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Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…
In this contribution, I will discuss two topics related to the clustering of atomic nuclei. The first is dual character of the ground state. Recently, it was pointed out that the ground states of atomic nuclei have dual character of shell…
The paper tackles the problem of clustering multiple networks, directed or not, that do not share the same set of vertices, into groups of networks with similar topology. A statistical model-based approach based on a finite mixture of…
The description of complex configuration is a difficult issue. We present a powerful technique for cluster identification and characterization. The scheme is designed to treat with and analyze the experimental and/or simulation data from…
Identifying and explaining the structure of complex networks at different scales has become an important problem across disciplines. At the mesoscale, modular architecture has attracted most of the attention. At the macroscale, other…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
In this paper, we explain why the chaotic model (CM) of Bahi and Michel (2008) accurately simulates gene mutations over time. First, we demonstrate that the CM model is a truly chaotic one, as defined by Devaney. Then, we show that…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
We study the dynamical properties of the ordered phases obtained in a coupled nonequilibrium system describing advection of two species of particles by a stochastically evolving landscape. The local dynamics of the landscape also gets…
Clustering of gene expression time series gives insight into which genes may be coregulated, allowing us to discern the activity of pathways in a given microarray experiment. Of particular interest is how a given group of genes varies with…
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement of strand-displacement DNA computing, a large class of…
A relational dataset is often analyzed by optimally assigning a label to each element through clustering or ordering. While similar characterizations of a dataset would be achieved by both clustering and ordering methods, the former has…
Perturbing fluids of neutrons and protons (nuclear matter) may lead, as the most catastrophic effect, to the rearrangement of the fluid into clusters of nucleons. A similar process may occur in a single atomic nucleus undergoing a violent…
We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a…
We study the synchronization of coupled maps on a variety of networks including regular one and two dimensional networks, scale free networks, small world networks, tree networks, and random networks. For small coupling strengths nodes show…
We review some recent work on the synchronization of coupled dynamical systems on a variety of networks. When nodes show synchronized behaviour, two interesting phenomena can be observed. First, there are some nodes of the floating type…
We show that "dry" active nematics, e.g. collections of shaken elongated granular particles, exhibit large-scale spatiotemporal chaos made of interacting dense, ordered, band-like structures in a parameter region including the linear onset…
Recent developments in many-body quantum chaos have raised the issue of correlations between different families of levels in the spectra of random fermionic systems. It seems that rotational invariance is sufficient to force an otherwise…
We demonstrate particle clustering on macroscopic scales in a coupled nonequilibrium system where two species of particles are advected by a fluctuating landscape and modify the landscape in the process. The phase diagram generated by…