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Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2 Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Euchromatin is an accessible phase of genetic material containing genes that encode proteins with increased expression levels. The structure of euchromatin in vitro has been described as a 30-nm fiber formed from ordered nucleosome arrays. However, recent advances in microscopy have revealed an in vivo euchromatin architecture that is much more disordered, characterized by variable-length linker DNA and sporadic nucleosome clusters. In this work, we develop a theoretical model to elucidate factors contributing to the disordered in vivo architecture of euchromatin. We begin by developing a 1D model of nucleosome positioning that captures the interactions between bound epigenetic reader proteins to predict the distribution of DNA linker lengths between adjacent nucleosomes. We then use the predicted linker lengths to construct 3D chromatin configurations consistent with the physical properties of DNA within the nucleosome array, and we evaluate the distribution of nucleosome cluster sizes in those configurations. Our model reproduces experimental cluster-size distributions, which are dramatically influenced by the local pattern of epigenetic marks and the concentration of reader proteins. Based on our model, we attribute the disordered arrangement of euchromatin to the heterogeneous binding of reader proteins and subsequent short-range interactions between bound reader proteins on adjacent nucleosomes. By replicating experimental results with our physics-based model, we propose a mechanism for euchromatin organization in the nucleus that impacts gene regulation and the maintenance of epigenetic marks. [ABSTRACT FROM AUTHOR]

In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross-over between two and four at contour lengths on the order of 30 kilo-base pairs. The anomalously high fractal dimension D = 4 is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times (Δ t) longer than tens of minutes to be proportional to Δ t 1/3. We validate our results with hybrid molecular dynamics--Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation. [ABSTRACT FROM AUTHOR]

Understanding and characterizing semi-crystalline models with crystalline and amorphous segments is crucial for industrial applications. A coarse-grained molecular dynamics (CGMD) simulations study probed the crystal network formation in high-density polyethylene (HDPE) from melt, and shed light on tensile properties for microstructure analysis. Modified Paul–Yoon–Smith (PYS/R) forcefield parameters are used to compute the interatomic forces among the PE chains. The isothermal crystallization at 300 K and 1 atm predicts the multi-nucleus crystal growth; moreover, the lamellar crystal stems and amorphous region are alternatively oriented. A one-dimensional density distribution along the alternative lamellar stems further confirms the ordering of the lamellar-stack orientation. Using this plastic model preparation approach, the semi-crystalline model density ( ρ c r ) of ca. 0.913 g·cm−3 and amorphous model density ( ρ a m ) of ca. 0.856 g·cm−3 are obtained. Furthermore, the ratio of ρ c r / ρ a m ≈ 1.06 is in good agreement with computational (≈1.096) and experimental (≈1.14) data, ensuring the reliability of the simulations. The degree of crystallinity ( χ c ) of the model is ca. 52% at 300 K. Nevertheless, there is a gradual increase in crystallinity over the specified time, indicating the alignment of the lamellar stems during crystallization. The characteristic stress–strain curve mimicking tensile tests along the z-axis orientation exhibits a reversible sharp elastic regime, tensile strength at yield ca. 100 MPa, and a non-reversible tensile strength at break of 350%. The cavitation mechanism embraces the alignment of lamellar stems along the deformation axis. The study highlights an explanatory model of crystal network formation for the PE model using a PYS/R forcefield, and it produces a microstructure with ordered lamellar and amorphous segments with robust mechanical properties, which aids in predicting the microstructure–mechanical property relationships in plastics under applied forces. [ABSTRACT FROM AUTHOR]

Single‐molecule force spectroscopy is a powerful tool for the quantitative investigation of the biophysics, polymer physics and mechanochemistry of individual polymer strands. One limitation of this technique is that the attachment between the tip of the atomic force microscope and the covalent or noncovalent analyte in a given pull is typically not strong enough to sustain the force at which the event of interest occurs, which makes the experiments time‐consuming and inhibits throughput. Here we report a polyelectrolyte handle for single‐molecule force spectroscopy that offers a combination of high (several hundred pN) attachment forces, good (~4%) success in obtaining a high‐force (>200 pN) attachment, a non‐fouling detachment process that allows for repetition, and specific attachment locations along the polymer analyte. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Shenzhen University Science & Engineering is the property of Editorial Department of Journal of Shenzhen University Science & Engineering and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Synthetic control over the shape, size, and interactions between nanoscale building blocks remains an open challenge in self‐assembly. Here, we propose to engineer triblock, star‐like polymers to design patterning on nanoparticles. We developed a theory that characterizes the structural organization of grafted polymers as a function of parameters such as grafting density, chain length, block fractions, and core shape/sizes. Stripe‐like patterning and corner/edge patch formation on arbitrarily shaped cores are readily accessible using our framework, all of which can be a priori predicted. Lastly, we employ assembly simulations to show that the resulting particles provide tighter control over structural and orientational orderings during self‐assembly. More importantly, they offer a way to pattern directional interactions that can override face–face alignment tendencies intrinsic to each core geometry. Our theory, therefore, creates a new handle for tuning nanoscale synthesis, enabling designs of complex building blocks that can target novel assemblies for materials fabrication. [ABSTRACT FROM AUTHOR]

Carbohydrate polymers are promising materials for an eco-friendly future due to their biodegradability and abundance in nature. However, due to their molecular characteristics and hydrophilicity, are often complicated to be investigated via spectroscopic methods. Thermoplastic starch plasticized by glycerol was prepared through melt processing conditions using twin screw extruder. Here we show how the presence of water molecules affects the dielectric response and charge transport dynamics over broad frequency (10−1 to 107 Hz) and temperature (− 140 to 150 oC) ranges. Overall, 7 dielectric processes were observed and differentiation between electronic and ionic conductivities was achieved. Two segmental relaxation processes were observed for each sample, ascribed to the starch-rich and glycerol-rich phases. Although the timescales of the two segmental relaxations were found different, both arise from the same temperature, giving thus an alternative explanation on what is reported in the literature. The origin of the σ-relaxation was attributed to hydrogen ions and was found to be proportional to the ionic conductivity according to the Barton, Nakajima and Namikawa relation. The presence of water molecules was found to enhance the ionic conductivity, indicating that water contributes charge carriers when compared to the dried sample. [ABSTRACT FROM AUTHOR]

Staudinger taught us that macromolecules were made up of covalently bonded monomer repeat units chaining up as polymer chains. This paradigm is not challenged in this paper. The main question raised in polymer physics remains: how do these long chains interact and move as a group when submitted to shear deformation at high temperature when they are viscous liquids? The current consensus is that we need to distinguish two cases: the deformation of "un-entangled chains" for macromolecules with molecular weight, M, smaller than Me, "the entanglement molecular weight", and the deformation of "entangled" chains for M > Me. The current paradigm stipulates that the properties of polymers derive from the statistical characteristics of the macromolecule itself, the designated statistical system that defines the thermodynamic state of the polymer. The current paradigm claims that the viscoelasticity of un-entangled melts is well described by the Rouse model and that the entanglement issues raised when M > Me, are well understood by the reptation model introduced by de Gennes and colleagues. Both models can be classified in the category of "chain dynamics statistics". In this paper, we examine in detail the failures and the current challenges facing the current paradigm of polymer rheology: the Rouse model for un-entangled melts, the reptation model for entangled melts, the time–temperature superposition principle, the strain-induced time dependence of viscosity, shear-refinement and sustained-orientation. The basic failure of the current paradigm and its inherent inability to fully describe the experimental reality is documented in this paper. In the discussion and conclusion sections of the paper, we suggest that a different solution to explain the viscoelasticity of polymer chains and of their "entanglement" is needed. This requires a change in paradigm to describe the dynamics of the interactions within the chains and across the chains. A brief description of our currently proposed open dissipative statistical approach, "the Grain-Field Statistics", is presented. [ABSTRACT FROM AUTHOR]

Medical devices often include polymeric components, which contain additives or contaminants that may leach into patients and pose a health risk. Previously, we proposed a mass transport model that conservatively estimates the leaching kinetics and only requires the solute's diffusion coefficient in the polymer, D, to be specified. Because determining D experimentally is time‐consuming, we also parameterized empirical models to estimate worst‐case D values using only the solute molecular weight, Mw. These models were based on a modest database and were limited to 19 polymers and larger solutes (Mw>100 g/mol). Here, we assemble a much larger database, which enables us to construct more accurate models using a robust statistical approach, expanding the coverage to 50 device‐relevant polymers and smaller solutes (Mw<100 g/mol). Then, we demonstrate several applications of these bounds, including modeling the release kinetics. Finally, we observe an interesting phenomenon, a discontinuous drop in D of up to 25,000× for solutes with Mw>50 g/mol in glassy polymers. Using molecular simulations and cheminformatics tools, we propose a novel definition of the effective diameter of free volume channels in polymers, and we show that solutes larger than this channel size diffuse much more slowly. [ABSTRACT FROM AUTHOR]

Molecular simulations are now an essential part of modern chemistry and physics, especially for the investigation of macromolecules. They have evolved into mature approaches that can be used effectively to understand the structure-to-property relationships of diverse macromolecular systems. In this article, we provide a tutorial on molecular simulations, focusing on the technical and practical aspects. Several prominent and classical simulation methods and software are introduced. The applications of molecular simulations in various directions of macromolecular science are then featured by representative systems, including self-assembly, crystallization, chemical reaction, and some typical non-equilibrium systems. This tutorial paper provides a useful overview of molecular simulations in the rapid progress of macromolecular science, and suggests guidance for researchers who start exploiting molecular simulations in their study. [ABSTRACT FROM AUTHOR]

Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins’ structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs’ amino acid sequence. Here, using small-angle X-ray scattering and time-resolved Förster resonance energy transfer (trFRET), we study the intramolecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt subsegments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments’ structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP’s sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intramolecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope that it will allow us to model their biological function. [ABSTRACT FROM AUTHOR]

A representation of polymer self‐consistent field theory equivalent to quantum density functional theory is given in terms of non‐orthogonal basis sets. Molecular integrals and self‐consistent equations for spherically symmetric systems using Gaussian basis functions are given, and the binding energies and radial electron densities of neutral atoms hydrogen through krypton are calculated. An exact electron self‐interaction correction is adopted and the Pauli‐exclusion principle is enforced through ideas of polymer excluded‐volume. The atoms hydrogen through neon are examined without some approximations which permit cancellation of errors and spontaneous shell structure is observed. Correlations are neglected in the interest of simplicity and comparisons are made with Hartree–Fock theory. The implications of the Pauli‐exclusion potential and its approximate form are discussed, and the Pauli model is analyzed using scaling theory for the uniform electron density case where the correct form of the Thomas–Fermi quantum kinetic energy and the Dirac exchange correction are recovered. [ABSTRACT FROM AUTHOR]

The active loop extrusion hypothesis proposes that chromatin threads through the cohesin protein complex into progressively larger loops until reaching specific boundary elements. We build upon this hypothesis and develop an analytical theory for active loop extrusion which predicts that loop formation probability is a nonmonotonic function of loop length and describes chromatin contact probabilities. We validate our model with Monte Carlo and hybrid Molecular Dynamics-Monte Carlo simulations and demonstrate that our theory recapitulates experimental chromatin conformation capture data. Our results support active loop extrusion as a mechanism for chromatin organization and provide an analytical description of chromatin organization that may be used to specifically modify chromatin contact probabilities. [ABSTRACT FROM AUTHOR]

Although electrons (fermions)and photons (bosons) produce the same interference patterns in the two-slit experiments, known in optics for photons since the 17th Century, the description of these patterns for electrons and photons thus far was markedly different. Photons are spin one, relativistic and massless particles while electrons are spin half massive particles producing the same interference patterns irrespective to their speed. Experiments with other massive particles demonstrate the same kind of interference patterns. In spite of these differences, in the early 1930s of the 20th Century, the isomorphism between the source-free Maxwell and Dirac equations was established. In this work, we were permitted replace the Born probabilistic interpretation of quantum mechanics with the optical. In 1925, Rainich combined source-free Maxwell equations with Einstein's equations for gravity. His results were rediscovered in the late 1950s by Misner and Wheeler, who introduced the word "geometrodynamics" as a description of the unified field theory of gravity and electromagnetism. An absence of sources remained a problem in this unified theory until Ranada's work of the late 1980s. However, his results required the existence of null electromagnetic fields. These were absent in Rainich–Misner–Wheeler's geometrodynamics. They were added to it in the 1960s by Geroch. Ranada's solutions of source-free Maxwell's equations came out as knots and links. In this work, we establish that, due to their topology, these knots/links acquire masses and charges. They live on the Dupin cyclides—the invariants of Lie sphere geometry. Symmetries of Minkowski space-time also belong to this geometry. Using these symmetries, Varlamov recently demonstrated group-theoretically that the experimentally known mass spectrum for all mesons and baryons is obtainable with one formula, containing electron mass as an input. In this work, using some facts from polymer physics and differential geometry, a new proof of the knotty nature of the electron is established. The obtained result perfectly blends with the description of a rotating and charged black hole. [ABSTRACT FROM AUTHOR]

Copyright of University Chemistry is the property of Peking University, College of Chemistry & Molecular Engineering and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In the present work, molecular dynamics simulations are carried out based on the bead‐spring model to indicate how the entanglement lockup manifests in the late stage of fast Rouse‐Weissnberg number (WiR>>1) uniaxial melt stretching of entangled polymer melts. At high strains, distinct features show up to reveal the emergence of an increasingly tightened entanglement network. Chain tension can build up, peaking at the middle of the chain, to a level for chain scission, through accumulated interchain interactions, as if there is a tug‐of‐war ongoing for each load‐bearing chain. Thanks to the interchain uncrossability, network junctions form by the pairing of two or more hairpins. It is hypothesized that the interchain entanglement at junctions can lockup through prevailing twist‐like interchain couplings as long as WiR > 9. In this limit, a significant fraction of chains act like cyclic chains to form a network held by interchain uncrossability, and appreciable chain tension emerges. [ABSTRACT FROM AUTHOR]

Fluorescence resonance energy transfer (FRET) is a non‐invasive characterization method for studying molecular structures and dynamics, providing high spatial resolution at nanometer scale. Over the past decades, FRET‐based measurements are developed and widely implemented in synthetic polymer systems for understanding and detecting a variety of nanoscale phenomena, enabling significant advances in polymer science. In this review, the basic principles of fluorescence and FRET are briefly discussed. Several representative research areas are highlighted, where FRET spectroscopy and imaging can be employed to reveal polymer morphology and kinetics. These examples include understanding polymer micelle formation and stability, detecting guest molecule release from polymer host, characterizing supramolecular assembly, imaging composite interfaces, and determining polymer chain conformations and their diffusion kinetics. Finally, a perspective on the opportunities of FRET‐based measurements is provided for further allowing their greater contributions in this exciting area. [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. [ABSTRACT FROM AUTHOR]

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, for example, 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 are varied. Furthermore, the transition from HW to HT phases is characterized by the spontaneous breaking of parity symmetry and the disappearance of perversions (that correspond to chirality-reversing localized defects). 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The pairing of homologous chromosomes (homologs) in meiosis is essential for distributing the correct numbers of chromosomes into haploid gametes. In budding yeast, pairing depends on the formation of 150 to 200 Spo11-mediated double-strand breaks (DSBs) that are distributed among 16 homolog pairs, but it is not known if all, or only a subset, of these DSBs contribute to the close juxtaposition of homologs. Having established a system to measure the position of fluorescently tagged chromosomal loci in three-dimensional space over time, we analyzed locus trajectories to determine how frequently and how long loci spend colocalized or apart. Continuous imaging revealed highly heterogeneous cell-to-cell behavior of foci, with the majority of cells exhibiting a “mixed” phenotype where foci move into and out of proximity, even at late stages of prophase, suggesting that the axial structures of the synaptonemal complex may be more dynamic than anticipated. The observed plateaus of the mean-square change in distance (MSCD) between foci informed the development of a biophysical model of two diffusing polymers that captures the loss of centromere linkages as cells enter meiosis, nuclear confinement, and the formation of Spo11-dependent linkages. The predicted number of linkages per chromosome in our theoretical model closely approximates the small number (approximately two to four) of estimated synapsis-initiation sites, suggesting that excess DSBs have negligible effects on the overall juxtaposition of homologs. These insights into the dynamic interchromosomal behavior displayed during homolog pairing demonstrate the power of combining time-resolved in vivo analysis with modeling at the granular level. [ABSTRACT FROM AUTHOR]

In higher eukaryotes, chromosomes have a complex three‐dimensional (3D) conformation in the cell nucleus serving vital functional purposes, yet their folding principles remain poorly understood at the single‐molecule level. Here, we summarize recent approaches from polymer physics to comprehend the physical mechanisms underlying chromatin architecture. In particular, we focus on two models that have been supported by recent, growing experimental evidence, the Loop Extrusion model and the Strings&Binders phase separation model. We discuss their key ingredients, how they compare to experimental data and some insight they provide on chromatin architecture and gene regulation. Progress in that research field are opening the possibility to predict how genomic mutations alter the network of contacts between genes and their regulators and how that is linked to genetic diseases, such as congenital disorders and cancer. [ABSTRACT FROM AUTHOR]

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]

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]

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]

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]

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. [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]

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]

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]

In the last decade, the developments of novel technologies, such as Hi-C or GAM methods, allowed to discover that chromosomes in the nucleus of mammalian cells have a complex spatial organization, encompassing the functional contacts between genes and regulators. In this work, we review recent progresses in chromosome modeling based on polymer physics to understand chromatin structure and folding mechanisms. As an example, we derive inmouse embryonic stemcells the full 3D structure of the Bmp7 locus, a genomic region that plays a key role in osteoblastic differentiation. Next, as an application to Neuroscience, we present the first 3D model for the mouse orthologoue of the Williams-Beuren syndrome 7q11.23 human locus. Deletions and duplications of the 7q11.23 region generate neurodevelopmental disorders with multi-system involvement and variable expressivity, and with autism. Understanding the impact of such mutations on the rewiring of the interactions of genes and regulators could be a new key to make sense of their related diseases, with potential applications in biomedicine. [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. [ABSTRACT FROM PUBLISHER]