arXiv subjects

Enzo Orlandini

Publications and source records attributed to Enzo Orlandini.

At least 55 records · Page 3Linked to original sources

arXiv2018

Topological Sieving of Rings According to their Rigidity

We present a novel mechanism for resolving the mechanical rigidity of nanoscopic circular polymers that flow in a complex environment. The emergence of a regime of negative differential mobility induced by topological interactions between the rings and the substrate is the key mechanism for selective sieving of circular polymers with distinct flexibilities. A simple model accurately describes the sieving process observed in molecular dynamics simulations and yields experimentally verifiable analytical predictions, which can be used as a reference guide for improving filtration procedures of circular filaments. The topological sieving mechanism we propose ought to be relevant also in probing the microscopic details of complex substrates.

cond-mat.soft↗

arXiv2018

Magnetic Polymer Models for Epigenomic Organisation and Phase Separation

The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks and three-dimensional genome folding. Yet, the physical principles underlying the dynamical coupling between three-dimensional genomic organisation and one-dimensional epigenetic patterns remain elusive. To shed light on this issue, here we study by mean field theory and Brownian dynamics simulations a magnetic polymer model for chromosomes, where each monomer carries a dynamic epigenetic mark. At the single chromosome level, we show that a first order transition describes the unlimited spreading of epigenetic marks, a phenomenon that is often observed in vivo. At the level of the whole nucleus, experiments suggest chromosomes form micro-phase separated compartments with distinct epigenetic marks. We here discover that for a melt of magnetic polymers such a morphology is thermodynamically unstable, but can be stabilised by a non- equilibrium and ATP-mediated epigenetic switch between different monomer states.

cond-mat.soft↗

arXiv2018

Rheology of an inverted cholesteric droplet under shear flow

The dynamics of a quasi two-dimensional isotropic droplet in a cholesteric liquid crystal medium under symmetric shear flow is studied by lattice Boltzmann simulations. We consider a geometry in which the flow direction is along the axis of the cholesteric, as this setup exhibits a significant viscoelastic response to external stress. We find that the dynamics depends upon the magnitude of the shear rate, the anchoring strength of the liquid crystal at the droplet interface and the chirality. While for low shear rate and weak interface anchoring the system shows a non-Newtonian behavior, a Newtonian-like response is observed at high shear rate and strong interface anchoring. This is investigated both by estimating the secondary flow profile, namely a flow emerging along the out-of-plane direction (absent in fully Newtonian fluids, such as water), and by monitoring defect formation and dynamics which alter significantly the rheological response of the system.

cond-mat.soft↗

arXiv2018

Lamellar ordering, droplet formation and phase inversion in exotic active emulsions

We study numerically the behaviour of a mixture of a passive isotropic fluid and an active polar gel, in the presence of a surfactant favouring emulsification. Focussing on parameters for which the underlying free energy favours the lamellar phase in the passive limit, we show that the interplay between nonequilibrium and thermodynamic forces creates a range of multifarious exotic emulsions. When the active component is contractile (e.g., an actomyosin solution), moderate activity enhances the efficiency of lamellar ordering, whereas strong activity favours the creation of passive droplets within an active matrix. For extensile activity (occurring, e.g., in microtubule-motor suspensions), instead, we observe an emulsion of spontaneously rotating droplets of different size. By tuning the overall composition, we can create high internal phase emulsions, which undergo sudden phase inversion when activity is switched off. Therefore, we find that activity provides a single control parameter to design composite materials with a strikingly rich range of morphologies.

physics.bio-ph↗

arXiv2017

Shaping Epigenetic Memory via Genomic Bookmarking

Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by "writer" proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or "readers", such as Polycomb Repressive Complexes and Transcription Factors. The coupling between readers and writers drives spreading of biochemical marks and sustains the memory of local chromatin states across replication and mitosis. In contrast, GBM-targeted perturbations destabilise the epigenetic patterns. Strikingly, we demonstrate that GBM alone can explain the full distribution of Polycomb marks in a whole Drosophila chromosome. We finally suggest that our model provides a starting point for an understanding of the biophysics of cellular differentiation and reprogramming.

q-bio.SC↗

arXiv2017

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to "epigenetic solitons" which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.

cond-mat.soft↗

arXiv2017

Exploring the correlation between the folding rates of proteins and the entanglement of their native states

The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native state of the protein. Contact order is related to the average length of the main chain loops formed by amino acids which are in contact. Here we argue that folding kinetics can be influenced also by the entanglement that loops may undergo within the overall three dimensional protein structure. In order to explore such possibility, we introduce a novel descriptor, which we call "maximum intrachain contact entanglement". Specifically, we measure the maximum Gaussian entanglement between any looped portion of a protein and any other non-overlapping subchain of the same protein, which is easily computed by discretized line integrals on the coordinates of the $C_α$ atoms. By analyzing experimental data sets of two-state and multistate folders, we show that also the new index is a good predictor of the folding rate. Moreover, being only partially correlated with previous methods, it can be integrated with them to yield more accurate predictions.

cond-mat.soft↗

arXiv2017

Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses

Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these systems arise due to topological interactions between polymers, or between the polymers and the environment, and it is often challenging to describe this quantitatively. Here we review recent research which suggests that a key role is played by inter-ring threadings (or penetrations), which become more abundant as the ring size increases. As we discuss, the physical consequences of such threadings are far-reaching: for instance, they lead to a topologically-driven glassy behaviour of ring polymer melts under pinning perturbations, while they can also account for the shape of experimentally observed patterns in two-dimensional gel electrophoresis of DNA knots.

cond-mat.soft↗

arXiv2017

Switching dynamics in cholesteric liquid crystal emulsions

In this work we numerically study the switching dynamics of a 2D cholesteric emulsion droplet immersed in an isotropic fluid under an electric field, which is either uniform or rotating with constant speed. The overall dynamics depend strongly on the magnitude and on the direction (with respect to the cholesteric axis) of the applied field, on the anchoring of the director at the droplet surface and on the elasticity. If the surface anchoring is homeotropic and a uniform field is parallel to the cholesteric axis, the director undergoes deep elastic deformations and the droplet typically gets stuck into metastable states which are rich in topological defects. When the surface anchoring is tangential, the effects due to the electric field are overall less dramatic, as a small number of topological defects form at equilibrium. The application of the field perpendicular to the cholesteric axis usually has negligible effects on the defect dynamics. The presence of a rotating electric field of varying frequency fosters the rotation of the defects and of the droplet as well, typically at lower speed than that of the field, due to the inertia of the liquid crystal. If the surface anchoring is homeotropic a periodic motion is found. Our results represent a first step to understand the dynamical response of a cholesteric droplet under an electric field and its possible application in designing novel liquid crystal-based devices.

cond-mat.soft↗

arXiv2016

A Polymer Model with Epigenetic Recolouring Reveals a Pathway for the de novo Establishment and 3D Organisation of Chromatin Domains

One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a "recolouring" process modelling the writing of epigenetic marks. Because many intra-chromatin interactions are mediated by bridging proteins, we consider a "two-state" model with self-attractive interactions between two epigenetic marks which are alike (either active or inactive). This model displays a first-order-like transition between a swollen, epigenetically disordered, phase, and a compact, epigenetically coherent, chromatin globule. If the self-attraction strength exceeds a threshold, the chromatin dynamics becomes glassy, and the corresponding interaction network freezes. By modifying the epigenetic read-write process according to more biologically-inspired assumptions, our polymer model with recolouring recapitulates the ultrasensitive response of epigenetic switches to perturbations, and accounts for multi-domain conformations, strikingly similar to the topologically-associating-domains observed in eukaryotic chromosomes.

cond-mat.soft↗

arXiv2016

Linking in domain-swapped protein dimers

The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, make such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter $G'$, termed Gaussian entanglement, is strongly correlated with the linking number. Based on $110$ non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with $|G'| > 1$. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties.

cond-mat.soft↗

arXiv2016

Single-file escape of colloidal particles from microfluidic channels

Single-file diffusion is a ubiquitous physical process exploited by living and synthetic systems to exchange molecules with their environment. It is paramount quantifying the escape time needed for single files of particles to exit from constraining synthetic channels and biological pores. This quantity depends on complex cooperative effects, whose predominance can only be established through a strict comparison between theory and experiments. By using colloidal particles, optical manipulation, microfluidics, digital microscopy and theoretical analysis we uncover the self-similar character of the escape process and provide closed-formula evaluations of the escape time. We find that the escape time scales inversely with the diffusion coefficient of the last particle to leave the channel. Importantly, we find that at the investigated {\bf microscale}, bias forces as tiny as $10^{-15}\;{\rm N}$ determine the magnitude of the escape time by drastically reducing interparticle collisions. Our findings provide crucial guidelines to optimize the design of micro- and nano-devices for a variety of applications including drug delivery, particle filtering and transport in geometrical constrictions.

cond-mat.soft↗

arXiv2015

Topological Patterns in Two-dimensional Gel Electrophoresis of DNA Knots

Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel, and in particular on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an "entanglement number", and yield a non-monotonic mobility at moderate fields. Consequently, in two-dimensional electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments.

cond-mat.soft↗

arXiv2015

Is the Kinetoplast DNA a Percolating Network of Linked Rings at its Critical Point?

In this work we present a computational study of the Kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation transition between a gas of unlinked rings and a network of linked loops which spans the whole system. Close to the percolation transition, we find that the mean valency of the network, i.e. the average number of loops which are linked to any one loop, is around 3 as found experimentally for the Kinetoplast DNA. Even more importantly, by simulating the digestion of the network by a restriction enzyme, we show that the distribution of oligomers, i.e. structures formed by a few loops which remain linked after digestion, quantitatively matches experimental data obtained from gel electrophoresis, provided that the density is, once again, close to the percolation transition. With respect to previous work, our analysis builds on a reduced number of assumptions, yet can still fully explain the experimental data. Our findings suggest that the Kinetoplast DNA can be viewed as a network of linked loops positioned very close to the percolation transition, and we discuss the possible biological implications of this remarkable fact.

cond-mat.soft↗

arXiv2014

Rings in Random Environments: Sensing Disorder Through Topology

In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby generating a disordered environment. Changes in the microscopic structure of the gel are captured by measuring the electrophoretic mobility of ring polymers moving through the medium, while their linear counterparts provide a control system as we show they are insensitive to these changes. We show that ring polymers provide a novel non-invasive way of exploiting topology to sense microscopic disorder. Finally, we compare the results from the simulations with an analytical model for the non-equilibrium differential mobility, and find a striking agreement between simulation and theory

cond-mat.soft↗

arXiv2014

Knotted globular ring polymers: how topology affects statistics and thermodynamics

The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter depending on the knot kind is an amplitude such that relative probabilities of knots do not vary with the temperature $T$, in the limit of long chains. We arrive at this conclusion by simulating interacting self-avoiding rings at low $T$ on the cubic lattice, both with unrestricted topology and with setups where the globule is divided by a slip link in two loops (preserving their topology) which compete for the chain length, either in contact or separated by a wall as for translocation through a membrane pore. These findings suggest that in macromolecular environments there may be entropic forces with a purely topological origin, whence portions of polymers holding complex knots should tend to expand at the expense of significantly shrinking other topologically simpler portions.

cond-mat.stat-mech↗

arXiv2014

Active Brownian Particles Escaping a Channel in Single File

Active particles may happen to be confined in channels so narrow that they cannot overtake each other (Single File conditions). This interesting situation reveals nontrivial physical features as a consequence of the strong inter-particle correlations developed in collective rearrangements. We consider a minimal model for active Brownian particles with the aim of studying the modifications introduced by activity with respect to the classical (passive) Single File picture. Depending on whether their motion is dominated by translational or rotational diffusion, we find that active Brownian particles in Single File may arrange into clusters which are continuously merging and splitting ({\it active clusters}) or merely reproduce passive-motion paradigms, respectively. We show that activity convey to self-propelled particles a strategic advantage for trespassing narrow channels against external biases (e.g., the gravitational field).

cond-mat.stat-mech↗

arXiv2014

Dynamics of Self-Threading Ring Polymers in a Gel

We study of the dynamics of ring polymers confined to diffuse in a background gel at low concentrations. We do this in order to probe the inter-play between topology and dynamics in ring polymers. We develop an algorithm that takes into account the possibility that the rings hinder their own motion by passing through themselves, i.e. "self-threading". Our results suggest that the number of self-threadings scales extensively with the length of the rings and that this is substantially independent of the details of the model. The slowing down of the rings' dynamics is found to be related to the fraction of segments that can contribute to the motion. Our results give a novel perspective on the motion of ring polymers in gel, for which a complete theory is still lacking, and may help us to understand the irreversible trapping of ring polymers in gel electrophoresis experiments.

cond-mat.soft↗