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Ribbons are a class of slender structures whose length, width, and thickness are widely separated from each other. This scale separation gives a ribbon unusual mechanical properties in athermal macroscopic settings, e.g. it can bend without twisting, but cannot twist without bending. Given the ubiquity of ribbon-like biopolymers in biology and chemistry, here we study the statistical mechanics of microscopic inextensible, fluctuating ribbons loaded by forces and torques. We show that these ribbons exhibit a range of topologically and geometrically complex morphologies exemplified by three phases - a twist-dominated helical phase (HT), a writhe-dominated helical phase (HW), and an entangled phase - that arise as the applied torque and force is varied. Furthermore, the transition from HW to HT phases is characterized by the spontaneous breaking of parity symmetry and the disappearance of perversions that characterize chirality reversals. This leads to a universal response curve of a topological quantity, the link, as a function of the applied torque that is similar to magnetization curves in second-order phase transitions., Comment: 10 pages, 4 figures

Simulating soft matter systems such as the cytoskeleton can enable deep understanding of experimentally observed phenomena. One challenge of modeling such systems is realistic description of the steric repulsion between nearby polymers. Previous models of the polymeric excluded volume interaction have the deficit of being non-analytic, being computationally expensive, or allowing polymers to erroneously cross each other. A recent solution to these issues, implemented in the MEDYAN simulation platform, uses analytical expressions obtained from integrating an interaction kernel along the lengths of two polymer segments to describe their repulsion. Here, we extend this model by re-deriving it for lower-dimensional geometrical configurations, deriving similar expressions using a steeper interaction kernel, comparing it to other commonly used potentials, and showing how to parameterize these models. We also generalize this new integrated style of potential by introducing a segmental Lennard-Jones potential, which enables modelling both attractive and repulsive interactions in semi-flexible polymer networks. These results can be further generalized to facilitate the development of effective interaction potentials for other finite elements in simulations of soft-matter systems., Comment: 18 pages, 6 figures

Since chemical shift interaction was discovered in 1953, nuclear magnetic resonance (NMR) spectroscopy has emerged as one of the most promising tools in polymer chemistry as well as polymer physics. In this chapter, basic principles of solution- and solid-state NMR spectroscopy will be introduced and recent NMR applications to polymer structure and dynamics will be reviewed.

Fluorescence in situ hybridization and chromosome conformation capture methods point to the same conclusion: that chromosomes appear to the external observer as compact structures with a highly nonrandom three-dimensional organization. In this work, we recapitulate the efforts made by us and other groups to rationalize this behavior in terms of the mathematical language and tools of polymer physics. After a brief introduction dedicated to some crucial experiments dissecting the structure of interphase chromosomes, we discuss at a nonspecialistic level some fundamental aspects of theoretical and numerical polymer physics. Then, we inglobe biological and polymer aspects into a polymer model for interphase chromosomes which moves from the observation that mutual topological constraints, such as those typically present between polymer chains in ordinary melts, induce slow chain dynamics and "constraint" chromosomes to resemble double-folded randomly branched polymer conformations. By explicitly turning these ideas into a multi-scale numerical algorithm which is described here in full details, we can design accurate model polymer conformations for interphase chromosomes and offer them for systematic comparison to experiments. The review is concluded by discussing the limitations of our approach and pointing to promising perspectives for future work.

Many emerging materials, such as ultrastable glasses1,2 of interest for phone displays and OLED television screens, owe their properties to a gradient of enhanced mobility at the surface of glass-forming liquids. The discovery of this surface mobility enhancement3–5 has reshaped our understanding of the behaviour of glass formers and of how to fashion them into improved materials. In polymeric glasses, these interfacial modifications are complicated by the existence of a second length scale—the size of the polymer chain—as well as the length scale of the interfacial mobility gradient6–9. Here we present simulations, theory and time-resolved surface nano-creep experiments to reveal that this two-scale nature of glassy polymer surfaces drives the emergence of a transient rubbery, entangled-like surface behaviour even in polymers comprised of short, subentangled chains. We find that this effect emerges from superposed gradients in segmental dynamics and chain conformational statistics. The lifetime of this rubbery behaviour, which will have broad implications in constraining surface relaxations central to applications including tribology, adhesion, and surface healing of polymeric glasses, extends as the material is cooled. The surface layers suffer a general breakdown in time−temperature superposition (TTS), a fundamental tenet of polymer physics and rheology. This finding may require a reevaluation of strategies for the prediction of long-time properties in polymeric glasses with high interfacial areas. We expect that this interfacial transient elastomer effect and TTS breakdown should normally occur in macromolecular systems ranging from nanocomposites to thin films, where interfaces dominate material properties5,10. Surface enhancements in glass mobility are complicated in polymers by the interplay of the surface mobile layer thickness with a second length scale (the size of the polymer chains), giving rise to a transient rubbery surface even in polymers with short chains.

Water-mediated interactions (WMIs) play diverse roles in molecular biology. They are particularly relevant in geometrically confined spaces such as the interior of the chaperonin, at the interface between ligands and their binding partners, and in the ribosome tunnel. Inspired in part by the geometry of the ribosome tunnel, we consider confinement effects on the stability of peptides. We describe results from replica exchange molecular dynamics simulations of a system containing a 23-alanine or 23-serine polypeptide confined to non-polar and polar nanotubes in the gas phase and when open to a water reservoir. We quantify the effect of water in determining the preferred conformational states of these polypeptides by calculating the difference in the solvation free energy for the helix and coil states in the open nanotube in the two phases. Our simulations reveal several possibilities. We find that nanoscopic confinement preferentially stabilizes the helical state of polypeptides with hydrophobic side chains, which is explained by the entropic stabilization mechanism proposed on the basis of polymer physics. Polypeptide chains with hydrophilic side chains can adopt helical structures within nanotubes, but helix formation is sensitive to the nature of the nanotube due to WMIs. We elaborate on the potential implications of our findings to the stability of peptides in the ribosome tunnel.

The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry of the building blocks of protein structures, alpha-helices and strands assembled into beta-sheets, with no adjustable parameters, no amino acid sequence information, and no chemistry. There is an almost perfect fit between the dictates of mathematics and physics and the rules of quantum chemistry. Our theory establishes an energy landscape that channels protein evolution by providing sequence-independent platforms for elaborating sequence-dependent functional diversity. Our work highlights the vital role of discreteness in life and has implications for the creation of artificial life and on the nature of life elsewhere in the cosmos., 32 pages, 6 figures, 2 tables; Added key sentence about the important role of amino acid side chains in providing steric constraints

We introduce a powerful, widely applicable approach to characterizing polymer conformational distributions, specifically the end-to-end distance distributions, P(Ree), accessed through double electron-electron resonance (DEER) spectroscopy in conjunction with molecular dynamics (MD) simulations. The technique is demonstrated on one of the most widely used synthetic, disordered, water-soluble polymers: poly(ethylene oxide) (PEO). Despite its widespread importance, no systematic experimental characterization of PEO's Ree conformational landscape exists. The evaluation of P(Ree) is particularly important for short polymers or (bio)polymers with sequence complexities that deviate from simple polymer physics scaling laws valid for long chains. In this study, we characterize the Ree landscape by measuring P(Ree) for low molecular weight (MW: 0.22-2.6 kDa) dilute PEO chains. We use DEER with end-conjugated spin probes to resolve Ree populations from ∼2-9 nm and compare them with full distributions from MD. The P( Ree)'s from DEER and MD show remarkably good agreement, particularly at longer chain lengths where populations in the DEER-unresolvable range ( 10 kDa) PEO and the P(Ree)'s crossover to the theoretical distribution for an excluded volume chain.

Materials and design 196(109110), 1-11 (2020)., Published by Elsevier Science, Amsterdam [u.a.]

Since their inception, hydrogels have gained popularity among multiple fields, most significantly in biomedical research and industry. Due to their resemblance to biological tribosystems, a significant amount of research has been conducted on hydrogels to elucidate biolubrication mechanisms and their possible applications as replacement materials. This review is focused on lubrication mechanisms and covers friction models that have attempted to quantify the complex frictional characteristics of hydrogels. From models developed on the basis of polymer physics to the concept of hydration lubrication, assumptions and conditions for their applicability are discussed. Based on previous models and our own experimental findings, we propose the viscous-adhesive model for hydrogel friction. This model accounts for the effects of confinement of the polymer network provided by a solid surface and poroelastic relaxation as well as the (non) Newtonian shear of a complex fluid on the frictional force and quantifies the frictional response of hydrogels-solid interfaces. Finally, the review delineates potential areas of future research based on the current knowledge.

We study the structural ensembles of human chromosomes across different cell types. Using computer simulations, we generate cell-specific 3D chromosomal structures and compare them to recently published chromatin structures obtained through microscopy. We demonstrate using a combination of machine learning and polymer physics simulations that epigenetic information can be used to predict the structural ensembles of multiple human cell lines. The chromosomal structures obtained in silico are quantitatively consistent with those obtained through microscopy as well as DNA-DNA proximity ligation assays. Theory predicts that chromosome structures are fluid and can only be described by an ensemble, which is consistent with the observation that chromosomes exhibit no unique fold. Nevertheless, our analysis of both structures from simulation and microscopy reveals that short segments of chromatin make transitions between a closed conformation and an open dumbbell conformation. This conformational transition appears to be consistent with a two-state process with an effective free energy cost of about four times the effective information theoretic temperature. Finally, we study the conformational changes associated with the switching of genomic compartments observed in human cell lines. Genetically identical but epigenetically distinct cell types appear to rearrange their respective structural ensembles to expose segments of transcriptionally active chromatin, belonging to the A genomic compartment, towards the surface of the chromosome, while inactive segments, belonging to the B compartment, move to the interior. The formation of genomic compartments resembles hydrophobic collapse in protein folding, with the aggregation of denser and predominantly inactive chromatin driving the positioning of active chromatin toward the surface of individual chromosomal territories.

A study applies polymer physics to assess the advantages and limitations of three sequencing-based approaches for determining the structure of genomes and genomic domains.

Chains dynamics, specially when repulsive interactions come at play, remains an unsolved problem of polymer physics, although understanding this dynamics could improve our knowledge about crucial phenomena at the cellular level. For instance, the transport of RNA across the nuclear pore or the injection of viral DNA plasmid by bacteriophages into a bacteria. Alas, studying repulsive polymers in confined geometries is as experimentally difficult as it is biologically relevant. In spite of recent advances in ≪ nanorheology ≫, from the Brownian motion of local probes, or in com- puter simulation, designing experiments matching the biological parameters is near impossible. All this leads to unchallenged theoretical tools. Even the straightforward problem of polymer translocation remains lively debated. As a way out of this impasse, we propose to use granular chain as a macroscopic equivalent of a polymer. First we were interested in the internal structure of a stack of granular chains at rest and we rationalized it with polymer analogy. Then we added energy in our experimental system via mechanical excitations which appears to be analogous to the equilibration with a thermal bath. Finally we studied the dynamics of chains in specific confined geometries and compared it to both molecular dynamics simulation and theoretical tools., La dynamique des chaînes est encore de nos jours une question ouverte en physique des polymères, tout particulièrement lorsque les interactions répulsives sont prises en compte. Néanmoins, répondre à cette question améliorerait nos connaissances sur la machinerie cellulaire. On peut penser, par exemple, au transport de l’ARN du noyau au cytoplasme ou encore à l’injection du matériel génétique de bactériophages dans les bactéries. Malheureusement, étudier ces polymères en situation confinée est aussi expérimentalement difficile que biologiquement pertinent. En dépit des récentes avancées en nanorhéologie et en simulation de dynamique moléculaire, concevoir des expériences reprenant les mêmes paramètres que rencontrés in vivo est proche de l’impossible. Les théories en place ne peuvent donc être contestées par l’expérience. Même le problème, simple en apparence, de la translocation est encore aujourd’hui âprement discuté. Nous proposons, pour sortir de l’impasse actuelle, d’utiliser un équivalent d’un polymère à l’échelle macroscopique : la chaîne granulaire. Nous nous sommes tout d’abord intéressé à la structure interne d’un empilement de chaînes granulaires, au repos, et nous proposons pour la comprendre d’adopter une analogie avec les polymères. Après quoi, nous introduisons, par le biais d’une excitation mécanique, de l’énergie dans notre système expérimental et nous montrons que c’est statistiquement analogue à l’équilibre thermique à l’échelle microscopique. Enfin, nous étudions la dynamique de chaînes granulaires dans des géométries confinées et nous comparons nos résultats à ceux obtenus par simulation de dynamique moléculaire et ceux théoriquement attendus.

Electronics that can be stretched and feature skin-inspired functionalities are opening doors for opportunities in health and environmental monitoring, sustainability, and next-generation consumer products. Degradability is an important attribute for applications on dynamic surfaces where manual recovery would be logistically or financially unpractical. A key step to realize such electronics is the development of a stretchable and degradable transistor with electrical performance independent of large mechanical stress. Herein, we decouple the design of stretchability and transience by harmonizing polymer physics principles and molecular design in order to demonstrate for the first time a material that simultaneously possesses three disparate attributes: semiconductivity, intrinsic stretchability, and full degradability. This polymeric system represents a promising advance towards developing multifunctional materials for skin-inspired electronics.

The generation of localized temperature gradients is accompanied by new fundamental physics and also provides new tools for the control of molecules, particles or more complex matter in solution. We describe experiments, which use metal nano- and microstructures as optically pumped heat sources. Heat flowing from these structures along solid/liquid interfaces sets liquids into motion. With the help of such thermo-osmotic creep flows, we can trap particles and single molecules suspended in liquids without body forces but with forces balances. Also, the compression of macro-molecules becomes accessible. The inhomogeneous temperature, however, also modifies the Brownian dynamics. We report applications in the field polymer physics and protein aggregation, where such trapping techniques provide a unique new insight. We address the dynamics of heated colloids in optical tweezers with nanosecond time resolution and picometer spatial resolution to understand thermal non-equilibrium effects.

We consider the polymer physics of a possible molecular mechanism for disentangled melt states observed recently. We find that the route from molten, but only marginally-overlapping single crystals to the equilibrium state must pass over a free-energy barrier that becomes large at high molecular weights. The penalty arises from elastic distortions of the entanglement network as the chains diffuse. A critical molecular weight arises naturally from the competition of elastic distortion and the free-energy of confinement. We calculate the barrier and critical molecular weight at both a simple single-chain level, and at a “one-loop” level of co-operative motion, finding that many-chain effects alter the physics quantitatively, but not qualitatively. Several new experiments are suggested.

The shapes of living organisms are formed and maintained by precise control in time and space of growth, which is achieved by dynamically fine-tuning the mechanical (viscous and elastic) properties of their hierarchically built structures from the nanometer up. Most organisms on Earth including plants grow by yield (under pressure) of cell walls (bio-polymeric matrices equivalent to extracellular matrix in animal tissues) whose underlying nanoscale viscoelastic properties remain unknown. Multifrequency atomic force microscopy (AFM) techniques exist that are able to map properties to a small subgroup of linear viscoelastic materials (those obeying the Kelvin-Voigt model), but are not applicable to growing materials, and hence are of limited interest to most biological situations. Here, we extend existing dynamic AFM methods to image linear viscoelastic behaviour in general, and relaxation times of cells of multicellular organisms in vivo with nanoscale resolution (~80 nm pixel size in this study), featuring a simple method to test the validity of the mechanical model used to interpret the data. We use this technique to image cells at the surface of living Arabidopsis thaliana hypocotyls to obtain topographical maps of storage E′ = 120–200 MPa and loss E″ = 46–111 MPa moduli as well as relaxation times τ = 2.2–2.7 µs of their cell walls. Our results demonstrate that (taken together with previous studies) cell walls, despite their complex molecular composition, display a striking continuity of simple, linear, viscoelastic behaviour across scales–following almost perfectly the standard linear solid model–with characteristic nanometer scale patterns of relaxation times, elasticity and viscosity, whose values correlate linearly with the speed of macroscopic growth. We show that the time-scales probed by dynamic AFM experiments (microseconds) are key to understand macroscopic scale dynamics (e.g. growth) as predicted by physics of polymer dynamics.

Biology offers new systems for Physics, namely proteins and molecular motors in interaction with biopolymers like DNA and messenger RNA. This field is at the interface between active matter, polymer physics, and physics of colloids. Interestingly, cells also need to increase locally concentrations of proteins in a phase transition-like mechanism to realize vital function like cell division, DNA repair, DNA segregation etc. During this HDR defense, I will offer a physical perspective of intracellular phase transition with the example of bacterial DNA segregation. I will also discuss the motion of ribosomes along messenger RNA, an example of unidimensional inhomogeneous transport giving rise to different dynamical regimes.; Biology offers new systems for Physics, namely proteins and molecular motors in interaction with biopolymers like DNA and messenger RNA. This field is at the interface between active matter, polymer physics, and physics of colloids. Interestingly, cells also need to increase locally concentrations of proteins in a phase transition-like mechanism to realize vital function like cell division, DNA repair, DNA segregation etc. During this HDR defense, I will offer a physical perspective of intracellular phase transition with the example of bacterial DNA segregation. I will also discuss the motion of ribosomes along messenger RNA, an example of unidimensional inhomogeneous transport giving rise to different dynamical regimes.

The statistics of self-avoiding random walks have been used to model polymer physics for decades. A self-avoiding walk that grows one step at a time on a lattice will eventually trap itself, which occurs after an average of 71 steps on a square lattice. Here, we consider the effect of nearest-neighbor attractive interactions on the growing self-avoiding walk, and examine the effect that self-attraction has both on the statistics of trapping as well as on chain statistics through the transition between expanded and collapsed walks at the theta point. We find the trapping length increases exponentially with the nearest-neighbor contact energy, but that there is a local minimum in trapping length for weakly self-attractive walks. While it has been controversial whether growing self-avoiding walks have the same asymptotic behavior as traditional self-avoiding walks, we find that the theta point is not at the same location for growing self-avoiding walks, and that the persistence length converges much more rapidly to a smaller value., 9 pages, 8 figures + 2 in appendix

In concentrated electrolytes with asymmetric or irregular ions, such as ionic liquids and solvent-in-salt electrolytes, ion association is more complicated than simple ion-pairing. Large branched aggregates can form at significant concentrations at even moderate salt concentrations. When the extent of ion association reaches a certain threshold, a percolating ionic gel network can form spontaneously. Gelation is a phenomenon that is well known in polymer physics, but it is practically unstudied in concentrated electrolytes. However, despite this fact, the ion-pairing description is often applied to these systems for the sake of simplicity. In this work, drawing strongly from established theories in polymer physics, we develop a simple thermodynamic model of reversible ionic aggregation and gelation in concentrated electrolytes accounting for the competition between ion solvation and ion association. Our model describes, with the use of several phenomenological parameters, the populations of ionic clusters of different sizes as a function of salt concentration; it captures the onset of ionic gelation and also the post-gel partitioning of ions into the gel. We discuss the applicability of our model, as well as the implications of its predictions on thermodynamic, transport, and rheological properties.

The spatial organization of chromosomes has key functional roles, yet how chromosomes fold remains poorly understood at the single-molecule level. Here, we employ models of polymer physics to investigate DNA loci in human HCT116 and IMR90 wild-type and cohesin depleted cells. Model predictions on single-molecule structures are validated against single-cell imaging data, providing evidence that chromosomal architecture is controlled by a thermodynamics mechanism of polymer phase separation whereby chromatin self-assembles in segregated globules by combinatorial interactions of chromatin factors that include CTCF and cohesin. The thermodynamics degeneracy of single-molecule conformations results in broad structural and temporal variability of TAD-like contact patterns. Globules establish stable environments where specific contacts are highly favored over stochastic encounters. Cohesin depletion reverses phase separation into randomly folded states, erasing average interaction patterns. Overall, globule phase separation appears to be a robust yet reversible mechanism of chromatin organization where stochasticity and specificity coexist., The molecular and physical mechanisms underlying chromatin folding at the single DNA molecule level remain poorly understood. Here, the authors use polymer modeling to investigate the conformations of two 2Mb-wide DNA loci in normal and cohesin depleted cells, and provide evidence that the architecture of the studied loci is controlled by a thermodynamics mechanism of polymer phase separation whereby chromatin self-assembles in segregated globules.

Summary: We investigate the three-dimensional (3D) conformations of the α-globin locus at the single-allele level in murine embryonic stem cells (ESCs) and erythroid cells, combining polymer physics models and high-resolution Capture-C data. Model predictions are validated against independent fluorescence in situ hybridization (FISH) data measuring pairwise distances, and Tri-C data identifying three-way contacts. The architecture is rearranged during the transition from ESCs to erythroid cells, associated with the activation of the globin genes. We find that in ESCs, the spatial organization conforms to a highly intermingled 3D structure involving non-specific contacts, whereas in erythroid cells the α-globin genes and their enhancers form a self-contained domain, arranged in a folded hairpin conformation, separated from intermingling flanking regions by a thermodynamic mechanism of micro-phase separation. The flanking regions are rich in convergent CTCF sites, which only marginally participate in the erythroid-specific gene-enhancer contacts, suggesting that beyond the interaction of CTCF sites, multiple molecular mechanisms cooperate to form an interacting domain. : Chiariello et al. use polymer physics models to infer the 3D conformations of the murine α-globin locus. In the transition from ESCs to erythroid cells, the locus rearranges from an inactive highly intermingled conformation to an active, hairpin-shaped structure, marked by cell-specific three-way contacts accurately predicted by the models. Keywords: globin loci, higher-order chromatin organization, polymer physics, gene regulation

New theoretical and experimental work suggests that 10-nm chromatin fiber is folded into tree-like domains in single cells., With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggest that this irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing three-dimensional genome into tree data structures on top of, and in striking contrast to, the linear topology of DNA double helix. These functional modules need to be connected and isolated by an open backbone that results in porous and heterogeneous packing in a quasi–self-similar manner, as revealed by our electron and optical imaging. Our multiscale theoretical and experimental results suggest the existence of higher-order universal folding principles for a disordered chromatin fiber to avoid entanglement and fulfill its biological functions.

Intrinsically disordered linkers control avidity, auto-inhibition, catalysis, and liquid-liquid phase separation in multidomain proteins. Linkers enforce effective concentrations that directly affect the kinetics and equilibrium positions of intramolecular reactions. Mechanistic understanding of the role of linkers thus requires measurements of the effective concentrations in supramolecular complexes. Here, we describe an experimental protocol for measuring the effective concentrations enforced by a linker using a competition assay. The experiment uses a FRET biosensor that is titrated by a competitor peptide. The assay is designed for parallel analysis of several constructs in a fluorescent plate reader and has been used to study hundreds of synthetic disordered linkers.

Background Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes. How condensin contributes to chromatin organization in interphase is less well understood. Results Here, we use efficient conditional depletion of fission yeast condensin to determine its contribution to interphase chromatin organization. We deplete condensin in G2-arrested cells to preempt confounding effects from cell cycle progression without condensin. Genome-wide chromatin interaction mapping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitatively similar to those observed in mitosis, but quantitatively far less prevalent. Despite their low abundance, chromatin mobility tracking shows that condensin markedly confines interphase chromatin movements. Without condensin, chromatin behaves as an unconstrained Rouse polymer with excluded volume, while condensin constrains its mobility. Unexpectedly, we find that condensin is required during interphase to prevent ongoing transcription from eliciting a DNA damage response. Conclusions In addition to establishing mitotic chromosome architecture, condensin-mediated long-range chromatin interactions contribute to shaping chromatin organization in interphase. The resulting structure confines chromatin mobility and protects the genome from transcription-induced DNA damage. This adds to the important roles of condensin in maintaining chromosome stability.

Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular biological phenomenon. This process is driven by the formation of chromosome loops. The ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE), we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the available experimental data quantitatively, and suggests that condensin must undergo a large conformational change, induced by ATP binding, bringing distant parts of the motor to proximity. Simulations using a simple model confirm that the motor transitions between an open and a closed state in order to extrude loops by a scrunching mechanism, similar to that proposed in DNA bubble formation during bacterial transcription. Changes in the orientation of the motor domains are transmitted over ~50 nm, connecting the motor head and the hinge, thus providing an allosteric basis for LE., How chromosomes, which are polymers with nearly billion base pairs, are packaged in the restricted nuclear volume is not well understood. Here, the authors combine polymer physics, nonequilibrium fluctuation theorem, and simulations to quantitatively predict the force-dependent velocity and step-size distribution of condensin, which facilitates the folding of chromosomes by loop extrusion.

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., Comment: 21 pages, 12 figures, submitted for publication

Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo "Non-equilibrium chromosome looping via molecular slip-links", Physical Review Letters 119, 138101 (2017), Comment: 7 pages, 3 figures

Innovative experimental protocols from Molecular Biology provided in recent years quantitative data about the structure of the cell nucleus. These technologies, such as Hi-C, GAM or SPRITE, revealed that the genome has a non-random three-dimensional (3D) spatial organization, which serves functional purposes. In order to dissect the complexity of chromosome folding, models from Polymer Physics have been employed, highlighting many key aspects of large-scale chromatin organization. A deep understanding of the molecular mechanisms underlying the genome architecture is currently a crucial problem in Biology, since chromatin misfolding or structural variants can reconfigure chromatin domains, thereby resulting in pathogenic phenotypes and disease. Here, we discuss a numerical Polymer-Physics-based approach (PRISMR), able to model 3D chromatin folding by using Machine Learning strategies informed with experimental data. Using as a case study the Pitx1 locus, a genomic region critically involved in hindlimb development, we show that the PRISMR algorithm reproduces in silico with high accuracy the experimental contact data, thus providing a powerful computational tool for analyzing and predicting the 3D chromatin structure.

Ultra-High Molecular Weight semi-crystalline polymers, such as Ultra-High Molecular Weight PolyEthylene (UHMWPE) exhibit strong wear and impact resistance, making them good candidates for structural applications in many industrial fields. At high strain rate and large strain, mechanisms of deformation are quite different from those involved in classical semi-crystalline polymers, mainly because chain disentanglements are almost impossible for very long macromolecules even at temperature far above the melting point. Thus, there is a need to develop specific models for these materials and, from the works of Deplancke and her co-workers (Deplancke et al., 2019; Deplancke et al., 2015) who developed a scalar description based on polymer physics, three-dimensional constitutive equations are developed in this work. The developed model proposes an innovative way to take into account the repartition of strain for a semi-crystalline polymer and more generally for a two-phase material. Moreover, by modelling the evolution of microstructure during the plastic deformation of the material, the model is able to reproduce quite fairly the mechanical behavior of UHMWPE for both loading and unloading.

Microscopy and sequencing-based technologies are providing increasing insights into chromatin architecture. Nevertheless, a full comprehension of chromosome folding and its link with vital cell functions is far from accomplished at the molecular level. Recent theoretical and computational approaches are providing important support to experiments to dissect the three-dimensional structure of chromosomes and its organizational mechanisms. Here, we review, in particular, the String&Binders polymer model of chromatin that describes the textbook scenario where contacts between distal DNA sites are established by cognate binders. It has been shown to recapitulate key features of chromosome folding and to be able at predicting how phenotypes causing structural variants rewire the interactions between genes and regulators.

The constant development of sophisticated technologies is allowing to dissect three-dimensional chromatin structure at high resolution level. The tremendous amount of quantitative experimental data available today requires a conceptual framework able to make sense of them. In this perspective, polymer physics offers a key tool to interpret chromatin architecture data and to unveil the basic mechanisms shaping its structure. In the very last years, several polymer models have been proposed and have allowed to capture complex features emerging from the data. The major peculiarity distinguishing the different models is represented by the more or less complicated physical mechanism used to explain chromatin folding. Here, we review very popular models which have been recently developed and which represent brilliant examples from this interdisciplinary research field. In order to highlight the wide range of practical applications they have, we discuss the cases of the murine Pitx1 and the human EPHA4 loci, showing that polymer physics allows to effectively study chromatin structure in different cell lines and to predict the impact of pathogenic structural variants on the genome three-dimensional architecture. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Theoretical and Physical Chemistry > Statistical Mechanics.

A sterically π-congested ortho-phenylated poly(p-phenylene) (PPP) has been synthesized with unprecedentedly high molecular weights up to 29 kDa after fractionation, as confirmed by gel permeation chromatography coupled with a multiangle laser light scattering detector. The chain translation diffusion coefficient obtained from dynamic light scattering experiments displayed strong scaling (∼Lw–0.8) to the chain contour length, indicating a rodlike shape with remarkably high rigidity of this novel PPP. These results provide an interesting insight into the relationship between the structure and the chain stiffness of PPP-based polymers and challenge the validity of the existing diffusion models in polymer physics.