DORIGNAC Jerome
Organisme : Université Montpellier
Maître de Conférences
Jerome.DORIGNAC
umontpellier.fr
0467144692
Bureau: 40, Etg: 1, Bât: 13  Site : Campus Triolet
Administration Nationale: 
Curriculum Vitae: 
 1995/00: PhD, Ecole Polytechnique (CPHT, Palaiseau).  2000/02: MaxPlanckInstitut (MPIPKS, Dresden)  2002/04: LOCNET Fellow, Warwick University & HeriotWatt University (Edinburgh).  2004/08: Research Assistant Prof. (Boston University, Boston) 
Activités de Recherche: 
Main Research Topics:  Discrete Nonlinear Schrodinger Equations  Discrete Breathers (classical and quantum)  Vibration of Complex Mechanical Structures (MEMs and NEMs)  Nonlinear supratransmission. 
Domaines de Recherche:  Science non linéaire/Formation de Structures et Solitons [nlin.PS]
 Physique/Mécanique/Mécanique des structures
 Science non linéaire/Systèmes Solubles et Intégrables [nlin.SI]
 Physique/Matière Condensée/Gaz Quantiques

Dernieres productions scientifiques :


Looping and clustering model for the organization of partitioning proteins on the bacterial genome
Auteur(s): Walter J.C., David G., Dorignac J., Geniet F., Palmeri J., Parmeggiani A., Wingreen Ned s., Broedersz Chase p.
(Document sans référence bibliographique) 20170630
Ref HAL: hal01561696_v1
Ref Arxiv: 1707.01373
Ref. & Cit.: NASA ADS
Exporter : BibTex  endNote
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 ParBDNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIPSeq experiments show that ParB proteins localize around centromerelike 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 DNAbound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this proteinDNA 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 proteinDNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNAbound proteins. Conceptually, the structure of the proteinDNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this proteinDNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy proteinDNA complex. With this approach we consider the genomic organization of such a proteinDNA cluster around a single highaffinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParBlike proteins around a cognate (parS) binding site.
Commentaires: 14 pages, 7 figures, submitted



Surfing on protein waves: proteophoresis as a mechanism for bacterial genome partitioning
Auteur(s): Walter J.C., Dorignac J., Lorman V., Rech Jérôme, Bouet Jeanyves, Nollmann Marcelo, Palmeri J., Parmeggiani A., Geniet F.
(Article) Publié:
Physical Review Letters, vol. 119 p.028101 (2017)
Ref HAL: hal01493262_v1
Ref Arxiv: 1702.07372
DOI: 10.1103/PhysRevLett.119.028101
Ref. & Cit.: NASA ADS
Exporter : BibTex  endNote
Résumé: Efficient bacterial chromosome segregation typically requires the coordinated action of a threecomponent machinery, fueled by adenosine triphosphate, called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reactiondiffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from proteinprotein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation, and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a nonlinear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and traveling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.
Commentaires: 6 pages, 3 figures



The growth of windwaves in finite depth
Auteur(s): Montalvo P., Dorignac J., Manna M., Kharif C., Branger H.
(Article) Publié:
Coastal Engineering, vol. p.4956 (2013)
Ref HAL: hal00749901_v1
Ref Arxiv: 1206.1491
DOI: 10.1016/j.coastaleng.2013.02.008
Ref. & Cit.: NASA ADS
Exporter : BibTex  endNote
3 citations
Résumé: In order to study the growth of wind waves in finite depth we extend Miles' theory to the finite depth domain. A depthdependent wave growth rate is derived from the dispersion relation of the wind/water interface. A suitable dimensionless finite depth wave age parameter allows us to plot a family of wave growth curves, each family member characterized by the water depth. Two major results are that for small wave age, the wave growth rates are comparable to those of deep water and for large wave age, a finitedepth waveagelimited growth is reached, with wave growth rates going to zero. The corresponding limiting wave length and limiting phase speed are explicitely calculated in the shallow and in the deep water cases. A qualitative agreement with wellknown empirical results is established and shows the robust consistency of the linear theoretical approach.



Nonlinear supratransmission revisited
Auteur(s): Dorignac J.
Conférence invité: Nonlinear Waves in Optics NWO11 (, FR, 20110628)
Actes de conférence: , vol. p. ()
Ref HAL: hal00819807_v1
Exporter : BibTex  endNote
Résumé: Nonlinear Supratransmission (NST) was discovered by J. Léon and F. Geniet [Phys. Rev. Lett. 89, 134102 (2002)] in a chain of coupled pendula forced harmonically at one end with a frequency lying within the chain forbidden band gap. When the forcing amplitude is low enough, an evanescent wave is formed that becomes unstable at a critical value above which a sudden energy transfer occurs through the emission of gap solitons: this is NST. This phenomenon has since been observed in many different contexts and in particular in some continuous non integrable multicomponent Nonlinear Schrödinger like models used in Optics. For such models, the NST threshold is a surface whose dimension is equal to the number of components (fields) involved. I shall present an asymptotic method that permits its determination and also talk about an ultradiscrete (monomer) approach that yields both simple and reliable analytical expressions for NST manifolds.



Generation and dynamics of quadratic birefringent spatial gap solitons
Auteur(s): AnghelVasilescu P., Dorignac J., Geniet F., Léon J., Taki A.
(Article) Publié:
Physical Review A: Atomic, Molecular And Optical Physics, vol. 83 p.043836 (2011)
Ref HAL: hal00628026_v1
DOI: 10.1103/PhysRevA.83.043836
Exporter : BibTex  endNote
4 citations
Résumé: A method is proposed to generate and study the dynamics of spatial light solitons in a birefringent medium with quadratic nonlinearity. Although no analytical expression for propagating solitons has been obtained, our numerical simulations show the existence of stable localized spatial solitons in the frequency forbidden band gap of the medium. The dynamics of these objects is quite rich and manifests for instance elastic reflections, or inelastic collisions where two solitons merge and propagate as a single solitary wave. We derive the dynamics of the slowly varying envelopes of the three fields (second harmonic pump and twocomponent signal) and study this new system theoretically. We show that it does present a threshold for nonlinear supratransmission that can be calculated from a series expansion approach with a very high accuracy. Specific physical implications of our theoretical predictions are illustrated on LiGaTe2 (LGT) crystals. Once irradiated by a cw laser beam of 10 mu m wavelength, at an incidence beyond the extinction angle, such crystals will transmit light, in the form of spatial solitons generated in the nonlinear regime above the nonlinear supratransmission threshold.

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