arXiv subjects

Jean-Marc Victor

Publications and source records attributed to Jean-Marc Victor.

15 recordsLinked to original sources

arXiv2026

Distribution of the Radius of Gyration for an ISAW

We aim at calculating an explicit expression for the finite-size probability distribution of the radius of gyration $R$ of an Interacting Self-Avoiding Walk (ISAW), as a function of chain length $N$ and monomer-monomer interaction energy $\varepsilon$. We first derive the explicit free energy expression for a non-interacting Self-Avoiding Walk, introducing a new natural scale variable $t = \rho^g$ expressed as a power of the density $\rho$. Then, thanks to a cumulant expansion approach introduced by Lhuillier, Victor and coworkers, we extend it to the interacting case, capturing both the coil-globule transition and finite-size corrections to scaling, including entropic and surface-energy contributions. The radius of gyration distribution determined by the new free energy expression is then compared, using Bayesian inference to estimate the model parameters, to results from extensive Monte Carlo simulations of three-dimensional ISAWs, showing excellent agreement except very close to the $\Theta$-point, where finite chain lengths limit the accessible scaling regime. This validates our resulting free energy expression and allows us, as an application, to construct a phase diagram of the coil-globule transition.

cond-mat.stat-mech↗

arXiv2016

The physics of epigenetics

In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the daughter cells. This intriguing phenomenon is achieved by a variety of processes that have been collectively termed epigenetics: the stable and inheritable changes in gene expression patterns. This article reviews the extremely rich and exquisitely multi-scale physical mechanisms that govern the biological processes behind the initiation, spreading and inheritance of epigenetic states. These include not only the changes in the molecular properties associated with the chemical modifications of DNA and histone proteins, such as methylation and acetylation, but also less conventional ones, such as the physics that governs the three-dimensional organization of the genome in cell nuclei. Strikingly, to achieve stability and heritability of epigenetic states, cells take advantage of many different physical principles, such as the universal behavior of polymers and copolymers, the general features of non-equilibrium dynamical systems, and the electrostatic and mechanical properties related to chemical modifications of DNA and histones. By putting the complex biological literature under this new light, the emerging picture is that a limited set of general physical rules play a key role in initiating, shaping and transmitting this crucial "epigenetic landscape". This new perspective not only allows to rationalize the normal cellular functions, but also helps to understand the emergence of pathological states, in which the epigenetic landscape becomes dysfunctional.

physics.bio-ph↗

arXiv2015

Theory and simulations of toroidal and rod-like structures in single-molecule DNA condensation

DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical condensation forces have been used to estimate the amplitude of the attractive DNA-DNA interactions. Here, to describe these experiments, we developed an analytical model and a rigid body Langevin dynamics assay to investigate the behavior of a polymer with self-interactions, in the presence of a traction force applied at its extremities. We model self-interactions using a pairwise attractive potential, thereby treating the counterions implicitly. The analytical model allows to accurately predict the equilibrium structures of toroidal and rod-like condensed structures, and the dependence of the critical condensation force on the DNA length. We find that the critical condensation force depends strongly on the length of the DNA, and finite-size effects are important for molecules of length up to 10^5 μm. Our Langevin dynamics simulations show that the force-extension behavior of the rod-like structures is very different from the toroidal ones, so that their presence in experiments should be easily detectable. In double-stranded DNA condensation experiments, the signature of the presence of rod-like structures was not unambiguously detected, suggesting that the polyamines used to condense DNA may protect it from bending sharply as needed in the rod-like structures

cond-mat.soft↗

arXiv2014

Conformational Manipulation of DNA in Nanochannels Using Hydrodynamics

The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics, although the physics of soft matter in nanoscale flows has raised considerable interest over the past decade. In this report the migration of DNA is studied in nanochannels of lateral dimension spanning 100 to 500 nm using both actuation principles. We show that the relaxation kinetics are 3-fold slowed down and the extension increases up to 3-fold using hydrodynamics. We propose a model to account for the onset in elongation with the flow, which assumes that DNA response is determined by the shear-driven lift forces mediated by the proximity of the channels' walls. Overall, we suggest that hydrodynamic actuation allows for an improved manipulation of DNA in nanochannels.

physics.bio-ph↗

arXiv2009

Non-specific DNA-protein interaction: Why proteins can diffuse along DNA

The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between proteins and DNA play a role during the target search even far from the specific site. It is unclear how these non-specific interactions optimize the search process, and how the protein structure comes into play. Each nucleotide being negatively charged, one may think that the positive surface of DNA-BPs should electrostatically collapse onto DNA. Here we show by means of Monte Carlo simulations and analytical calculations that a counter-intuitive repulsion between the two oppositely charged macromolecules exists at a nanometer range. We also show that this repulsion is due to a local increase of the osmotic pressure exerted by the ions which are trapped at the interface. For the concave shape of DNA-BPs, and for realistic protein charge densities, we find that the repulsion pushes the protein in a free energy minimum at a distance from DNA. As a consequence, a favourable path exists along which proteins can slide without interacting with the DNA bases. When a protein encounters its target, the osmotic barrier is completely counter-balanced by the H-bond interaction, thus enabling the sequence recognition.

q-bio.BM↗

arXiv2009

Poisson-Boltzmann for oppositely charged bodies: an explicit derivation

The interaction between charged bodies in an ionic solution is a general problem in colloid physics and becomes a central topic in the study of biological systems where the electrostatic interaction between proteins, nucleic acids, membranes is involved. This problem is often described starting from the simple one-dimensional model of two parallel charged plates. Several different approaches to this problem exist, focusing on different features. In many cases, an intuitive expression of the pressure exerted on the plates is proposed, which includes an electrostatic plus an osmotic contribution. We present an explicit and self-consistent derivation of this formula for the general case of any charge densities on the plates and any salt solution, obtained in the framework of the Poisson-Boltzmann theory. We also show that, depending on external constraints, the correct thermodynamic potential can differ from the usual PB free energy. The resulting expression predicts, for asymmetric, oppositely charged plates, the existence of a non trivial equilibrium position with the plates separated by a finite distance. It is therefore crucial, in order to study the kinetic stability of the corresponding energy minimum, to obtain its explicit dependence on the plates charge densities and on the ion concentration. An analytic expression for the position and value of the corresponding energy minimum has been derived in 1975 by Ohshima [Ohshima H., Colloid and Polymer Sci. 253, 150-157 (1975)] but, surprisingly, this important result seems to be overlooked today. We retrieve the expressions obtained by Ohshima in a simpler formalism, more familiar to the physics community, and give a physical interpretation of the observed behavior.

cond-mat.soft↗

arXiv2007

Nucleosome Chiral Transition under Positive Torsional Stress in Single Chromatin Fibers

Using magnetic tweezers to investigate the mechanical response of single chromatin fibers, we show that fibers submitted to large positive torsion transiently trap positive turns, at a rate of one turn per nucleosome. A comparison with the response of fibers of tetrasomes (the (H3-H4)2 tetramer bound with ~50 bp of DNA) obtained by depletion of H2A-H2B dimers, suggests that the trapping reflects a nucleosome chiral transition to a metastable form built on the previously documented righthanded tetrasome. In view of its low energy, <8 kT, we propose this transition is physiologically relevant and serves to break the docking of the dimers on the tetramer which in the absence of other factors exerts a strong block against elongation of transcription by the main RNA polymerase.

q-bio.BM↗

arXiv2007

A Physical Model for the Condensation and Decondensation of Eukaryotic Chromosomes

During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this paper, we propose a scenario for chromatin structural reorganization during mitosis, which bridges all the different scales involved in chromatin architecture, from nucleosomes to chromatin loops. We build a model for chromatin, based on available data, taking into account both physical and topological constraints DNA has to deal with. Our results suggest that the mitotic chromosome condensation/decondensation process is induced by a structural change at the level of the nucleosome itself.

q-bio.SC↗

arXiv2007

Structural plasticity of single chromatin fibers revealed by torsional manipulation

Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucleosome, which are determined by the crossing status of the entry/exit DNAs (positive, null or negative). Torsional strain, in displacing that equilibrium, extensively reorganizes the fiber architecture. The model explains a number of long-standing topological questions regarding DNA in chromatin, and may provide the ground to better understand the dynamic binding of most chromatin-associated proteins.

q-bio.BM↗

arXiv2004

How does the chromatin fiber deal with topological constraints?

In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of the so-called 30 nm chromatin fiber and accordingly imposes strong topological constraints. We present a general method for computing both the twist and the writhe of any winding pattern. An explicit derivation is implemented for the chromatin fiber which provides the linking number of DNA in eukaryotic chromosomes. We show that there exists one and only one unwinding path which satisfies both topological and mechanical constraints that DNA has to deal with during condensation/decondensation processes.

q-bio.SC↗

arXiv2002

Adaptive elastic properties of chromatin fiber

Chromatin is a complex of DNA and specific proteins forming an intermediary level of organization of eukaryotic genomes, between double-stranded DNA and chromosome. Within a generic modeling of the chromatin assembly, we investigate the interplay between the mechanical properties of the chromatin fiber and its biological functions. A quantitative step is to relate the mechanics at the DNA level and the mechanics described at the chromatin fiber level. It allows to calculate the complete set of chromatin elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant), in terms of DNA elastic properties and geometric features of the fiber. These elastic constants are strongly sensitive to the local architecture of the fiber and we argue that this tunable elasticity might be a key feature in chromatin functions, for instance in the initiation and regulation of transcription. Moreover, this analysis provides a framework to interpret micromanipulations studies of chromatin fiber and suggests further experiments involving intercalators to scan the tunable elasticity of the fiber.

cond-mat.stat-mech↗

arXiv2002

Intercalation and buckling instability of DNA linker within locked chromatin fiber

The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the nucleosomes are strongly end constrained. Longitudinal thermal fluctuations in these linkers allow intercalative mode of protein binding. We show that mechanical constraints generated in the first stage of the binding process induce linker DNA buckling; buckling in turn modifies the binding energies and activation barriers and creates a force of decondensation at the chromatin fiber level. The unique structure and properties of DNA thus yield a novel physical mechanism of buckling instability that might play a key role in the regulation of gene expression.

cond-mat.stat-mech↗

arXiv2001

Chromatin: a tunable spring at work inside chromosomes

This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the ``extensible worm-like rope'', allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.

cond-mat.soft↗

arXiv2000

Anomalous tricritical behaviour in the coil-globule transition of a single polymer chain

We investigate a model of self-avoiding walk exhibiting a first-order coil-globule transition. This first-order nature, unravelled through the coexistence of distinct coil and globule populations, has observable consequences on the scaling properties. A thorough analysis of the size dependence of the mean radius of gyration evidences a breakdown of the plain tricritical scaling behaviour. In some regimes, anomalous exponents are observed in the transition region and logarithmic corrections arise along the coexistence curve.

cond-mat.stat-mech↗

arXiv2000

First-order theta-point of a single polymer chain

Conformational transitions of a single macromolecule of finite size $N$ cannot be described within standard thermodynamic framework. Taking as a basis a simple model of homopolymer exhibiting a coil-globule transition, we show that a relevant approach is to describe the thermal equilibrium distribution $P_N^{(β)}(t)$ of some variable $t$ characterizing the conformation. Although the mean order parameter exhibits a second-order behaviour in the infinite-size limit, the $Θ$-point arises from the coexistence of two distinct populations, associated with two well-separated peaks of $P_N^{(β)}(t)$ and identified respectively with a coil state and a globule state. Remarkably, this first-order feature increases with the size of the chain. It allows to describe the transition within a two-state model, well-suited to analyse experimental data.

cond-mat.stat-mech↗