of the Bekenstein's conjecture.

Dynamical horizon entropy and equilibrium thermodynamics of generalized gravity theories

We study the relation between the thermodynamics and field equations of generalized gravity theories on the dynamical trapping horizon with sphere symmetry. We assume the entropy of a dynamical horizon as the Noether charge associated with the Kodama vector and point out that it satisfies the second law when a Gibbs equation holds. We generalize two kinds of Gibbs equations to Gauss-Bonnet gravity on any trapping horizon. Based on the quasilocal gravitational energy found recently for f(R) gravity and scalar-tensor gravity in some special cases, we also build up the Gibbs equations, where the nonequilibrium entropy production, which is usually invoked to balance the energy conservation, is just absorbed into the modified Wald entropy in the Friedmann-Robertson-Walker spacetime with slowly varying horizon. Moreover, the equilibrium thermodynamic identity remains valid for f(R) gravity in a static spacetime. Our work provides an alternative treatment to reinterpret the nonequilibrium correction and supports the idea that the horizon thermodynamics is universal for generalized gravity theories.

Entropy of Kaluza-Klein black hole from Kerr/CFT correspondence

We extend the recently proposed Kerr/CFT correspondence to examine the dual conformal field theory of four-dimensional Kaluza-Klein black hole in Einstein-Maxwell-Dilaton theory. For the extremal Kaluza-Klein black hole, the central charge and temperature of the dual conformal field are calculated following the approach of Guica, Hartman, Song and Strominger. Meanwhile, we show that the microscopic entropy given by the Cardy formula agrees with Bekenstein-Hawking entropy of extremal Kaluza-Klein black hole. For the non-extremal case, by studying the near-region wave equation of a neutral massless scalar field, we investigate the hidden conformal symmetry of Kaluza-Klein black hole, and find the left and right temperatures of the dual conformal field theory. Furthermore, we find that the entropy of non-extremal Kaluza-Klein black hole is reproduced by Cardy formula. (C) 2010 Elsevier B.V. All rights reserved.

Enthalpy/entropy compensation: Influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes

The effect of the context of the flanking sequence on ligand binding to DNA oligonucleotides that contain consensus binding sites was investigated for the binding of the intercalator 7-amino actinomycin D. Seven self-complementary DNA oligomers each containing a centrally located primary binding site, 5'-A-G-C-T-3', flanked on either side by the sequences (AT)(n) or (AA)(n) (with n = 2, 3, 4) and AA(AT)(2), were studied. For different flanking sequences, (AA)(n)-series or (AT)(n)-series, differential fluorescence enhancements of the ligand due to binding were observed. Thermodynamic studies indicated that the flanking sequences not only affected DNA stability and secondary structure but also modulated ligand binding to the primary binding site. The magnitude of the ligand binding affinity to the primary site was inversely related to the sequence dependent stability. The enthalpy of ligand binding was directly measured by isothermal titration calorimetry, and this made it possible to parse the binding free energy into its energetic and entropic terms.

Martensitic transformation under impact with high strain rate

This paper deals with the quantitative prediction of the volume fraction of martensitic transformation in a austenitic steel that undergoes impact with high strain rate. The coupling relations between strain, stress, strain rate, transformation rate and transformed fraction were derived from the OTC model and modified Bodner-Partom equations, where the impact process was considered as an adiabatic and no entropy-increased process (pressure less than or equal to 20GPa). The one-dimensional results were found to model and predict various experimental results obtained on 304 stainless steel under impact with high strain rate.

Direct dynamical test for deterministic chaos and optimal embedding of a chaotic time-series

We propose here a local exponential divergence plot which is capable of providing an alternative means of characterizing a complex time series. The suggested plot defines a time-dependent exponent and a ''plus'' exponent. Based on their changes with the embedding dimension and delay time, a criterion for estimating simultaneously the minimal acceptable embedding dimension, the proper delay time, and the largest Lyapunov exponent has been obtained. When redefining the time-dependent exponent LAMBDA(k) curves on a series of shells, we have found that whether a linear envelope to the LAMBDA(k) curves exists can serve as a direct dynamical method of distinguishing chaos from noise.

Direct dynamical test for deterministic chaos

We present a direct and dynamical method to distinguish low-dimensional deterministic chaos from noise. We define a series of time-dependent curves which are closely related to the largest Lyapunov exponent. For a chaotic time series, there exists an envelope to the time-dependent curves, while for a white noise or a noise with the same power spectrum as that of a chaotic time series, the envelope cannot be defined. When a noise is added to a chaotic time series, the envelope is eventually destroyed with the increasing of the amplitude of the noise.

Some comments on the stability theory of mhd shock waves

The stability (evolutionarity) problem for a kind of MHD shock waves is discussed in this paper. That is to solve the interaction problem of MHD shock waves with (2-dimensional) oblique incident disturbances. In other words, the result of gasdynamic shocks is generalized to the case of MHD shocks. The previous conclusion of stability theory of MHD shock waves obtained from the solution of interaction problem of MHD shock wave with (one-dimensional) normal shock wave is that only fast and slow shocks are stable, and intermediate shocks are unstable. However, the results of this paper show that when the small disturbances are the Alfven waves a new stability condition which is related to the parameters in front of and behind the shock wave is derived. When the disturbances are entropy wave and fast and slow magneto acoustic waves the stability condition is related to the frequency of small disturbances. As the limiting ease, i. e. when a normal incident (reflection, refraction) is consid...更多ered, the fast and slow shocks are unstable. The results also show that the conclusion drawn by Kontorovich is invalid for the stability theory of shock waves.

Spatiotemporal segmentation based on two-dimensional spatiotemporal entropic thresholding

A novel spatiotemporal segmentation technique is further developed for extracting uncovered background and moving objects from the image sequences, then the following motion estimation is performed only on the regions corresponding to moving objects. The frame difference contrast (FCON) and local variance contrast (LCON), which are related to the temporal and spatial homogeneity of the image sequence, are selected to form the 2-D spatiotemporal entropy. Then the spatial segmentation threshold is determined by maximizing the 2-D spatiotemporal entropy, and the temporal segmentation point is selected to minimize the complexity measure for image sequence coding. Since both temporal and spatial correlation of an image sequence are exploited, this proposed spatiotemporal segmentation technique can further be used to determine the positions of reference frames adaptively, hence resulting in a low bit rate. Experimental results show that this segmentation-based coding scheme is more efficient than usual fixed-size coding algorithms. (C) 1997 Society of Photo-Optical Instrumentation Engineers.