Ref HAL: hal-01561696_v1
Ref Arxiv: 1707.01373
DOI: 10.1088/1367-2630/aaad39
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4 Citations
Résumé:

The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. With this approach we consider the genomic organization of such a protein-DNA cluster around a single high-affinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Commentaires: 14 pages, 7 figures

Ref HAL: hal-01517340_v1
Ref Arxiv: 1705.00855
DOI: 10.1063/1.5006924
WoS: 000431291900023
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5 Citations
Résumé:

In a dense colloidal suspension at a volume fraction slightly lower than that of its glass transition, we follow the trajectories of an assembly of tracers over a large time window. We define a local activity, which quantifies the local tendency of the system to rearrange. We determine the statistics of the time and space integrated activity, and we argue that it develops a low activity tail that comes on a par with the onset of glassy behavior and heterogeneous dynamics. These rare events may be interpreted as the reflection of an underlying dynamic phase transition.

Commentaires: 10 pages, 15 figures

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Ref Arxiv: 1702.05497
DOI: 10.1007/s00220-018-3114-z
WoS: WOS:000428927100008
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7 Citations
Résumé:

We analyze the modular properties of D3-brane instanton corrections to the hypermultiplet moduli space in type IIB string theory compactified on a Calabi-Yau threefold. In Part I, we found a necessary condition for the existence of an isometric action of S-duality on this moduli space: the generating function of DT invariants in the large volume attractor chamber must be a vector-valued mock modular form with specified modular properties. In this work, we prove that this condition is also sufficient at two-instanton order. This is achieved by producing a holomorphic action of SL(2,Z) on the twistor space which preserves the holomorphic contact structure. The key step is to cancel the anomalous modular variation of the Darboux coordinates by a local holomorphic contact transformation, which is generated by a suitable indefinite theta series. For this purpose we introduce a new family of theta series of signature (2,n-2), find their modular completion, and conjecture sufficient conditions for their convergence, which may be of independent mathematical interest.

Commentaires: 24+24 pages

Ref HAL: hal-02090515_v1
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Une méthode permettant la mesure spectrocolorimétrique des solutions opaques très diffusantes, de type jus de fruits, dans leur packaging d'origine. Les appareils courants sur le marché (spectrocolorimètres) ne permettent pas de réaliser cette mesure. La méthode s'affranchit des contraintes présentes dans ces appareils.

Ref HAL: hal-01334181_v1
Ref Arxiv: 1606.05495
DOI: 10.1007/s00029-018-0444-9
WoS: WOS:000449794800003
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7 Citations
Résumé:

Theta series for lattices with indefinite signature $(n_+,n_-)$ arise in many areas of mathematics including representation theory and enumerative algebraic geometry. Their modular properties are well understood in the Lorentzian case ($n_+=1$), but have remained obscure when $n_+\geq 2$. Using a higher-dimensional generalization of the usual (complementary) error function, discovered in an independent physics project, we construct the modular completion of a class of `conformal' holomorphic theta series ($n_+=2$). As an application, we determine the modular properties of a generalized Appell-Lerch sum attached to the lattice ${\operatorname A}_2$, which arose in the study of rank 3 vector bundles on $\mathbb{P}^2$. The extension of our method to $n_+>2$ is outlined.

Commentaires: 30 pages, 2 figures