اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدMinimum-Free-Energy Distribution of RNA Secondary Structures: Entropic and Thermodynamic Properties of Rare Events
145
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
We study the distribution of the minimum free energy (MFE) for the Turner model of pseudoknot free RNA secondary structures over ensembles of random RNA sequences. In particular, we are interested in those rare and intermediate events of unexpected low MFEs. Generalized ensemble Markov-chain Monte Carlo methods allow us to explore the rare-event tail of the MFE distribution down to probabilities like $10^{-70}$ and to study the relationship between the sequence entropy and structural properties for sequence ensembles with fixed MFEs. Entropic and structural properties of those ensembles are compared with natural RNA of the same reduced MFE (z-score).
قيم البحث
اقرأ أيضاً
We perform numerical simulations to study the optimal path problem on disordered hierarchical graphs with effective dimension d=2.32. Therein, edge energies are drawn from a disorder distribution that allows for positive and negative energies. This i
nduces a behavior which is fundamentally different from the case where all energies are positive, only. Upon changing the subtleties of the distribution, the scaling of the minimum energy path length exhibits a transition from self-affine to self-similar. We analyze the precise scaling of the path length and the associated ground-state energy fluctuations in the vincinity of the disorder critical point, using a decimation procedure for huge graphs. Further, using an importance sampling procedure in the disorder we compute the negative-energy tails of the ground-state energy distribution up to 12 standard deviations away from its mean. We find that the asymptotic behavior of the negative-energy tail is in agreement with a Tracy-Widom distribution. Further, the characteristic scaling of the tail can be related to the ground-state energy flucutations, similar as for the directed polymer in a random medium.
A complete understanding of real networks requires us to understand the consequences of the uneven interaction strengths between a systems components. Here we use the minimum spanning tree (MST) to explore the effect of weight assignment and network
topology on the organization of complex networks. We find that if the weight distribution is correlated with the network topology, the MSTs are either scale-free or exponential. In contrast, when the correlations between weights and topology are absent, the MST degree distribution is a power-law and independent of the weight distribution. These results offer a systematic way to explore the impact of weak links on the structure and integrity of complex networks.
We show that, in a broad class of continuous time random walks (CTRW), a small external field can turn diffusion from standard into anomalous. We illustrate our findings in a CTRW with trapping, a prototype of subdiffusion in disordered and glassy ma
terials, and in the Levy walk process, which describes superdiffusion within inhomogeneous media. For both models, in the presence of an external field, rare events induce a singular behavior in the originally Gaussian displacements distribution, giving rise to power-law tails. Remarkably, in the subdiffusive CTRW, the combined effect of highly fluctuating waiting times and of a drift yields a non-Gaussian distribution characterized by long spatial tails and strong anomalous superdiffusion.
We carefully investigate the two fundamental assumptions in the Stillinger-Weber analysis of the inherent structures (ISs) in the energy landscape and come to conclude that they cannot be validated. This explains some of the conflicting results betwe
en their conclusions and some recent rigorous and exact results. Our analysis shows that basin free energies, and not ISs, are useful for understanding glasses.
Local entropic loss functions provide a versatile framework to define architecture-aware regularization procedures. Besides the possibility of being anisotropic in the synaptic space, the local entropic smoothening of the loss function can vary durin
g training, thus yielding a tunable model complexity. A scoping protocol where the regularization is strong in the early-stage of the training and then fades progressively away constitutes an alternative to standard initialization procedures for deep convolutional neural networks, nonetheless, it has wider applicability. We analyze anisotropic, local entropic smoothenings in the language of statistical physics and information theory, providing insight into both their interpretation and workings. We comment some aspects related to the physics of renormalization and the spacetime structure of convolutional networks.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
