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Search Results: 1 - 10 of 7500 matches for " Ivan Junier "
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Local energy approach to the dynamic glass transition
Ivan Junier
Physics , 2006, DOI: 10.1209/epl/i2006-10181-x
Abstract: We propose a new class of phenomenological models for dynamic glass transitions. The system consists of an ensemble of mesoscopic regions to which local energies are allocated. At each time step, a region is randomly chosen and a new local energy is drawn from a distribution that self-consistently depends on the global energy of the system. Then, the transition is accepted or not according to the Metropolis rule. Within this scheme, we model an energy threshold leading to a mode-coupling glass transition as in the p-spin model. The glassy dynamics is characterized by a two-step relaxation of the energy autocorrelation function. The aging scaling is fully determined by the evolution of the global energy and linear violations of the fluctuation dissipation relation are found for observables uncorrelated with the energies. Interestingly, our mean-field approach has a natural extension to finite dimension, that we briefly discuss.
Unstructured intermediate states in single protein force experiments
Ivan Junier,Felix Ritort
Physics , 2008, DOI: 10.1002/prot.21802
Abstract: Recent single-molecule force measurements on single-domain proteins have highlighted a three-state folding mechanism where a stabilized intermediate state (I) is observed on the folding trajectory between the stretched state and the native state. Here we investigate on-lattice protein-like heteropolymer models that lead to a three-state mechanism and show that force experiments can be useful to determine the structure of I. We have mostly found that I is composed of a core stabilized by a high number of native contacts, plus an unstructured extended chain. The lifetime of I is shown to be sensitive to modifications of the protein that spoil the core. We then propose three types of modifications--point mutations, cuts, and circular permutations--aiming at: (1) confirming the presence of the core and (2) determining its location, within one amino acid accuracy, along the polypeptide chain. We also propose force jump protocols aiming to probe the on/off-pathway nature of I.
Single-domain protein folding: a multi-faceted problem
Ivan Junier,Felix Ritort
Physics , 2008, DOI: 10.1063/1.2345624
Abstract: We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape approach. As far as experiments are concerned, we focus on the recent development of single-molecule techniques. In particular, we compare the results obtained with two main techniques: single protein force measurements with optical tweezers and single-molecule fluorescence in studies on the same protein (RNase H). This allows us to point out some controversial issues such as the nature of the denatured and intermediate states and possible folding pathways. After reviewing the various numerical simulation techniques, we show that on-lattice protein-like models can help to understand many controversial issues.
Synteny in Bacterial Genomes: Inference, Organization and Evolution
Ivan Junier,Olivier Rivoire
Quantitative Biology , 2013,
Abstract: Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized genes from multiple genomes, describe their organization, and study their evolutionary history. In bacterial genomes, we thus identify synteny units, or "syntons", which are clusters of proximal genes that encompass and extend operons. The size distribution of these syntons divide them into large syntons, which correspond to fundamental macro-molecular complexes of bacteria, and smaller ones, which display a remarkable exponential distribution of sizes. This distribution is "universal" in two respects: it holds for vastly different genomes, and for functionally distinct genes. Similar statistical laws have been reported previously in studies of bacterial genomes, and generally attributed to purifying selection or neutral processes. Here, we perform a new analysis based on the concept of parsimony, and find that the prevailing evolutionary mechanism behind the formation of small syntons is a selective process of gene aggregation. Altogether, our results imply a common evolutionary process that selectively shapes the organization and diversity of bacterial genomes.
Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization
Ivan Junier,Olivier Martin ,Fran?ois Képès
PLOS Computational Biology , 2010, DOI: 10.1371/journal.pcbi.1000678
Abstract: Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close by. This is motivated by recurrent evidence that there exist physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.
Periodic pattern detection in sparse boolean sequences
Ivan Junier, Joan Hérisson, Fran?ois Képès
Algorithms for Molecular Biology , 2010, DOI: 10.1186/1748-7188-5-31
Abstract: The algorithm is particularly robust with respect to strong signal distortions such as the addition of 1's at arbitrary positions (contaminated data), the deletion of existing 1's in the sequence (missing data) and the presence of disorder in the position of the 1's (noise). This robustness property stems from an appropriate exploitation of the remarkable alignment properties of periodic points in solenoidal coordinates.The efficiency of the algorithm is demonstrated in situations where standard Fourier-based spectral methods are poorly adapted. We also show how the proposed framework allows to identify the 1's that participate in the periodic trends, i.e. how the framework allows to allocate a positional score to genes, in the same spirit of the sequence score. The software is available for public use at http://www.issb.genopole.fr/MEGA/Softwares/iSSB_SolenoidalApplication.zip webcite.There is increasing evidence that the organization of the genome plays a crucial role in the interplay between genetic regulation and chromosome structure. At the smallest scale, several experimental studies have highlighted the importance of the positions of the transcription factor binding sites in the functioning of small transcriptional regulatory networks [1-3]. At a larger - but still local - scale, in bacteria many transcription units are known to be located along the DNA close to the gene that encodes their regulating transcription factors [4-6]. At the global scale of the chromosome, both in Escherichia coli and in Saccharomyces cerevisiae, it has been previously realized that the genes that are regulated by the same transcription factor have a tendency to be periodically spaced along the DNA [7,8]. Recently, the relative positions of phylogenetically conserved gene pairs were also shown to tend to periodically organize along the DNA in E. coli [9]. Such periodic organization has been proposed to be responsible for the spatial co-localization of co-regulated genes [10]; indee
Recovery of free energy branches in single molecule experiments
Ivan Junier,Alessandro Mossa,Maria Manosas,Felix Ritort
Physics , 2009, DOI: 10.1103/PhysRevLett.102.070602
Abstract: We present a method for determining the free energy of coexisting states from irreversible work measurements. Our approach is based on a fluctuation relation that is valid for dissipative transformations in partially equilibrated systems. To illustrate the validity and usefulness of the approach, we use optical tweezers to determine the free energy branches of the native and unfolded states of a two-state molecule as a function of the pulling control parameter. We determine, within 0.6 kT accuracy, the transition point where the free energies of the native and the unfolded states are equal.
Experimental free energy measurements of kinetic molecular states using fluctuation theorems
Anna Alemany,Alessandro Mossa,Ivan Junier,Felix Ritort
Quantitative Biology , 2013, DOI: 10.1038/nphys2375
Abstract: Recent advances in non-equilibrium statistical mechanics and single molecule technologies make it possible to extract free energy differences from irreversible work measurements in pulling experiments. To date, free energy recovery has been focused on native or equilibrium molecular states, whereas free energy measurements of kinetic states (i.e. finite lifetime states that are generated dynamically and are metastable) have remained unexplored. Kinetic states can play an important role in various domains of physics, such as nanotechnology or condensed matter physics. In biophysics, there are many examples where they determine the fate of molecular reactions: protein and peptide-nucleic acid binding, specific cation binding, antigen-antibody interactions, transient states in enzymatic reactions or the formation of transient intermediates and non-native structures in molecular folders. Here we demonstrate that it is possible to obtain free energies of kinetic states by applying extended fluctuation relations. This is shown by using optical tweezers to mechanically unfold and refold DNA structures exhibiting intermediate and misfolded kinetic states.
CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus
Ivan Junier,Ryan Dale,Chunhui Hou,Fran?ois Képès,Ann Dean
Quantitative Biology , 2012, DOI: 10.1093/nar/gks536
Abstract: The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the 3-dimensional folding of a 1 Mbp region of human chromosome 11 containing the {\beta}-globin genes by integrating looping interactions of the insulator protein CTCF determined comprehensively by chromosome conformation capture (3C) into a polymer model of chromatin. We find that CTCF-mediated cell type specific interactions in erythroid cells are organized to favor contacts known to occur in vivo between the {\beta}-globin locus control region (LCR) and genes. In these cells, the modeled {\beta}-globin domain folds into a globule with the LCR and the active globin genes on the periphery. By contrast, in non-erythroid cells, the globule is less compact with few but dominant CTCF interactions driving the genes away from the LCR. This leads to a decrease in contact frequencies that can exceed 1000-fold depending on the stiffness of the chromatin and the exact positioning of the genes. Our findings show that an ensemble of CTCF contacts functionally affects spatial distances between control elements and target genes contributing to chromosomal organization required for transcription.
Tailoring symmetry groups using external alternate fields
I. Junier,J. Kurchan
Physics , 2002, DOI: 10.1209/epl/i2003-00583-2
Abstract: Macroscopic systems with continuous symmetries subjected to oscillatory fields have phases and transitions that are qualitatively different from their equilibrium ones. Depending on the amplitude and frequency of the fields applied, Heisenberg ferromagnets can become XY or Ising-like -or, conversely, anisotropies can be compensated -thus changing the nature of the ordered phase and the topology of defects. The phenomena can be viewed as a dynamic form of "order by disorder".
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