相关论文: Analysis of correlation structures in the Synechoc…
Resurgence theory implies that the non-perturbative (NP) and perturbative (P) data in a QFT are quantitatively related, and that detailed information about non-perturbative saddle point field configurations of path integrals can be…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression…
Complex periodic structures inherit spectral properties from the constituent parts of their unit cells, chiefly their spectral band gaps. Exploiting this intuitive principle, which is made precise in this work, means spectral features of…
Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory…
A full understanding of transport in dense, interacting suspensions requires analysis frameworks sensitive to self and collective dynamics across all relevant spatial and temporal scales. Here we introduce a trajectory-free approach to…
Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. In the form of the correlation distance of nucleotide…
We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from binding…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Understanding the function of network motifs in an attempt to gain insight into how their combinations create larger reaction networks that drive cellular functions, has been a longstanding pursuit of systems biology. One specific objective…
Stochastic systems feature, in general, both coherent dynamics and incoherent transitions between different states. We propose a method to identify the coherent part in the full counting statistics for the transitions. The proposal is…
Sensory stimuli in animals are encoded into spike trains by neurons, offering advantages such as sparsity, energy efficiency, and high temporal resolution. This paper presents a signal processing framework that deterministically encodes…
Out of equilibrium, the lack of reciprocity is the rule rather than the exception. Non-reciprocal interactions occur, for instance, in networks of neurons, directional growth of interfaces, and synthetic active materials. While wave…
Entangled qubits transported through space is a key element in many prospective quantum information systems, from long-distance quantum communication to large modular quantum processors. The moving qubits are decohered by time- and…
The richness of many complex systems stems from the interactions among their components. The higher-order nature of these interactions, involving many units at once, and their temporal dynamics constitute crucial properties that shape the…
Previous investigation of coding sequence lengths (CDS) in the bacterial circular chromosome revealed short range correlation in the series of these data. We have further analyzed the averaged periodograms of these series and we found that…
We propose a quantum-Hamiltonian-learning-based sequential reconstruction framework for dynamic two-dimensional magnetic-field maps using a local likelihood model derived from a nitrogen-vacancy-center spin-1 Hamiltonian. Local measurements…
Short tandem repeats (STRs) are low-entropy regions in the genome, consisting of a short (1-6 bp) unit that is consecutively repeated multiple times. They are known for high mutational instability, due to so-called stutter-mutations, in…
We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function,…
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.…