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The nuclear pore complex (NPC) is a critical gateway regulating molecular transport between the nucleus and cytoplasm. It allows small molecules to pass freely, while larger molecules require nuclear transport receptors to traverse the barrier. This selective permeability is maintained by phenylalanine-glycine-rich nucleoporins (FG-Nups), intrinsically disordered proteins that fill the NPC's central channel. The disordered and flexible nature of FG-Nups complicates their spatial characterization with conventional structural biology techniques. To address this challenge, polymer physics offers a valuable framework for describing FG-Nup behavior, reducing their complex structures to a few key parameters. In this review, we explore how polymer physics models FG-Nups using these parameters and discuss experimental efforts to quantify them in various contexts, providing insights into the conformational properties of FG-Nups.

Interactions between polymer molecules and inorganic nanoparticles can play a dominant role in nanocomposite material mechanics, yet control of such interfacial interaction dynamics remains a significant challenge particularly in water. This study presents insights on how to engineer hydrogel material mechanics via nanoparticle interface-controlled cross-link dynamics. Inspired by the adhesive chemistry in mussel threads, we have incorporated iron oxide nanoparticles (Fe3O4 NPs) into a catechol-modified polymer network to obtain hydrogels cross-linked via reversible metal-coordination bonds at Fe3O4 NP surfaces. Unique material mechanics result from the supra-molecular cross-link structure dynamics in the gels; in contrast to the previously reported fluid-like dynamics of transient catechol-Fe(3+) cross-links, the catechol-Fe3O4 NP structures provide solid-like yet reversible hydrogel mechanics. The structurally controlled hierarchical mechanics presented here suggest how to develop hydrogels with remote-controlled self-healing dynamics.

The development of novel experimental technologies able to map genome-wide chromatin contacts, as Hi-C, GAM or SPRITE, allowed to derive detailed information about the spatial structure of chromosomes in the cell nucleus. They revealed that the genome has a complex spatial organisation, which is highly connected with its activity. In the last years, such an abundance of experimental data prompted the development of quantitative models based on Polymer Physics to describe the chromatin architecture, clarifying many aspects about the molecular mechanisms underlying genome folding. Efficient algorithms are thus fundamental to perform massive numerical simulations for testing the accuracy of these models and provide a good description for small genomic regions or for whole chromosomes. Here, we consider the performances of Molecular Dynamics (MD) implementation of commonly used polymer physics models. Such models can be combined with Machine Learning approaches informed with experimental data to produce more accurate descriptions of real genomic regions. However, the execution times increase as a power-law with the size of the input data, which ultimately reflects the complexity of the investigated system. The best strategy is therefore a convenient trade-off between the accuracy in the description and the availability of computational resources. The combination of innovative experimental data and polymer physics theories allow to reconstruct the 3D genome structure. This is achieved by the use of machine learning approaches and massive parallel computing. Efficient algorithms and computational resources are then fundamental to produce models of increasingly high accuracy. [ABSTRACT FROM AUTHOR]

Abstract 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.

Understanding the mechanisms underlying the complex 3D architecture of mammalian genomes poses, at a more fundamental level, the problem of how two or multiple genomic sites can establish physical contacts in the nucleus of the cells. Beyond stochastic and fleeting encounters related to the polymeric nature of chromatin, experiments have revealed specific, privileged patterns of interactions that suggest the existence of basic organizing principles of folding. In this review, we focus on two major and recently proposed physical processes of chromatin organization: loop-extrusion and polymer phase-separation, both supported by increasing experimental evidence. We discuss their implementation into polymer physics models, which we test against available single-cell super-resolution imaging data, showing that both mechanisms can cooperate to shape chromatin structure at the single-molecule level. Next, by exploiting the comprehension of the underlying molecular mechanisms, we illustrate how such polymer models can be used as powerful tools to make predictions in silico that can complement experiments in understanding genome folding. To this aim, we focus on recent key applications, such as the prediction of chromatin structure rearrangements upon disease-associated mutations and the identification of the putative chromatin organizing factors that orchestrate the specificity of DNA regulatory contacts genome-wide.

Biomolecular condensation and phase separation are increasingly understood to play crucial roles in cellular compartmentalization and spatiotemporal regulation of cell machinery implicated in function and pathology. A key aspect of current research is to gain insight into the underlying physical mechanisms of these processes. Accordingly, concepts of soft matter and polymer physics, the thermodynamics of mixing, and material science have been utilized for understanding condensation mechanisms of multivalent macromolecules resulting in viscoelastic mesoscopic supramolecular assemblies. Here, we focus on two topological concepts that have recently been providing key mechanistic understanding in the field. First, we will discuss how percolation provides a network-topology-related framework that offers an interesting paradigm to understand the complex networking of dense ‘connected’ condensate structures and, therefore, their phase behavior. Second, we will discuss the idea of entanglement as another topological concept that has deep roots in polymer physics and important implications for biomolecular condensates. We will first review some historical developments and fundamentals of these concepts, then we will discuss current advancements and recent examples. Our discussion ends with a few open questions and the challenges to address them, hinting at unveiling fresh possibilities for the modification of existing knowledge as well as the development of new concepts relevant to condensate science.

Spontaneous locomotion is a common feature of most metazoan cells, generally attributed to the properties of actomyosin networks. This force-producing machinery has been studied down to the most minute molecular details, especially in lamellipodium-driven migration. Nevertheless, how actomyosin networks work inside contraction-driven amoeboid cells still lacks unifying principles. Here, using stable motile blebs from HeLa cells as a model amoeboid motile system, we imaged the dynamics of the actin cortex at the single filament level and revealed the co-existence of three distinct rheological phases. We introduce "advected percolation," a process where rigidity percolation and active advection synergize, spatially organizing the actin network's mechanical properties into a minimal and generic locomotion mechanism. Expanding from our observations on simplified systems, we speculate that this model could explain, down to the single actin filament level, how amoeboid cells, such as cancer or immune cells, can propel efficiently through complex 3D environments., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

An array of motor proteins consumes chemical energy in setting up the architectures of chromosomes. Here, we explore how the structure of ideal polymer chains is influenced by two classes of motors. The first class which we call "swimming motors" acts to propel the chromatin fiber through three-dimensional space. They represent a caricature of motors such as RNA polymerases. Previously, they have often been described by adding a persistent flow onto Brownian diffusion of the chain. The second class of motors, which we call "grappling motors" caricatures the loop extrusion processes in which segments of chromatin fibers some distance apart are brought together. We analyze these models using a self-consistent variational phonon approximation to a many-body Master equation incorporating motor activities. We show that whether the swimming motors lead to contraction or expansion depends on the susceptibility of the motors, that is, how their activity depends on the forces they must exert. Grappling motors in contrast to swimming motors lead to long-ranged correlations that resemble those first suggested for fractal globules and that are consistent with the effective interactions inferred by energy landscape analyses of Hi-C data on the interphase chromosome., Competing Interests: Competing interests statement:The authors declare no competing interest.

Summary: All kingdoms of life have evolved tip‐growing cells able to mine their environment or deliver cargo to remote targets. The basic cellular processes supporting these functions are understood in increasing detail, but the multiple interactions between them lead to complex responses that require quantitative models to be disentangled. Here, I review the equations that capture the fundamental interactions between wall mechanics and cell hydraulics starting with a detailed presentation of James Lockhart's seminal model. The homeostatic feedbacks needed to maintain a steady tip velocity are then shown to offer a credible explanation for the pulsatile growth observed in some tip‐growing cells. Turgor pressure emerges as a central variable whose role in the morphogenetic process has been a source of controversy for more than 50 yr. I argue that recasting Lockhart's work as a process of chemical stress relaxation can clarify how cells control tip growth and help us internalise the important but passive role played by turgor pressure in the morphogenetic process. [ABSTRACT FROM AUTHOR]

The effects of molecular weight ( M w ) of polystyrene (PS) latex particles on optical and electrical percolations of multi-walled carbon nanotube (MWCNT)-added nanocomposite films were reported. Three different latex particle solutions, each having different M w , were first mixed with MWCNT dispersions at various mass fractions between 0 and 20 wt.% to prepare nanocomposites, and then the drop-casting method was employed to coat glass substrates by nanocomposite films. Surface resistivity, photon transmission and scanning electron microscopy measurements were performed on prepared films. As a result, the M w of latex particles had no influence on both optical, φ o and electrical percolation, φ c thresholds and the same threshold values were determined as 1.5 wt.%. Upon decreasing the latex M w , a steady reduction from 3.99 to 2.28 was observed for the critical exponents of electrical percolation, β c whereas almost similar critical exponents of optical percolation (averaged β o ≈ 0.20) were found without any trend. [ABSTRACT FROM AUTHOR]

Simulating soft matter systems such as the cytoskeleton can enable deep understanding of experimentally observed phenomena. One challenge of modelling 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 parameterise these models. We also generalise 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 generalised to facilitate the development of effective interaction potentials for other finite elements in simulations of softmatter systems. [ABSTRACT FROM AUTHOR]

Recent super-resolution imaging technologies enable tracing chromatin conformation with nanometer-scale precision at the single-cell level. They revealed, for example, that human chromosomes fold into a complex three-dimensional structure within the cell nucleus that is essential to establish biological activities, such as the regulation of the genes. Yet, to decode from imaging data the molecular mechanisms that shape the structure of the genome, quantitative methods are required. In this review, we consider models of polymer physics of chromosome folding that we benchmark against multiplexed FISH data available in human loci in IMR90 fibroblast cells. By combining polymer theory, numerical simulations and machine learning strategies, the predictions of the models are validated at the single-cell level, showing that chromosome structure is controlled by the interplay of distinct physical processes, such as active loop-extrusion and thermodynamic phase-separation.

Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular interactions greatly influence chain dynamics. In this work, we directly observe the dynamics of DNA rings in semidilute ring-linear polymer blends using single molecule techniques. We systematically investigate ring polymer relaxation dynamics from high extension and transient and steady-state stretching dynamics in a planar extensional flow for a series of ring-linear blends with varying ring fraction. Our results show multiple molecular subpopulations for ring relaxation in ring-linear blends, as well as large conformational fluctuations for rings in a steady extensional flow, even long after the initial transient stretching process has subsided. We further quantify the magnitude and characteristic time scales of ring conformational fluctuations as a function of blend composition. Interestingly, we find that the magnitude of ring conformational fluctuations follows a nonmonotonic response with increasing ring fraction, first increasing at low ring fraction and then substantially decreasing at large ring fraction in ring-linear blends. A unique set of ring polymer conformations are observed during the transient stretching process, which highlights the prevalence of molecular individualism and supports the notion of complex intermolecular interactions in ring-linear polymer blends. In particular, our results suggest that transient intermolecular structures form in ring-linear blends due to a combination of direct forces due to linear chains threading through open rings and indirect forces due to hydrodynamic interactions; these combined effects lead to large conformational fluctuations of rings over distributed time scales. Taken together, our results provide a new molecular understanding of ring polymer dynamics in ring-linear blends in the nonequilibrium flow. [ABSTRACT FROM AUTHOR]

We report the effect of graphene oxide (GO) on film formation and morphological properties of GO-doped polystyrene (PS) latex nanocomposite (PS latex/GO) films using UV-visible absorption spectroscopy and scanning electron microscopy (SEM). PS latex particles were synthesized through emulsion polymerization technique and then nanocomposite blends, each containing different concentrations of GO ranging from 0 wt% to 70 wt%, were obtained. Prepared blends were deposited on glass plates via drop-casting method and coated substrates were annealed at different temperatures between 100 °C and 250 °C. At each annealing temperature, transmitted light intensity of nanocomposite films was recorded. Void closure and Prager-Tirrell models were employed to interpret the film formation behavior. Activation energy of viscous flow (ΔH) decreased from 21.80 kcal·mol-1 to 5.91 kcal·mol-1 when the amount of GO content increased in film composition. However, activation energy of interdiffusion (ΔE) varied between 1.08 kcal·mol-1 and 6.94 kcal·mol-1 without any trend upon the addition of GO nanofillers. SEM images of films agreed well with calculated activation energies. Although the interdiffusion process of GO-doped latex films remained unaffected by added GO nanofillers, optical transparency of the films enhanced up to 92.5%, demonstrating that thermally resistant and highly transparent GO-rich nanocomposite films can be fabricated. [ABSTRACT FROM AUTHOR]

Genome architecture plays a pivotal role in gene regulation. The use of high-throughput methods for chromatin profiling and 3-D interaction mapping provide rich experimental data sets describing genome organization and dynamics. These data challenge development of new models and algorithms connecting genome architecture with epigenetic marks. In this review, we describe how chromatin architecture could be reconstructed from epigenetic data using biophysical or statistical approaches. We discuss the applicability and limitations of these methods for understanding the mechanisms of chromatin organization. We also highlight the emergence of new predictive approaches for scoring effects of structural variations in human cells.

Within cell nuclei, several biophysical processes occur in order to allow the correct activities of the genome such as transcription and gene regulation. To quantitatively investigate such processes, polymer physics models have been developed to unveil the molecular mechanisms underlying genome functions. Among these, phase-separation plays a key role since it controls gene activity and shapes chromatin spatial structure. In this paper, we review some recent experimental and theoretical progress in the field and show that polymer physics in synergy with numerical simulations can be helpful for several purposes, including the study of molecular condensates, gene-enhancer dynamics, and the three-dimensional reconstruction of real genomic regions.

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. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Genome architecture plays a pivotal role in gene regulation. The use of high-throughput methods for chromatin profiling and 3-D interaction mapping provide rich experimental data sets describing genome organization and dynamics. These data challenge development of new models and algorithms connecting genome architecture with epigenetic marks. In this review, we describe how chromatin architecture could be reconstructed from epigenetic data using biophysical or statistical approaches. We discuss the applicability and limitations of these methods for understanding the mechanisms of chromatin organization. We also highlight the emergence of new predictive approaches for scoring effects of structural variations in human cells. [ABSTRACT FROM AUTHOR]

Elastomers used in everyday life are always reinforced with rigid nanoparticles (carbon black or silica). The addition of rigid nanoparticles to an elastomer gives it very specific viscoelastic properties. In this article, we discuss the current understanding of mechanical properties of a polymer matrix around its glass transition, focusing on the situation of polymers confined between two rigid surfaces with a nanometric gap. Then, we will explain how the properties of the matrix can help to understand the properties of filled or reinforced elastomers. We will then explain that in reinforced rubbers, the mechanical properties are dominated by stress propagation between neighboring aggregates through a nanometric polymer gap, thus by confined polymer bridges.We will discuss how knowledge of the dynamics of confined polymers allows us to understand the temperature dependence, the pressure dependence and the non-linearities observed for strain below 0.1 of reinforced elastomers. [ABSTRACT FROM AUTHOR]

Different semicrystalline polymers including poly(l‐lactic acid), poly(ethylene terephthalate), syndiotactic polystyrene, and polyamide 12 are studied in terms of their mechanical response to uniaxial compression deformation. Apparent decoupling of yielding of amorphous and crystalline phases is identified as separate peaks in the stress–strain curve in the vicinity of the glass transition temperature. The same feature is also observed for the uniaxial extension of predrawn semicrystalline poly(ethylene terephthalate). It is indicated that in absence of a strong amorphous phase a semicrystalline polymer is unable to yield and undergo plastic deformation and it fails in a brittle manner in the uniaxial compression. Treating a semicrystalline polymer as a composite of amorphous and crystalline phases, putting emphasis on the crucial role of amorphous phase in acting as connectors between crystalline domains and indicating that the yielding of amorphous phase is a prerequisite for yielding of crystalline phase, work toward a better understanding of the mechanical properties of semicrystalline polymers at the molecular level is done. [ABSTRACT FROM AUTHOR]

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 BiophysicsMolecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo MethodsTheoretical and Physical Chemistry > Statistical Mechanics [ABSTRACT FROM AUTHOR]

Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target-probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety. [ABSTRACT FROM AUTHOR]

We incorporate the Boltzmann factors for inter‐monomer bending energy into the monomer growth direction choice in Rosenbluth's algorithm to model chains of arbitrary nearest‐neighbor rigidity. This allows for the consideration of compact (bent state lower in energy), free (straight and bent state equal in energy), or extended chains (bent state higher). We validate against, and compare to, various other results, showing very good agreement with known results for short chains and demonstrate the ability to model chains up to 500 segments long, far beyond the length at which the normal Rosenbluth method becomes unstable for reasonable nonzero bending energies. This approach is easily generalizable both to other energies determinable during chain growth, for example, polymers composed of more than one type of monomer with differing monomer interaction energies, as well as to other chain production algorithms. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 1684–1691 [ABSTRACT FROM AUTHOR]

Conjugated polymers are promising candidates for next‐generation low‐cost flexible electronics. Field‐effect transistors comprising conjugated polymers have witnessed significant improvements in device performance, notably the field‐effect mobility, in the last three decades. However, to truly make these materials commercially competitive, a better understanding of charge‐transport mechanisms in these structurally heterogeneous systems is needed for providing systematic guides for further improvements. This review assesses the key microstructural features of conjugated polymers across multiple length scales that can influence charge transport, with special attention given to the underlying polymer physics. The mechanistic understanding from collective experimental and theoretical studies point to the importance of interconnected ordered domains given the macromolecular nature of the polymeric semiconductors. Based on the criterion, optimization to improve charge transport can be broadly characterized by efforts to (a) promote intrachain transport, (b) establish intercrystallite connectivity, and (c) enhance interchain coupling. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 1559–1571 [ABSTRACT FROM AUTHOR]

The genome is 3-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are regulated within and across the domains according to their organization, whereas the chromatin itself is highly dynamic. However, the details of such dynamic organization of chromatin domains in living cells remain unclear. To unify chromatin dynamics and organization, we recently demonstrated that structural information of chromatin domains in living human cells can be extracted from analyses of the subdiffusive nucleosome movement using mathematical modeling. Our mathematical analysis suggested that as the chromatin domain becomes smaller and more compact, nucleosome movement becomes increasingly restricted. Here, we show the implication of these results for bridging the gap between chromatin dynamics and organization, and provide physical insight into chromatin domains as efficient units to conduct genome functions in the thermal noisy environment of the cell.

Thermotropic polymeric tissues have attracted considerable scientific interest for their useful biomedical applications. The complex coupling of van der Waals and steric interactions influences the thermal response of polymers’ molecular structure. Comprehensive theories that govern the molecular reorganization define the intramolecular interactions as the interactions between segments of the same polymer, and intermolecular interactions as the interactions between different polymers' segments of differ. The attractive interactions between polymer segments are determined via exact calculations of the intramolecular interactions, while the intermolecular interactions are treated with a self-consistent approximation, which leads to the double counting of the intermolecular interactions. Our decoupled self-consistent field theory (SCF) corrects for that double counting. The results show that the decoupled SCF theory considers less attractive energy than the standard one. These results improve the calculations of several parameters, such as the polymers end-to-end distance, and distinguish the critical parameters that lead to the formation of micelles.

Many multidomain proteins contain disordered linkers that regulate interdomain contacts, and thus the effective concentrations that govern intramolecular reactions. Effective concentrations are rarely measured experimentally, and therefore little is known about how they relate to linker architecture. We have directly measured the effective concentrations enforced by disordered protein linkers using a fluorescent biosensor. We show that effective concentrations follow simple geometric models based on polymer physics, offering an indirect method to probe the structural properties of the linker. The compaction of the disordered linker depends not only on net charge, but also on the type of charged residues. In contrast to theoretical predictions, we found that polyampholyte linkers can contract to similar dimensions as globular proteins. Hydrophobicity has little effect in itself, but aromatic residues lead to strong compaction, likely through π-interactions. Finally, we find that the individual contributors to chain compaction are not additive. We thus demonstrate that direct measurement of effective concentrations can be used in systematic studies of the relationship between sequence and structure of intrinsically disordered proteins. A quantitative understanding of the relationship between effective concentration and linker sequence will be crucial for understanding disorder-based allosteric regulation in multidomain proteins. [ABSTRACT FROM AUTHOR]

Highly controlled polymers and nanostructures are increasingly translated from the lab to the industry. Together with the industrialization of complex systems from renewable sources, a paradigm change in the processing of plastics and rubbers is underway, requiring a new generation of analytical tools. Here, we present the recent developments in time domain NMR (TD-NMR), starting with an introduction of the methods. Several examples illustrate the new take on traditional issues like the measurement of crosslink density in vulcanized rubber or the monitoring of crystallization kinetics, as well as the unique information that can be extracted from multiphase, nanophase and composite materials. Generally, TD-NMR is capable of determining structural parameters that are in agreement with other techniques and with the final macroscopic properties of industrial interest, as well as reveal details on the local homogeneity that are difficult to obtain otherwise. Considering its moderate technical and space requirements of performing, TD-NMR is a good candidate for assisting product and process development in several applications throughout the rubber, plastics, composites and adhesives industry. [ABSTRACT FROM AUTHOR]

Delayed capillary break-up of viscoelastic filaments presents scientific and technical challenges relevant for drop formation, dispensing, and adhesion in industrial and biological applications. The flow kinematics are primarily dictated by the viscoelastic stresses contributed by the polymers that are stretched and oriented in a strong extensional flow field resulting from the streamwise gradients created by the capillarity-driven squeeze flow. After an initial inertiocapillary (IC) or viscocapillary (VC) regime, where elastic effects seem to play no role, the interplay of capillarity and viscoelasticity can lead to an elastocapillary (EC) response characterized by exponentially-slow thinning of neck radius (extensional relaxation time is determined from the delay constant). Less frequently, a terminal visco-elastocapillary (TVEC) response with linear decay in radius can be observed and used for measuring terminal, steady extensional viscosity. However, both IC/VC-EC and EC-TVEC transitions are inaccessible in devices that create stretched necks by applying a step strain to a liquid bridge (e.g., capillary breakup extensional rheometer). In this study, we use dripping-onto-substrate rheometry to obtain radius evolution data for unentangled polymer solutions. We deduce that the plots of transient extensional viscosity vs. Hencky strain (scaled by the respective values at the EC-TVEC transition) emulate the functional form of the birefringence-macromolecular strain relationship based on Peterlin's theory. We quantify the duration and strain between the IC/VC-EC and the EC-TVEC transitions using measures we term elastocapillary span and elastocapillary strain increment and find both measures show values directly correlated with the corresponding variation in extensional relaxation time. [ABSTRACT FROM AUTHOR]

Chromosome organization and chromatin mobility are central to DNA metabolism. In particular, it has been recently shown by several labs that double strand breaks (DSBs) in yeast induce a change in chromatin mobility at the site of the damage. Intriguingly, DSB also induces a global mobility of the genome, at others, potentially undamaged positions. How mobility is regulated and what are the functional outcomes of these global changes in chromatin dynamics are, however, not yet fully understood. We present the current state of knowledge in light of the recent literature and discuss some perspectives opened by these discoveries towards genome stability. [ABSTRACT FROM AUTHOR]

Combining atomistic and coarse-grained (CG) models is a promising approach for quantitative prediction of polymer properties. However, the gaps between the length and time scales of atomistic and CG models still need to be bridged. Here, the scale gaps of the atomistic model of polyethylene melts, the bead−spring Kremer−Grest model, and dissipative particle dynamics with the slip-spring model were investigated. A single set of spatial and temporal scaling factors was determined between the atomistic model and each CG model. The results of the CG models were rescaled using the set of scaling factors and compared with those of the atomistic model. For each polymer property, a threshold value indicating the onset of static or dynamic universality of polymers was obtained. The scaling factors also revealed the computational efficiency of each CG model with respect to the atomistic model. The performance of the CG models of polymers was systematically evaluated in terms of both the accuracy and computational efficiency.

We develop a deep neural network (DNN) that accounts for the phase behaviors of polymer-containing liquid mixtures. The key component in the DNN consists of a theory-embedded layer that captures the characteristic features of the phase behavior via coarse-grained mean-field theory and scaling laws and substantially enhances the accuracy of the DNN. Moreover, this layer enables us to reduce the size of the DNN for the phase diagrams of the mixtures. This study also presents the predictive power of the DNN for the phase behaviors of polymer solutions and salt-free and salt-doped diblock copolymer melts.

In eukaryotes, chromatin is coated with epigenetic marks which induce differential gene expression profiles and eventually lead to different cellular phenotypes. One of the challenges of contemporary cell biology is to relate the wealth of epigenomic data with the observed physical properties of chromatin. In this study, we present a polymer physics framework that takes into account the sizes of epigenomic domains. We build a model of chromatin as a block copolymer made of domains with various sizes. This model produces a rich set of conformations which is well explained by finite-size scaling analysis of the coil-globule transition of epigenomic domains. Our results suggest that size-dependent folding of epigenomic domains may be a crucial physical mechanism able to provide chromatin with tissue-specific folding states, these being associated with differential gene expression.

Chromatin has a complex, dynamic architecture in the interphase nucleus, which regulates the accessibility of the underlying DNA and plays a key regulatory role in all the cellular functions using DNA as a template, such as replication, transcription or DNA damage repair. Here, we review the recent progresses in the understanding of the interplay between chromatin architecture and DNA repair mechanisms. Several reports based on live cell fluorescence imaging show that the activation of the DNA repair machinery is associated with major changes in the compaction state and the mobility of chromatin. We discuss the functional consequences of these changes in yeast and mammals in the light of the different repair pathways utilized by these organisms. In the final section of this review, we show how future developments in high-resolution light microscopy and chromatin modelling by polymer physics should contribute to a better understanding of the relationship between the structural changes in chromatin and the activity of the repair processes.

Mammalian chromatin is spatially organized at many scales showing two prominent features in interphase: (i) alternating regions (1-10 Mb) of active and inactive chromatin that spatially segregate into different compartments, and (ii) domains (<1 Mb), that is, regions that preferentially interact internally [topologically associating domains (TADs)] and are central to gene regulation. There is growing evidence that TADs are formed by active extrusion of chromatin loops by cohesin, whereas compartmentalization is established according to local chromatin states. Here, we use polymer simulations to examine how loop extrusion and compartmental segregation work collectively and potentially interfere in shaping global chromosome organization. A model with differential attraction between euchromatin and heterochromatin leads to phase separation and reproduces compartmentalization as observed in Hi-C. Loop extrusion, essential for TAD formation, in turn, interferes with compartmentalization. Our integrated model faithfully reproduces Hi-C data from puzzling experimental observations where altering loop extrusion also led to changes in compartmentalization. Specifically, depletion of chromatin-associated cohesin reduced TADs and revealed finer compartments, while increased processivity of cohesin strengthened large TADs and reduced compartmentalization; and depletion of the TAD boundary protein CTCF weakened TADs while leaving compartments unaffected. We reveal that these experimental perturbations are special cases of a general polymer phenomenon of active mixing by loop extrusion. Our results suggest that chromatin organization on the megabase scale emerges from competition of nonequilibrium active loop extrusion and epigenetically defined compartment structure. [ABSTRACT FROM AUTHOR]

Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like conformations. Additionally, they can fold into well-defined three-dimensional structures or remain partially or entirely disordered. Recent discoveries have shown that the tendency for proteins to collapse or remain expanded is not intrinsically coupled to their ability to fold. These observations suggest that proteins do not have to form compact globules in aqueous solutions. They can be intrinsically disordered, collapsed, or expanded, and even form well-folded, elongated structures. This ability to decouple collapse from folding is determined by the sequence details of proteins. In this review, we highlight insights gleaned from studies over the past decade. Using a polymer physics framework, we explain how the interplay among sidechains, backbone units, and solvent determines the driving forces for collapsed versus expanded states in aqueous solvents. [ABSTRACT FROM AUTHOR]

Chromosome large‐scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high‐resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome. [ABSTRACT FROM AUTHOR]

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) [ABSTRACT FROM AUTHOR]

Actin filaments are critical components of the eukaryotic cytoskeleton, playing important roles in a number of cellular functions, such as cell migration, organelle transport, and mechanosensation. They are helical polymers with awell-defined polarity, composed of globular subunits that bind nucleotides in one of three hydrolysis states (ATP,ADP-Pi, or ADP).Mean-field models of the dynamics of actin polymerization have succeeded in,among other things, determining the nucleotide profile of an average filament and resolving the mechanisms of accessory proteins.However, these models require numerical solution of a high-dimensional system of nonlinear ordinary differential equations. By truncating a set of recursion equations, the Brooks–Carlsson (BC) model reduces dimensionality to 11, but it still remains nonlinear and does not admit an analytical solution, hence, significantly hindering understanding of its resulting dynamics. In this work, by taking advantage of the fast time scales of the hydrolysis states of the filament tips,we propose two model reduction schemes: the quasi steady-state approximation model is five-dimensional and nonlinear,whereas the constant tip (CT)model is five-dimensional and linear, resulting from the approximation that the tip states are not dynamic variables.We provide an exact solution of the CT model and use it to shed light on the dynamical behaviours of the full BC model, highlighting the relative ordering of the timescales of various collective processes, and explaining some unusual dependence of the steady-state behavior on initial conditions. [ABSTRACT FROM AUTHOR]