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101.
W. Grüner R. Giegerich D. Strothmann C. Reidys J. Weber I. L. Hofacker P. F. Stadler P. Schuster 《Monatshefte für Chemie / Chemical Monthly》1996,127(4):355-374
Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).
Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke
Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.相似文献
102.
《Discrete Mathematics》2022,345(3):112721
This paper studies thresholds in random generalized Johnson graphs for containing large cycles, i.e. cycles of variable length growing with the size of the graph. Thresholds are obtained for different growth rates. 相似文献
103.
本文研究了无界域上的带有随机初值的复值Ginzburg-Landau方程.首先, 基于解过程的全局适定性, 建立了带有随机初值的Ginzburg-Landau方程的平均随机动力系统.然后, 证明了弱拉回平均随机吸引子的存在唯一性以及随机吸引子的周期性,并将其进一步推广到加权空间L2(?, L2σ(R)). 相似文献
104.
The computation ofL
1 smoothing splines on large data sets is often desirable, but computationally infeasible. A locally weighted, LAD smoothing spline based smoother is suggested, and preliminary results will be discussed. Specifically, one can seek smoothing splines in the spacesW
m
(D), with [0, 1]
n
D. We assume data of the formy
i
=f(t
i
)+
i
,i=1,..., N with {t
i
}
i=1
N
D, the
i
are errors withE(
i
)=0, andf is assumed to be inW
m
. An LAD smoothing spline is the solution,s
, of the following optimization problem
相似文献
105.
András Telcs 《Journal of Theoretical Probability》1995,8(1):77-96
This paper continues the study of exponentsd(x), d
(x), d
R
(x) andd
(x) for graphG; and the nearest neighbor random walk {X
n
}
nN
onG, if the starting pointX
0=x is fixed. These exponents are responsible for the geometric, resistance, diffusion and spectral properties of the graph. The main concern of this paper is the relation of these exponents to the spectral density of the transition matrix. A series of new exponentse, e
,e
R
,e
are introduced by allowingx to vary along the vertices. The results suggest that the geometric and resistance properties of the graph are responsible for the diffusion speed on the graph. 相似文献
106.
Let {X
t:0} denote random walk in the random waiting time model, i.e., simple random walk with jump ratew
–1(X
t), where {w(x):xd} is an i.i.d. random field. We show that (under some mild conditions) theintermediate scattering function
F(q,t)=E
0
(qd) is completely monotonic int (E
0 denotes double expectation w.r.t. walk and field). We also show that thedynamic structure factor
S(q, w)=2
0
cos(t)F(q, t) exists for 0 and is strictly positive. Ind=1, 2 it diverges as 1/||1/2, resp. –ln(||), in the limit 0; ind3 its limit value is strictly larger than expected from hydrodynamics. This and further results support the conclusion that the hydrodynamic region is limited to smallq and small such that ||D |q|2, whereD is the diffusion constant. 相似文献
107.
F. den Hollander 《Journal of statistical physics》1994,75(5-6):891-918
Some fifteen years ago, Shuler formulated three conjectures relating to the large-time asymptotic properties of a nearest-neighbor random walk on 2 that is allowed to make horizontal steps everywhere but vertical steps only on a random fraction of the columns. We give a proof of his conjectures for the situation where the column distribution is stationary and satisfies a certain mixing codition. We also prove a strong form of scaling to anisotropic Brownian motion as well as a local limit theorem. The main ingredient of the proofs is a large-deviation estimate for the number of visits to a random set made by a simple random walk on . We briefly discuss extensions to higher dimension and to other types of random walk.Dedicated to Prof. K. E. Shuler on the occasion of his 70th birthday, celebrated at a Symposium in his honor on July 13, 1992, at the University of California at San Diego, La Jolla, California. 相似文献
108.
Jerry W. Slootstra Wouter C. Puijk Gerard J. Ligtvoet Jan P. M. Langeveld Rob H. Meloen 《Molecular diversity》1996,1(2):87-96
Summary Two small random peptide libraries, one composed of 4550 dodecapeptides and one of 8000 tripeptides, were synthesized in newly developed credit-card format miniPEPSCAN cards (miniPEPSCAN libraries). Each peptide was synthesized in a discrete well (455 peptides/card). The two miniPEPSCAN libraries were screened with three different monoclonal antibodies (Mabs). Two other random peptide libraries, expressed on the wall of bacteria (recombinant libraries) and composed of 107 hexa- and octapeptides, were screened with the same three Mabs. The aim of this study was to compare the amino acid sequence of peptides selected from small and large pools of random peptides and, in this way, investigate the potential of small random peptide libraries. The screening of the two miniPEPSCAN libraries resulted in the identification of a surprisingly large number of antibody-binding peptides, while the screening of the large recombinant libraries, using the same Mabs, resulted in the identification of only a small number of peptides. The large number of peptides derived from the small random peptide libraries allowed the determination of consensus sequences. These consensus sequences could be related to small linear and nonlinear parts of the respective epitopes. The small number of peptides derived from the large random peptide libraries could only be related to linear epitopes that were previously mapped using small libraries of overlapping peptides covering the antigenic protein. Thus, with respect to the cost and speed of identifying peptides that resemble linear and nonlinear parts of epitopes, small diversity libraries based on synthetic peptides appear to be superior to large diversity libraries based on expression systems.Abbreviations ABTS
2,2-azino-di-3-ethylbenzthiazoline sulfonate
- EGF
epidermal growth factor
- Mab
monoclonal antibody
- ODccd
optical density obtained using CCD camera
- RAMPO
rabbit-antimouse peroxidase
- SDS
sodium dodecylsulfate
- TGEV
transmissible gastroenteritis virus 相似文献
109.
Richard C. Bradley 《Journal of Theoretical Probability》1996,9(3):659-678
Schmidt(10) showed that if the family of distributions of the partial sums of a strictly stationary random sequence is tight, then that random sequence is a coboundary. Here an analog of that result is proved for some sequences of random matrices, with partial sums replaced by matrix products. 相似文献
110.
We propose an algorithm for the computation ofL
1 (LAD) smoothing splines in the spacesW
M
(D), with
. We assume one is given data of the formy
i
=(f(t
i
) +
i
, i=1,...,N with {itti}
i=1
N D
, the
i
are errors withE(
i
)=0, andf is assumed to be inW
M
. The LAD smoothing spline, for fixed smoothing parameter0, is defined as the solution,s
, of the optimization problem
(1/N)
i=1
N
¦y
i
–g(t
i
¦+J
M
(g), whereJ
M
(g) is the seminorm consisting of the sum of the squaredL
2 norms of theMth partial derivatives ofg. Such an LAD smoothing spline,s
, would be expected to give robust smoothed estimates off in situations where the
i
are from a distribution with heavy tails. The solution to such a problem is a thin plate spline of known form. An algorithm for computings
is given which is based on considering a sequence of quadratic programming problems whose structure is guided by the optimality conditions for the above convex minimization problem, and which are solved readily, if a good initial point is available. The data driven selection of the smoothing parameter is achieved by minimizing aCV() score of the form
.The combined LAD-CV smoothing spline algorithm is a continuation scheme in 0 taken on the above SQPs parametrized in, with the optimal smoothing parameter taken to be that value of at which theCV() score first begins to increase. The feasibility of constructing the LAD-CV smoothing spline is illustrated by an application to a problem in environment data interpretation. 相似文献
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