arXiv subjects

Ralf Everaers

Publications and source records attributed to Ralf Everaers.

At least 19 recordsLinked to original sources

arXiv2026

Coherent modeling of double-folded ring polymers and their underlying random tree structure

Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have recently obtained expressions for the configurational entropy in ensembles with controlled branching activity. Here we demonstrate that they are equivalent up to a contribution originating from the number of distinct wrappings of a single tree. This allows us to develop a coherent framework for freely switching between the two representations. Importantly, the equivalence extends to interacting systems provided the interactions are treated consistently on the tree and on the ring level. To demonstrate the utility of the scheme, we introduce a generalization of the Amoeba Monte Carlo algorithm capable of generating the required ensembles of trees with fluctuating sizes. While the tree algorithm reproduces results obtained by dynamic simulations of the corresponding ring model, it is $O(N)$ faster for the purpose of sampling static properties and leverages the utility of the ring model for the study of dynamical properties, when used for the preparation of equilibrated starting states.

cond-mat.soft↗

arXiv2026

Plateau moduli of Kremer-Grest models for commodity polymer melts

We estimate the plateau moduli of highly entangled end-pinned bead-spring polymer melts with Z = 100 and Z = 200 from the time-dependent elastic response to a step strain, which we first extrapolate to infinite time and then interpolate to zero strain. We present data for systems deformed in the melt state as well as for systems deformed at the primitive path level following the recent iPPA protocol. We observe excellent agreement between the plateau moduli obtained via the two deformation protocols and good agreement with the available experimental data for commodity polymer melts using a common mapping on the Kuhn scale.

cond-mat.soft↗

arXiv2025

Configurational entropy of randomly double-folding ring polymers

Topologically constrained genome-like polymers often double-fold into tree-like configurations. Here we calculate the exact number of tightly double-folded configurations available to a ring polymer in ideal conditions. For this purpose, we introduce a scheme which allows us to define a ``code'' specifying how a ring wraps a randomly branching tree and calculate the number of admissible wrapping codes via a variant of Bertrand's ballot theorem. As a validation, we demonstrate that data from Monte Carlo simulations of an elastic lattice model of non-interacting tightly double-folded rings with controlled branching activity are in excellent agreement with exact expressions for branch-node and tree size statistics that can be derived from our expression for the ring entropy.

cond-mat.soft↗

arXiv2025

The emergent dynamics of double-folded randomly branching ring polymers

The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers migrating through an array of obstacles, as well as to the conformational statistics of eukaryotic chromosomes and melts of crumpled, non-concatenated ring polymers. Double-folded rings fall into different dynamical universality classes depending on whether the random tree-like graphs underlying the double-folding are quenched or annealed, and whether the trees can undergo unhindered Brownian motion in their spatial embedding. Locally, one can distinguish (i) repton-like mass transport around a fixed tree, (ii) the spontaneous creation and deletion of side branches, and (iii) displacements of tree node, where complementary ring segments diffuse together in space. Here we employ dynamic Monte Carlo simulations of a suitable elastic lattice polymer model of double-folded, randomly branching ring polymers to explore the mesoscopic dynamics that emerge from different combinations of the above local modes in three different systems: ideal non-interacting rings, self-avoiding rings, and rings in the melt state. We observe the expected scaling regimes for ring reptation, the dynamics of double-folded rings in an array of obstacles, and Rouse-like tree dynamics as limiting cases. Of particular interest, the monomer mean-square displacements of $g_1\sim t^{0.4}$ observed for crumpled rings with $ν=1/3$ are similar to the subdiffusive regime observed in bacterial chromosomes. In our analysis, we focus on the question to which extent contributions of different local dynamical modes to the emergent dynamics are simply additive. Notably, we reveal a non-trivial acceleration of the dynamics of interacting rings, when all three types of local motion are present.

cond-mat.soft↗

arXiv2025

The configurational entropy of random trees

We present a graph theoretical approach to the configurational statistics of random tree-like objects, such as randomly branching polymers. In particular, for ideal trees we show that Prüfer labelling provides: (i) direct access to the exact configurational entropy as a function of the tree composition, (ii) computable exact expressions for partition functions and important experimental observables for tree ensembles with controlled branching activity and (iii) an efficient sampling scheme for corresponding tree configurations and arbitrary static properties.

cond-mat.stat-mech↗

arXiv2024

Amoeba Monte Carlo algorithms for random trees with controlled branching activity: efficient trial move generation and universal dynamics

The reptation Monte Carlo algorithm is a simple, physically motivated and efficient method for equilibrating semi-dilute solutions of linear polymers. Here we propose two simple generalizations for the analogue {\it Amoeba} algorithm for randomly branching chains, which allow to efficiently deal with random trees with controlled branching activity. We analyse the rich relaxation dynamics of Amoeba algorithms and demonstrate the existence of an unexpected scaling regime for the tree relaxation. In particular, our results suggests that the equilibration time for Amoeba algorithms scales in general like $N^2 \langle n_{\rm lin}\rangle^Δ$, where $N$ denotes the number of tree nodes, $\langle n_{\rm lin}\rangle$ the mean number of linear segments the trees are composed of and $Δ\simeq 0.4$.

cond-mat.soft↗

arXiv2023

DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling

DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation. Highlighted in vitro and in vivo in the 1960s and 1970s, respectively, the first physical models were proposed concomitantly in order to predict the deformation properties of the double helix. About fifteen years later, polymer physics models demonstrated on larger scales the plectonemic nature and the tree-like organization of supercoiled DNA. Since then, many works have tried to establish a better understanding of the multiple structuring and physiological properties of bacterial DNA in thermodynamic equilibrium and far from equilibrium. The purpose of this essay is to address upcoming challenges by thoroughly exploring the relevance, predictive capacity, and limitations of current physical models, with a specific focus on structural properties beyond the scale of the double helix. We discuss more particularly the problem of DNA conformations, the interplay between DNA supercoiling with gene transcription and DNA replication, its role on nucleoid formation and, finally, the problem of scaling up models. Our primary objective is to foster increased collaboration between physicists and biologists. To achieve this, we have reduced the respective jargon to a minimum and we provide some explanatory background material for the two communities.

q-bio.BM↗

arXiv2022

Multiscale equilibration of highly entangled isotropic model polymer melts

We present a computationally efficient multiscale method for preparing equilibrated, isotropic long chain model polymer melts. As an application we generate Kremer-Grest melts of $1000$ chains with $200$ entanglements and $25000$-$2000$ beads per chain, which cover the experimentally relevant bending rigidities up to and beyond the limit of the isotropic-nematic transition. In the first step, we employ Monte Carlo simulations of a lattice model to equilibrate the large-scale chain structure above the tube scale while ensuring a spatially homogeneous density distribution. We then use theoretical insight from a constrained mode tube model to introduce the bead degrees of freedom together with random walk conformational statistics all the way down to the Kuhn scale of the chains. This is followed by a sequence of simulations with carefully parameterized force-capped bead-spring models, which slowly introduce the local bead packing while reproducing the larger scale chain statistics of the target Kremer-Grest system at all levels of force-capping. Finally we can switch to the full Kremer-Grest model without perturbing the structure. The resulting chain statistics is in excellent agreement with literature results on all length scales accessible in brute-force simulations of shorter chains.

cond-mat.soft↗

arXiv2020

Single-molecule stretching experiments of flexible (wormlike) chain molecules in different ensembles: Theory and a potential application of finite chain length effects to nick-counting in DNA

We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the asymptotic behavior and finite chain length corrections. In particular, we apply this formalism to our previously developed interpolation formula for the wormlike chain end-to-end distance distribution. The resulting expression for the asymptotic limit of infinite chain length is of similar quality as the numerical evaluation of Marko's and Siggia's variational theory and considerably more precise than their interpolation formula. A comparison to numerical data suggests, that our analytical expressions for the finite-chain length corrections are of similar quality. As an application of our results we discuss the possibility of inferring the changing number of nicks in a double-stranded DNA molecule in single-molecule stretching experiments from the accompanying changes in the effective chain length.

cond-mat.soft↗

arXiv2019

Kremer-Grest models for commodity polymer melts: Linking theory, experiment and simulation at the Kuhn scale

The Kremer-Grest (KG) polymer model is a standard model for studying generic polymer properties in Molecular Dynamics simulations. It owes its popularity to its simplicity and computational efficiency, rather than its ability to represent specific polymers species and conditions. Here we show, that by tuning the chain stiffness it is possible to adapt the KG model to model melts of real polymers. In particular, we provide mapping relations from KG to SI units for a wide range of commodity polymers. The connection between the experimental and the KG melts is made at the Kuhn scale, i.e. at the crossover from chemistry-specific small scale to the universal large scale behavior. We expect Kuhn scale-mapped KG models to faithfully represent universal properties dominated by the large scale conformational statistics and dynamics of flexible polymers. In particular, we observe very good agreement between entanglement moduli of our KG models and the experimental moduli of the target polymers.

cond-mat.soft↗

arXiv2019

Characteristic time and length scales in melts of Kremer-Grest bead-spring polymers with wormlike bending stiffness

The Kremer-Grest (KG) model is a standard for studying generic polymer properties. Here we have equilibrated KG melts up to and beyond $200$ entanglements per chain for varying chain stiffness. We present methods for estimating the Kuhn length corrected for incompressibility effects, for estimating the entanglement length corrected for chain stiffness, for estimating bead frictions and Kuhn times taking into account entanglement effects. These are the key parameters for enabling quantitative, accurate, and parameter free comparisons between theory, experiment and simulations of KG polymer models with varying stiffness. We demonstrate this for the mean-square monomer displacements in moderately to highly entangled melts as well as for the shear relaxation modulus for unentangled melts, which are found to be in excellent agreement with the predictions from standard theories of polymer dynamics.

cond-mat.soft↗

arXiv2019

Local loop opening in untangled ring polymer melts: A detailed "Feynman test" of models for the large scale structure

The conformational statistics of ring polymers in melts or dense solutions is strongly affected by their quenched microscopic topological state. The effect is particularly strong for untangled (i.e. non-concatenated and unknotted) rings, which are known to crumple and segregate. Here we study these systems using a computationally efficient multi-scale approach, where we combine massive simulations on the fiber level with the explicit construction of untangled ring melt configurations based on theoretical ideas for their large scale structure. We find (i) that topological constraints may be neglected on scales below the standard entanglement length, $L_e$, (ii) that rings with a size $1 \le L_r/L_e \le 30$ exhibit nearly ideal lattice tree behavior characterized by primitive paths which are randomly branched on the entanglement scale, and (iii) that larger rings are compact with gyration radii $\langle R_g^2(L_r) \rangle \propto L_r^{2/3}$. The detailed comparison between equilibrated and constructed ensembles allows us to perform a `Feynman test' of our understanding of untangled rings: can we convert ideas for the large-scale ring structure into algorithms for constructing (nearly) equilibrated ring melt samples? We show that most structural observables are quantitatively reproduced by two different construction schemes: hierarchical crumpling and ring melts derived from the analogy to interacting branched polymers. However, the latter fail the `Feynman test' with respect to the magnetic radius, $R_m$, which we have defined based on an analogy to magnetostatics. While $R_m$ is expected to vanish for double-folded structures, the observed values of $\langle R_m^2(L_r) \rangle \propto \langle R_g^2(L_r) \rangle$ provide a simple and computationally convenient measure of the presence of a non-negligible amount of local loop opening in crumpled rings.

cond-mat.soft↗

arXiv2018

Conformational statistics of randomly-branching double-folded ring polymers

The conformations of topologically constrained double-folded ring polymers can be described as wrappings of randomly branched primitive trees. We extend previous work on the tree statistics under different (solvent) conditions to explore the conformational statistics of double-folded rings in the limit of tight wrapping. In particular, we relate the exponents characterizing the ring statistics to those describing the primitive trees and discuss the distribution functions $p(\vec r | \ell)$ and $p(L | \ell)$ for the spatial distance, $\vec r$, and tree contour distance, $L$, between monomers as a function of their ring contour distance, $\ell$.

cond-mat.soft↗

arXiv2018

Kremer-Grest models for universal properties of specific common polymer species

The Kremer-Grest (KG) bead-spring model is a near standard in Molecular Dynamic simulations of generic polymer properties. It owes its popularity to its computational efficiency, rather than its ability to represent specific polymer species and conditions. Here we investigate how to adapt the model to match the universal properties of a wide range of chemical polymers species. For this purpose we vary a single parameter originally introduced by Faller and Müller-Plathe, the chain stiffness. Examples include polystyrene, polyethylene, polypropylene, cis-polyisoprene, polydimethylsiloxane, polyethyleneoxide and styrene-butadiene rubber. We do this by matching the number of Kuhn segments per chain and the number of Kuhn segments per cubic Kuhn volume for the polymer species and for the Kremer-Grest model. We also derive mapping relations for converting KG model units back to physical units, in particular we obtain the entanglement time for the KG model as function of stiffness allowing for a time mapping. To test these relations, we generate large equilibrated well entangled polymer melts, and measure the entanglement moduli using a static primitive-path analysis of the entangled melt structure as well as by simulations of step-strain deformation of the model melts. The obtained moduli for our model polymer melts are in good agreement with the experimentally expected moduli.

cond-mat.soft↗

arXiv2016

Beyond Flory theory: Distribution functions for interacting lattice trees

While Flory theories provide an extremely useful framework for understanding the behavior of interacting, randomly branching polymers, the approach is inherently limited. Here we use a combination of scaling arguments and computer simulations to go beyond a Gaussian description. We analyse distributions functions for a wide variety of quantities characterising the tree connectivities and conformations for the four different statistical ensembles, which we have studied numerically in [Rosa and Everaers, J. Phys. A (2016, published) and J. Chem. Phys. (2016, to appear)]: (a) ideal randomly branching polymers, (b) $2d$ and $3d$ melts of interacting randomly branching polymers, (c) $3d$ self-avoiding trees with annealed connectivity and (d) $3d$ self-avoiding trees with quenched ideal connectivity. In particular, we investigate the distributions (i) $p_N(n)$ of the weight, $n$, of branches cut from trees of mass $N$ by severing randomly chosen bonds; (ii) $p_N(l)$ of the contour distances, $l$, between monomers; (iii) $p_N(\vec r)$ of spatial distances, $\vec r$, between monomers, and (iv) $p_N(\vec r|l)$ of the end-to-end distance of paths of length $l$. Data for different tree sizes superimpose, when expressed as functions of suitably rescaled observables $\vec x = \vec r/\langle r^2(N) \rangle$ or $x =l/\langle l(N) \rangle$. In particular, we observe a generalised Kramers relation for the branch weight distributions (i) and find that all the other distributions (ii-iv) are of Redner-des Cloizeaux type, $q(\vec x) = C \, |x|^θ \exp \left( -(K |x|)^t \right)$. We propose a coherent framework, including generalised Fisher-Pincus relations, relating most of the RdC exponents to each other and to the contact and Flory exponents for interacting trees.

cond-mat.stat-mech↗

arXiv2016

Computer simulations of melts of randomly branching polymers

Randomly branching polymers with {\em annealed} connectivity are model systems for ring polymers and chromosomes. In this context, the branched structure represents transient folding induced by topological constraints. Here we present computer simulations of melts of annealed randomly branching polymers of $3 \le N \le 1800$ segments in $d=2$ and $d=3$ dimensions. In all cases, we perform a detailed analysis of the observed tree connectivities and spatial conformations. Our results are in excellent agreement with an asymptotic scaling of the average tree size of $R \sim N^{1/d}$, suggesting that the trees behave as compact, {\it territorial} fractals. The observed swelling relative to the size of ideal trees, $R\sim N^{1/4}$, demonstrates that excluded volume interactions are only partially screened in melts of annealed trees. Overall, our results are in good qualitative agreement with the predictions of Flory theory. In particular, we find that the trees swell by the combination of modified branching and path stretching. However, the former effect is subdominant and difficult to detect in $d=3$ dimensions.

cond-mat.stat-mech↗

arXiv2016

Computer simulations of randomly branching polymers: Annealed vs. quenched branching structures

We present computer simulations of three systems of randomly branching polymers in d=3 dimensions: ideal trees and self-avoiding trees with annealed and quenched connectivities. In all cases, we performed a detailed analysis of trees connectivities, spatial conformations and statistical properties of linear paths on trees, and compare the results to the corresponding predictions of Flory theory. We confirm that, overall, the theory predicts correctly that trees with quenched ideal connectivity exhibit {\it less} overall swelling in good solvent than corresponding trees with annealed connectivity even though they are more strongly stretched on the path level. At the same time, we emphasize the inadequacy of the Flory theory in predicting the behaviour of other, and equally relevant, observables like contact probabilities between tree nodes. We show, then, that contact probabilities can be aptly characterized by introducing a novel critical exponent, $θ_{path}$, which accounts for how they decay as a function of the node-to-node path distance on the tree.

cond-mat.stat-mech↗

arXiv2016

Multiscale approach to equilibrating model polymer melts

We present an effective and simple multiscale method for equilibrating Kremer Grest model polymer melts of varying stiffness. In our approach, we progressively equilibrate the melt structure above the tube scale, inside the tube and finally at the monomeric scale. We make use of models designed to be computationally effective at each scale. Density fluctuations in the melt structure above the tube scale are minimized through a Monte Carlo simulated annealing of a lattice polymer model. Subsequently the melt structure below the tube scale is equilibrated via the Rouse dynamics of a force-capped Kremer-Grest model that allows chains to partially interpenetrate. Finally the Kremer-Grest force field is introduced to freeze the topological state and enforce correct monomer packing. We generate $15$ melts of $500$ chains of $10.000$ beads for varying chain stiffness as well as a number of melts with $1.000$ chains of $15.000$ monomers. To validate the equilibration process we study the time evolution of bulk, collective and single-chain observables at the monomeric, mesoscopic and macroscopic length scales. Extension of the present method to longer, branched or polydisperse chains and/or larger system sizes is straight forward.

cond-mat.soft↗