Papers by Christophe Oguey
Journal of Physics: Conference Series, 2017
We study the quantum diffusion of charge carriers in octagonal tilings. Our numerical results sho... more We study the quantum diffusion of charge carriers in octagonal tilings. Our numerical results show a power law decay of the wave-packet spreading, L(t) ∝ t β , characteristic of critical states in quasicrystals at large time t. For many energies states are sub-diffusive, i.e. β < 0.5, and thus conductivity increases when the amount of defects (static defects and/or temperature) increases.
Journal of Biomolecular Structure and Dynamics, 2015
Journal of chemical theory and computation, Jan 20, 2017
The nucleosome is the fundamental unit of eukaryotic genome packaging in the chromatin. In this c... more The nucleosome is the fundamental unit of eukaryotic genome packaging in the chromatin. In this complex, the DNA wraps around eight histone proteins to form a super-helical double helix. The resulting bending, stronger than anything observed in free DNA, raises the question to how such a distortion is stabilized by the proteic and solvent environments. In this work, the DNA-histone interface in solution was exhaustively analyzed from nucleosome structures generated by molecular dynamics. An original Voronoi tessellation technique, measuring the topology of interacting elements without any empirical or subjective adjustment, was used to characterize the interface in terms of contact area and occurrence. Our results revealed an interface more robust than previously known, combining extensive, long-lived non-electrostatic and electrostatic interactions between DNA and both structured and unstructured histone regions. Cation accumulation makes the proximity of juxtaposed DNA gyres in th...
arXiv: Disordered Systems and Neural Networks, 2002
Geometrically, foams or covalent graphs can be decomposed into successive layers or strata. Disor... more Geometrically, foams or covalent graphs can be decomposed into successive layers or strata. Disorder of the underlying structure imposes a characteristic roughening of the layers. Our main results are hysteresis and convergence in the layer sequences. 1) If the direction of construction is reversed, the layers are different in the up and down sequences (irreversibility); nevertheless, under suitable but non-restrictive conditions, the layers come back, exactly, to the initial profile, a hysteresis phenomenon. 2) Layer sequences based on different initial conditions (e.g. different starting cells) converge, at least in the cylindrical geometry. Jogs in layers may be represented as pairs of opposite dislocations, moving erratically due to the disorder of the underlying structure and ending up annihilating when colliding.
PLOS Computational Biology, 2015
The accurate prediction of the structure and dynamics of DNA remains a major challenge in computa... more The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI $ BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0 εζOLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition.
Geometrically, foams or covalent graphs can be decomposed into successive layers or strata. Disor... more Geometrically, foams or covalent graphs can be decomposed into successive layers or strata. Disorder of the underlying structure imposes a characteristic roughening of the layers. Our main results are hysteresis and convergence in the layer sequences. 1) If the direction of construction is reversed, the layers are different in the up and down sequences (irreversibility); nevertheless, under suitable but non-restrictive conditions, the layers come back, exactly, to the initial profile, a hysteresis phenomenon. 2) Layer sequences based on different initial conditions (e.g. different starting cells) converge, at least in the cylindrical geometry. Jogs in layers may be represented as pairs of opposite dislocations, moving erratically due to the disorder of the underlying structure and ending up annihilating when colliding.
Sur l"effet d"écran dans les systèmes chargés quantiques
These Ecole polytechnique federale de Lausanne EPFL, n° 600 (1985) Reference doi:10.5075/epfl-the... more These Ecole polytechnique federale de Lausanne EPFL, n° 600 (1985) Reference doi:10.5075/epfl-thesis-600Print copy in library catalog Record created on 2005-03-16, modified on 2016-08-08
Geometrically, foams or covalent graphs can be decomposed into successive layers or strata. Disor... more Geometrically, foams or covalent graphs can be decomposed into successive layers or strata. Disorder of the underlying structure imposes a characteristic roughening of the layers. Our main results are hysteresis and convergence in the layer sequences. 1) If the direction of construction is reversed, the layers are different in the up and down sequences (irreversibility); nevertheless, under suitable but non-restrictive conditions, the layers come back, exactly, to the initial profile, a hysteresis phenomenon. 2) Layer sequences based on different initial conditions (e.g. different starting cells) converge, at least in the cylindrical geometry. Jogs in layers may be represented as pairs of opposite dislocations, moving erratically due to the disorder of the underlying structure and ending up annihilating when colliding.
Foams and Emulsions, 1999
Periodic minimal surfaces model a large variety of mesophases and crystals of films in ternary li... more Periodic minimal surfaces model a large variety of mesophases and crystals of films in ternary liquid systems typically composed of water, soap and oil. First I describe the Bonnet transformation with emphasis on the crystallographic aspects which are specific to periodic minimal surfaces. Then I consider other transformations which are non isometric but preserve minimality.
Journal of Physics A: Mathematical and General, 2001
A foam can be decomposed into successive layers of cells at the same topological distance to an o... more A foam can be decomposed into successive layers of cells at the same topological distance to an origin, which is either an arbitrary cell or a basal plane. The shape of these layers (profile and thickening) indicates the degree of randomness of the cellular pattern. To support this idea, we analyse the layer shapes in 2D rectangular models of foam. As confirmed by numerical simulations, the fluctuations in the direction normal to the layers are self-affine on a significant range of scales, with values of the exponents compatible with the KPZ universality class: ζ 0.5 for the roughness exponent and z 1.5 for the dynamic exponent measuring the increase of the intralayer correlation length ξ . These fluctuations are not sufficient, however, to affect the dominant behaviour of the number of cells per layer, found to saturate in cylindrical geometry, and to increase linearly in concentric geometry.
The European Physical Journal B - Condensed Matter, 2003
A foam is a space-filling cellular pattern, that can be decomposed into successive layers or stra... more A foam is a space-filling cellular pattern, that can be decomposed into successive layers or strata. Each layer contains all cells at the same topological distance to an origin (cell, cluster of cells, or basal layer). The disorder of the underlying structure imposes a characteristic roughening of the layers. In this paper, stratifications are described as the results a deterministic "invasion" process started from different origins in the same, given foam. We compare different stratifications of the same foam. Our main results are 1) hysteresis and 2) convergence in the sequence of layers. 1) If the progression direction is reversed, the layers in the up and down sequences differ (irreversibility of the invasion process); nevertheless, going back up, the layers return exactly to the top profile. This hysteresis phenomenon is established rigorously from elementary properties of graphs and processes. 2) Layer sequences based on different origins (e.g. different starting cells) converge, in cylindrical geometry. Jogs in layers may be represented as pairs of opposite dislocations, that move erratically because the underlying structure is disordered, and end up annihilating when colliding. Convergence is demonstrated and quantified by numerical simulations on a two dimensional columnar model.
Colloids and Surfaces A: Physicochemical and Engineering Aspects, 2005
This paper is concerned with elasticity and plasticity of two-dimensional cellular structures. Th... more This paper is concerned with elasticity and plasticity of two-dimensional cellular structures. The deformation of continuous media is defined by a mapping from the actual, deformed state of the material, into a reference (natural) state, where all elastic deformations have been relaxed. In two dimensions, the two states can be represented by a complex variable each, and the map, by a meromorphic function. Topological defects correspond to the singularity of the map: disclinations, dislocations and extra-matter, which appears as a fold or as a bulge. We show that these abstract concepts find a direct, geometric illustration in foams. The dual of a two-dimensional foam is a triangulation. The triangles are the finite elements for the two states of the material, with the vertices carrying the elementary defects. The meromorphic function can be analytically continued outside the basic triangle, and finite elements joined together in a natural fashion. The mapping enables us to define topological defects geometrically, and to compute their effect by contour integrals, and their image in the reference state. Disclinations alone can be defined intrinsically in the actual state of the material, without mapping into the reference state. For dislocation and extra matter, the mapping determines the (Burgers) contour integral, in its non-closure or its integral content, respectively. Before moulting, the crab has prepared its new shell that lies under the old one, folded, but metrically perfect and with all its topological intricacies. It stretches just after moulting through ingestion of salt water. Successive cellular divisions create the necessary folds.
Intrinsic flexibility of B-DNA: the experimental TRX scale
B-DNA flexibility, crucial for DNA–protein recogni-tion, is sequence dependent. Free DNA in solut... more B-DNA flexibility, crucial for DNA–protein recogni-tion, is sequence dependent. Free DNA in solution would in principle be the best reference state to uncover the relation between base sequences and their intrinsic flexibility; however, this has long been hampered by a lack of suitable experimental data. We investigated this relationship by compiling and analyzing a large dataset of NMR 31P chemical shifts in solution. These measurements reflect the BI $ BII equilibrium in DNA, intimately correlated to helicoi-dal descriptors of the curvature, winding and groove dimensions. Comparing the ten complementary DNA dinucleotide steps indicates that some steps are much more flexible than others. This malleability is primarily controlled at the dinucleotide level, modulated by the tetranucleotide environment. Our analyses provide an experimental scale called TRX that quantifies the intrinsic flexibility of the ten dinucleotide steps in terms of Twist, Roll, and X-disp (base pair displacemen...
Nucleic Acids Research, 2016
Experimental characterization of the structural couplings in free B-DNA in solution has been elus... more Experimental characterization of the structural couplings in free B-DNA in solution has been elusive, because of subtle effects that are challenging to tackle. Here, the exploitation of the NMR measurements collected on four dodecamers containing a substantial set of dinucleotide sequences provides new, consistent correlations revealing the DNA intrinsic mechanics. The difference between two successive residual dipolar couplings (RDCs) involving C6/8-H6/8, C3-H3 and C4-H4 vectors are correlated to the 31 P chemical shifts (␦P), which reflect the populations of the BI and BII backbone states. The ␦Ps are also correlated to the internucleotide distances (D inter) involving H6/8, H2 and H2 protons. Calculations of NMR quantities on high resolution X-ray structures and controlled models of DNA enable to interpret these couplings: the studied RDCs depend mostly on roll, while D inter are mainly sensitive to twist or slide. Overall, these relations demonstrate how ␦P measurements inform on key inter base parameters, in addition to probe the BI↔BII backbone equilibrium, and shed new light into coordinated motions of phosphate groups and bases in free B-DNA in solution. Inspection of the 5 and 3 ends of the dodecamers also supplies new information on the fraying events, otherwise neglected.
In random 2D cellular assemblies, maximum entropy inference yields a specific form for the topolo... more In random 2D cellular assemblies, maximum entropy inference yields a specific form for the topological pair correlation, bi-affine in the cell charges (6-polygonality). By a self-consistent method, we show that the long distance behaviour of the pair correlation function is related to sum rules involving moments of the quadratic coefficients of the bi-affine form. The correlation function is predicted to decay like the 4th power of inverse distance if the first moment does not vanish, faster otherwise. The lowest sum rule expresses the screening of topological charge in the foam. Comparison with sparse available experimental data is not conclusive. © 2011 Elsevier B.V. All rights reserved.
A dynamic view of DNA structure within the nucleosome: biological implications
Journal of Structural Biology
Structural explorations of NCp7-nucleic acid complexes give keys to decipher the binding process
Journal of Molecular Biology
In two dimensional foams at equilibrium, triangular bubbles can be freely exchanged with 3-fold s... more In two dimensional foams at equilibrium, triangular bubbles can be freely exchanged with 3-fold stars --three edges ending at a central vertex. This theorem is deduced here from Moukarzel's duality. Moreover, to probe the method, a few related properties are established: under slow gas diffusion, T2 processes are continuous for triangles but not for other types of bubbles. In general, the gas flow results in different configurations in the presence of a triangle than in the presence of a star.
Communications in Mathematical Physics, 1988
Tilings provide generalized frames of coordinates and as such they are used in different areas of... more Tilings provide generalized frames of coordinates and as such they are used in different areas of physics. The aim of the present paper is to present a unified and systematic description of a class of tilings which have appeared in contexts as disconnected as crystallography and dynamical systems. The tilings of this class show periodic or quasiperiodic ordering and the tiles are related to the unit cube through affine transformations. We present a section procedure generating canonical quasiperiodic tilings and we prove that true tilings are indeed obtained. Moreover, the procedure provides a direct and simple characterization of quasiperiodicity which is suitable for tilings but which does not refer to Fourier transform.
Scientific Reports
Given the tight relation between protein structure and function, we present a set of methods to a... more Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. The Laguerre partition specifies inter-atomic contacts, formalized in graphs. The deduced properties are the existence and count of water aggregates, possible passage ways and constrictions, the structure, connectivity, stability and depth of the water network. As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. Inside FepA, the solvent splits into isolated clusters and an intricate network connecting both sides of the lipid bilayer. The network is dynamic, connections set on and off, occasionally substantially relocating traversing paths. Subtle differences are detected between two forms of FepA, ligand-free and complexed with its natural iron carrier, the enterobactin. The complexed form has more constricted and more centered openings in the upper part whereas, in the lower part, constriction is released: two main channels between the plug and barrel lead directly to the periplasm. Reliability, precision and the variety of topological features are the main interest of the method.
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Papers by Christophe Oguey