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Theoretical and experimental approaches have been applied to study the polymer physics underlying the compaction of DNA in the bacterial nucleoid. Knowledge of the compaction mechanism is necessary to obtain a mechanistic understanding of the segregation process of replicating chromosome arms (replichores) during the cell cycle. The first part of this review discusses light microscope observations demonstrating that the nucleoid has a lower refractive index and thus, a lower density than the cytoplasm. A polymer physics explanation for this phenomenon was given by a theory discussed at length in this review. By assuming a phase separation between the nucleoid and the cytoplasm and by imposing equal osmotic pressure and chemical potential between the two phases, a minimal energy situation is obtained, in which soluble proteins are depleted from the nucleoid, thus explaining its lower density. This theory is compared to recent views on DNA compaction that are based on the exclusion of polyribosomes from the nucleoid or on the transcriptional activity of the cell. These new views prompt the question of whether they can still explain the lower refractive index or density of the nucleoid. In the second part of this review, we discuss the question of how DNA segregation occurs in Escherichia coli in the absence of the so-called active ParABS system, which is present in the majority of bacteria. How is the entanglement of nascent chromosome arms generated at the origin in the parental DNA network of the E. coli nucleoid prevented? Microscopic observations of the position of fluorescently-labeled genetic loci have indicated that the four nascent chromosome arms synthesized in the initial replication bubble segregate to opposite halves of the sister nucleoids. This implies that extensive intermingling of daughter strands does not occur. Based on the hypothesis that leading and lagging replichores synthesized in the replication bubble fold into microdomains that do not intermingle, a passive four-excluding-arms model for segregation is proposed. This model suggests that the key for segregation already exists in the structure of the replication bubble at the very start of DNA replication; it explains the different patterns of chromosome arms as well as the segregation distances between replicated loci, as experimentally observed.

In the 1960s, electron microscopy did not provide a clear answer regarding the compact or dispersed organization of the bacterial nucleoid. This was due to the necessary preparation steps of fixation and dehydration (for embedding) and freezing (for freeze-fracturing). Nevertheless, it was possible to measure the lengths of nucleoids in thin sections of slow-growing Escherichia coli cells, showing their gradual increase along with cell elongation. Later, through application of the so-called agar filtration method for electron microscopy, we were able to perform accurate measurements of cell size and shape. The introduction of confocal and fluorescence light microscopy enabled measurements of size and position of the bacterial nucleoid in living cells, inducing the concepts of “nucleoid occlusion” for localizing cell division and of “transertion” for the final step of nucleoid segregation. The question of why the DNA does not spread throughout the cytoplasm was approached by applying polymer-physical concepts of interactions between DNA and proteins. This gave a mechanistic insight in the depletion of proteins from the nucleoid, in accordance with its low refractive index observed by phase-contrast microscopy. Although in most bacterial species, the widely conserved proteins of the ParABS-system play a role in directing the segregation of newly replicated DNA strands, the basis for the separation and opposing movement of the chromosome arms was proposed to lie in preventing intermingling of nascent daughter strands already in the early replication bubble. E. coli, lacking the ParABS system, may be suitable for investigating this basic mechanism of DNA strand separation and segregation.

The cells and tissues that make up our body manage contradictory mechanical demands. It is crucial for their survival to be able to withstand large mechanical loads, but it is equally crucial for them to produce forces and actively change shape during biological processes such as tissue growth and repair. The mechanics of cells and tissues is determined by scaffolds of protein polymers known as the cytoskeleton and the extracellular matrix, respectively. Experiments on model systems reconstituted from purified components combined with polymer physics concepts have already uncovered some of the mechanisms that underlie the paradoxical mechanics of living matter. Initial work focused on explaining universal features, such as the nonlinear elasticity of cells and tissues, in terms of polymer network models. However, there is a growing recognition that living matter exhibits many advanced mechanical functionalities that are not captured by these coarse-grained theories. Here, we review recent experimental and theoretical insights that reveal how the porous structure, structural hierarchy, transient crosslinking and mechanochemical activity of biopolymers confer resilience combined with the ability to adapt and self-heal. These physical concepts increase our understanding of cell and tissue biology and provide inspiration for advanced synthetic materials.Biopolymer networks provide mechanical integrity and enable active deformation of cells and tissues. Here, we review recent experimental and theoretical studies of the mechanical behaviour of biopolymer networks with a focus on reductionist approaches.

Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects remains a challenge. Here we present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer–promoter contacts. PRISMR predicts higher-order chromatin structure from genome-wide chromosome conformation capture (Hi-C) data. Using the EPHA4 locus as a model, the effects of pathogenic SVs are predicted in silico and compared to Hi-C data generated from mouse limb buds and patient-derived fibroblasts. PRISMR deconvolves the folding complexity of the EPHA4 locus and identifies SV-induced ectopic contacts and alterations of 3D genome organization in homozygous or heterozygous states. We show that SVs can reconfigure topologically associating domains, thereby producing extensive rewiring of regulatory interactions and causing disease by gene misexpression. PRISMR can be used to predict interactions in silico, thereby providing a tool for analyzing the disease-causing potential of SVs. The authors present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer–promoter contacts. PRISMR correctly predicts ectopic contacts induced by pathogenic SVs at the mouse Epha4 locus.

Polymer materials provide solutions to some of the most pressing environmental, manufacturing and health-care challenges. Traditional thermoplastic and thermoset networks, however, have a limited capacity to reconfigure and restructure, and fail to match the dynamics required for many applications. Introducing dynamic bonding interactions into polymer networks can produce materials that are more easily processed, applied and recycled than their static counterparts. In this Review, we highlight an array of polymer materials designed with dynamic bonds and reconfigurable networks, and discuss the different classes of molecular-scale motifs used to realize dynamic behaviour. After surveying the fundamental polymer physics governing dynamic networks, we examine the many ways to engineer the time regimes of dynamic materials to suit particular applications. Finally, we conclude by discussing opportunities to further develop and integrate these dynamic concepts into existing processes and applications of polymer materials. Polymer materials that can reorganize over time or under specific conditions have enormous advantages over static polymer networks. This Review discusses the many classes of molecular bonding motifs used to introduce dynamicity to polymer materials and outlines the design rules for engineering the interaction timescales for desired applications.

We study the static and dynamical properties of a harmonically confined Rouse polymer coupled to a fluctuating correlated medium, which affect each other reciprocally during their stochastic evolution. The medium is modeled by a scalar Gaussian field which can feature modes with slow relaxation and long-range spatial correlations. We show that these modes affect the long-time behavior of the average position of the center of mass of the polymer, which, after a displacement, turns out to relax algebraically towards its equilibrium value. This is a manifestation of the non-Markovian nature of the effective evolution of the position of the center of mass, once the degrees of freedom of the medium have been integrated out. In contrast, we show that the coupling to the medium speeds up the relaxation of higher Rouse modes. We further characterize the typical size of the polymer as a function of its polymerization degree and of the correlation length of the medium, particularly when the system is driven out of equilibrium via the application of a constant external driving force. Finally, we study the response of a linear polymer to a tensile force acting on its terminal monomers.

The use of mechanical forces to chemically transform polymers dates back decades. In recent years, the use of mechanochemistry to direct constructive transformations in polymers has resulted in a range of engineered molecular responses that span optical, mechanical, electronic and thermal properties. The chemistry that has been developed is now well positioned for use in materials science, polymer physics, mechanics and additive manufacturing. Here, we review the historical backdrop of polymer mechanochemistry, give an overview of the existing toolbox of mechanophores and associated theoretical methods, and speculate as to emerging opportunities in materials science for which current capabilities are seemingly well suited. Non-linear mechanical responses and internal, amplifying stimulus–response feedback loops, including those enabled by, or coupled to, microstructured metamaterial architectures, are seen as particularly promising. Polymer mechanochemistry converts mechanical forces in materials to chemical reactions through the response of functional groups known as mechanophores. This Review discusses the colorimetric, mechanical, chemical and electronic responses of mechanophores that may be useful in materials for strain sensing and strengthening, soft devices and additive manufacturing.

The electronic devices that play a vital role in our daily life are primarily based on silicon and are thus rigid, opaque, and relatively heavy. However, new electronics relying on polymer semiconductors are opening up new application spaces like stretchable and self-healing sensors and devices, and these can facilitate the integration of such devices into our homes, our clothing, and even our bodies. While there has been tremendous interest in such technologies, the widespread adoption of these organic electronics requires low-cost manufacturing techniques. Fortunately, the realization of organic electronics can take inspiration from a technology developed since the beginning of the Common Era: printing. This review addresses the critical issues and considerations in the printing methods for organic electronics, outlines the fundamental fluid mechanics, polymer physics, and deposition parameters involved in the fabrication process, and provides future research directions for the next generation of printed polymer electronics. A primary advantage of polymer semiconductors compared to silicon-based semiconductors lies in its capability of being solution-processed for the large-scale fabrication of electronics that can be flexible, stretchable, implantable, biodegradable, and self-healing. Here, Gu and Shaw et al. review recent developments in meniscus-guided coating that can control thin-film morphology.

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.

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.