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The main focus of this thesis lies on confining and/or pulling on two important biopolymers, i.e. cellulose nanofibrils (CNF) and amyloid fibrils. The results of these studies have implications for understanding in vivo biopolymer systems, improving the engineering of novel green materials, and furthering concepts in polymer physics. The first chapter introduces the reader to the motivations behind this work, as well as provides background information on CNF and amyloid fibrils and on the major polymer physics theories needed to devise experiments and simulations. In the second chapter, an experiment to study CNF under weak rectangular confinement is displayed. CNF were adsorbed into slits, previously obtained by thermal scanning probe nanolithography. Atomic force microscopy (AFM) coupled with single-molecule statistics allowed me to observe the alignment and self-folding of CNF under confinement. Simulations confirmed that the slits were not simply selecting a preexisting fibril population, but that the CNF were folding upon themselves as a result of the confinement. In addition, a kink preferential bending direction and an inverse correlation between kink angle and number of kinks, i.e. the fewer kinks the higher the angle, were noted. The combination of these observations provides further evidence that the kinks are a result of mechanical breaking. In the third chapter, an experiment to study subtle interplay between concurrent pulling and confinement of amyloid fibrils is explained. This was achieved by pulling the fibrils into a microcapillary device. AFM allowed a detailed single molecule statistics of the system. These results indicated that the extension of the fibrils was force- or confinement dominated at short and large length scales, respectively. This was in contrast to the order of the system, which was confinement-dominated at all length scales. Simulations both confirmed this result and brought to light the existence of other regimes. Therefore displaying the potential to tailor the system through the fine-tuning of the contribution of either effect. This data may in addition help understand in vivo amyloid phenomena in blood vessels, as well as other physiological occurrences involving the stretching and confining of semi-flexible biopolymers. The fourth chapter focuses on a technique to deposit gradients of amyloid fibrils from the liquid-liquid interface while under simultaneous compression, thus imposing macroscopic confinement. Orientation was induced perpendicularly to the compression, from isotropic to nematic. Reproducible transitions, from a monolayer to a bilayer and from a bilayer to a multilayer, were observed. This method brings forth an approach to overcome the engineering challenge associated with manipulating sticky amyloid fibrils. It further shows great potential for investigating amyloid aggregation at interfaces, which is of great relevance for understanding the propagation of certain amyloid fibril-related diseases. In conclusion, confinement successfully produced alignment, independently of the polymer and of the length scale. The effects of confinement can be modulated by adding a pulling force to the system. These experiments may not only be valid for CNF and amyloids, but show great potential for investigating divers biopolymers.

The depth and complexity of data now available on chromosome 3D architecture, derived by new technologies such as Hi-C, have triggered the development of models based on polymer physics to explain the observed patterns and the underlying molecular folding mechanisms. Here, we give an overview of some of the ideas and models from physics introduced to date, along with their progresses and limitations in the description of experimental data. In particular, we focus on the Strings&Binders and the Loop Extrusion model of chromatin architecture. This article is categorized under: Analytical and Computational Methods > Computational Methods.

Chromatin fibers within the interior of the nucleus of the cell make stable interactions with the nucleoskeleton, an ensemble of 'extra-chromatin' structures which help ensuring genome stability. Although the role of these interactions appears crucial to the correct behavior of the cell, their impact on chromatin structure and dynamics remains to be elucidated. In order to tackle this important issue, in this work we introduce a simple polymer model for chromatin fibers in interphase which takes into account the two generic properties of chain-versus-chain mutual uncrossability and the presence of stable binding interactions to an extra-chromatin nuclear matrix. To study how these constraints affect chromatin structure from small to large scales, we employ extensive molecular dynamics computer simulations and we monitor the motion of nanoprobes of different sizes embedded within the polymer medium. Our results demonstrate that nanoprobes show hampered motion whenever their linear size becomes larger than chromatin stiffness. This transition is also displaying features which usually belong to the realm of glassy systems, namely long-tail correlations in the distribution functions of nanoprobe spatial displacements and heterogeneous behavior accompanied by ergodicity breaking.

Polymer injection to improve and/or accelerate oil recovery is a widespread technique with numerous ongoing and successful projects. In recent years, many field cases have been reported with injected polymer viscosity ranging from 5 to 160cP, producing large incremental oil volumes, without major injectivity issues. These field results often contradict pessimistic predictions of injectivity from prior studies. Despite abundant publications on the subject, there is no standard explanation of the reasons for discrepancies between forecast and actual behavior, and many questions are not yet fully answered. Will it be possible to inject the polymer solution at target viscosity? How much to inject? How fast? Will high pressures lead to fracturing or polymer degradation? Should the polymer solution be pre-treated, pre-sheared? What should be done if planned injection rates are not achievable? Will injectivity decline over time? These questions are very topical when it comes to building a business case for EOR, using 3D reservoir simulation models for forecasting production and calculating the economics of the project. In this paper, we present a critical review of selected field cases from the literature, analyzing reservoir characteristics and development history as well as properties of the injected solution. We discuss the mechanisms which can affect injectivity, including polymer solution rheology, near-well flow regimes, reservoir heterogeneity and geomechanical effects, and how these mechanisms can be represented in reservoir simulation models. Based on this investigation, we propose appropriate methodologies for dynamic modeling of polymer injection, considering the impact on predicted flow behavior of assumptions about polymer physics, selection of key parameters for sensitivity studies and the issues of upscaling from core experiments to the field. We suggest guidelines for using laboratory measurements and field observations, and for implementing forecasting workflows. Finally, we make recommendations on designing a practical field injection and monitoring program, to obtain data for calibrating models and improving future predictions.

Polyelectrolyte complex micelles (PCMs, core-shell nanoparticles formed by complexation of a polyelectrolyte with a polyelectrolyte-hydrophilic neutral block copolymer) offer a solution to the critical problem of delivering therapeutic nucleic acids, Despite this, few systematic studies have been conducted on how parameters such as polycation charge density, hydrophobicity, and choice of charged group influence PCM properties, despite evidence that these strongly influence the complexation behavior of polyelectrolyte homopolymers. In this article, we report a comparison of oligonucleotide PCMs and polyelectrolyte complexes formed by poly(lysine) and poly((vinylbenzyl) trimethylammonium) (PVBTMA), a styrenic polycation with comparatively higher charge density, increased hydrophobicity, and a permanent positive charge. All of these differences have been individually suggested to provide increased complex stability, but we find that PVBTMA in fact complexes oligonucleotides more weakly than does poly(lysine), as measured by stability versus added salt. Using small angle X-ray scattering and electron microscopy, we find that PCMs formed from both cationic blocks exhibit very similar structure-property relationships, with PCM radius determined by the cationic block size and shape controlled by the hybridization state of the oligonucleotides. These observations narrow the design space for optimizing therapeutic PCMs and provide new insights into the rich polymer physics of polyelectrolyte self-assembly.

Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.

The mechanical behavior of polymers such as their probability density function (PDF), strain energy, and entropic force, has long been described by the non-Gaussian statistical model. Non-Gaussian models are often approximated by the Kuhn-Grun (KG) distribution function, which is derived from the first-order approximation of the complex Rayleigh's exact Fourier integral distribution. The KG function is widely accepted in polymer physics, where the non-Gaussian theory is often used to describe energy of the chains with various flexibility ratios. However, the KG function is shown to be relevant only for long chains and becomes extremely inaccurate for chains with fewer than 40 segments. In comparison to the KG model, other approximations of the non-Gaussian statistical model are often less accurate, and those with higher accuracy are usually too complex to be implemented in large-scale simulations. Here a new accurate approximation of the non-Gaussian PDF, entropic force, and strain energy of a single chain subsequently is developed to describe the mechanics of a polymer chain. With a similar level of complexity, the presented approximations of non-Gaussian PDF, strain energy, and entropic force are at least 10 times more accurate than KG approximations and thus are an excellent alternative option to be used in micromechanical constitutive models.

Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.

One of the most intriguing properties of rod-like polymers is the ability to form a nematic phase. Among a broad variety of external stimuli to promote the isotropic (I)-nematic (N) transition, a shear-induced nematic phase represents one of the most fascinating phenomena in polymer physics. Here, after reviewing some relevant findings on quiescent and shear-induced nematics, we present the novel shear-induced isotropic-nematic transition exhibited by poly(ether ether ketone) (PEEK) melts of various chain lengths. The key factor is the significant rigidity of the PEEK chain that makes it a rod-like polymer. The molecular weight (Mw) dependence of the zero-shear viscosity ( η 0 ) of PEEK in the isotropic phase, follows the Doi-Edwards theoretical prediction for rod-like polymers in the entangled regime; η 0 ∼ M w 6 . The shear-induced I-N transition manifests in the apparent shear viscosity dependence on the shear rate (flow curves) with three regimes: I) an isotropic response with no measurable birefringence at low shear rates, II) an I-N transition with an isotropic-nematic biphase, two steady state values of apparent viscosity and mild birefringence at intermediate shear rates, and III) a continuous nematic phase with strong birefringence at high shear rates with η ∼ γ ˙ − 1 / 2 . Additionally, the observed threshold shear rates for regimes II and III for the four PEEK samples were used to construct a dynamic phase diagram of PEEK at 370°C, revealing that such a transition is stress-controlled.

The understanding of polymer solution thermodynamics and characterization of pressure effects on fundamental polymer physics of macromolecular systems is significant in the manufacturing of polyolefins. Consequently, numerous experimental and theoretical efforts have been made towards understanding phase behavior of polymer solutions at elevated pressures. Despite this progress, only limited efforts are directed towards understanding the underlying phenomena behind the influence of high pressure upon the thermophysical properties of ternary polymer solutions at a molecular level. The present paper, therefore, reports on the influence of supercritical ethylene on the density of PE + hydrocarbon solvent system by exploring ternary mixtures of PE + hexane + ethylene for ethylene concentrations up to 10 wt% at varied temperatures and in a pressure range from 100 to 1000 bar via fully-atomistic molecular dynamics (MD) simulations. Additionally, the modified Sanchez-Lacombe equation of state (EOS) model is iteratively solved to capture the pressure, concentration, and temperature dependence of ternary PE solution density. It is shown that the small amounts of ethylene dissolved in the liquid mixtures of PE + hexane significantly decreases the polymer solution density. The presence of unreacted monomer in the solution polymerization process utilized in PE manufacturing was found to substantially lower the PE solution density particularly at the lower end of the investigated pressure range. This noteworthy reduction in mixture density as a consequence impacts design and operation of the liquid-liquid phase separator in manufacturing of PE via solution polymerization. Another key point to bear in mind is that the mixture density exhibits fairly less sensitivity to ethylene amount as external pressure raises. Nevertheless, pressure, solvent composition, and temperature dependence of density display less sensitivity as pressure increases. In relation to the characterization of the impact of addition of ethylene an atomistic-level insight is provided, which proves to be of great value in revealing intermolecular interactions in the binary subsystems of polymer/solvent/monomer. The MD computations are shown to be in excellent agreement with the theoretical EOS model, confirming the validity of the proposed methodology. Furthermore, the adopted OPLS-AA has been found a reliable atomistic force field, which provides detailed molecular information on the thermophysical properties of polyolefin in hydrocarbon solutions. Ultimately, it is demonstrated that the MD simulations complement parametric EOS predictions and costly experimental approaches.

A combination of nano-focus X-ray scattering and nanocalorimetry was used to re-explore the phenomenon of multiple melting behavior of a typical semirigid-chain polymer, poly(trimethylene terephthalate), PTT. The multiple melting of semirigid-chain polymers constitutes one of the long-standing issues in polymer physics. By using very high heating and cooling rates the micro-structure of PTT corresponding to different stages of melting has been arrested by quenching it to room temperature. Although the recrystallization of PTT can be largely precluded under these conditions, the nanocalorimetric curve exhibits two melting events. By employing an in-situ small-angle X-ray scattering, SAXS, it is observed that the low-temperature melting peak corresponds to formation of streaky SAXS patterns. At this stage, the crystalline lamellar stacks lose their long-range order due to melting of the crystals confined in the smallest amorphous gaps, which can be explained by the negative stresses imposed on these crystals. This low-melting crystal fraction can be selectively molten away by performing a fast heating just above the corresponding melting point, and the subsequent heating does not reveal the double-melting behavior anymore. Therefore the phenomenon of the double (or multiple) melting behavior is not necessarily coupled to the melting–recrystallization processes and can be observed even in the absence of any recrystallization.

Polymer films on solid substrates present significant interest for fundamental polymer physics and industrial applications. For their mesoscale study, we develop a hybrid particle-based representation where polymers are modeled as worm-like chains and non-bonded interactions are introduced through a simple density functional. The mesoscale description is parameterized to match a generic microscopic model, which nevertheless can represent real materials. Choosing poly (methyl methacrylate) adsorbed on silica as a case study, the consistency of both models in describing conformational and structural properties in polymer films is investigated. We compare selected quantifiers of chain-shape, the structure of the adsorbed layer, as well as the statistics of loops, tails, and trains. Overall, the models are found to be consistent with each other. Some deviations in conformations and structure of adsorbed layer can be attributed to the simplified description of polymer/surface interactions and local liquid packing in the mesoscale model. These results are encouraging for a future development of pseudo-dynamical schemes, parameterizing the kinetics in the hybrid model via the dynamics of the generic microscopic model.

We carry out simultaneous mechanical and IR-thermal-imaging-based temperature measurements of tensile extension on untreated, milled (mechanically “rejuvenated”) and melt-stretched bisphenol A-polycarbonate (PC). The extension is found to cause significant buildup of both excess internal energy u 2 and plastic dissipation. The magnitude of u 2 is one to two orders of magnitude higher than the energy involved in rubbery elastic deformation. While the ratio of u 2 to the mechanical work w decreases with increasing rate of extension for untreated PC, milled PC is found to be more dissipative at lower rates. Homogeneous extension of melt-stretched PC in the post-yield regime including strain hardening behavior reveals largely non-dissipative responses, emphasizing the plastic deformation of glassy polymer may not be fully dissipative. The experimental results clearly indicate that a significant component of stress can be intrasegmental leading to the observed buildup of internal energy by distortions of covalent bonds. The glassy polymer physics at the chain level complements the more familiar idea of inter-segmental dissipation as the dominant event during plastic deformation.

A theoretical investigation on the mechanism of the tailored side-chain architecture of benzil-like voltage stabilizers for enhanced dielectric electrical breakdown strength of cross-linked polyethylene at the atomic and molecular levels is accomplished. The HOMO–LUMO energy gaps, the ionization potentials, and the electron affinities at the ground states of a series of benzil-like molecules are obtained at the B3LYP/6-311+G(d,p) level. The 8 isomerization reactions at the S0 state, including the harmonic vibration frequencies of the equilibrium geometries and the minimum energy paths (MEP) found using the intrinsic reaction coordinate (IRC) theory, are obtained at the same level. The substituent group effect, functional group effect, and electronic effect of the different heteroatoms (O, N, S) in substituent groups have been evaluated. The results show that benzil-like molecules, which have much smaller HOMO–LUMO energy gaps, much lower ionization potentials, and much larger electron affinities than those of aliphatic chains, can increase the electrical breakdown strength effectively as voltage stabilizers in cross-linked polyethylene. This result is consistent with Jarvid’s suggestions (Journal of Polymer Science, Part B: Polymer Physics, 2014, 52(16): 1047–1054).

Creation of polymers comprised of repeat units that can create topologically planar macromolecules (rather than linear) has been the topic of several recent studies in the field of synthetic polymer chemistry. Such novel macromolecules, known as 2D polymers, are the result of advanced synthetic methodology which allows creation of monolayer sheets with a periodic internal structure and functional groups placed at predetermined sites under mild conditions. Given the promising potentials of 2D polymers, this feature paper aims at discussing the concept of these novel macromolecules from a topological viewpoint in Section 1. This is followed by spotlighting the expected behavior of 2D polymers in the context of polymer physics (entropy elasticity, strength, percolation, and persistence) and polymer chemistry (copolymers and growth kinetics) in Section 2. Section 3 delineates synthetic and analytical matters associated with 2D polymers followed by a brief final section highlighting the potential of these sheet-like macromolecules for application purposes. We hope this article will trigger the interest of chemists, physicists and engineers to help develop this encouraging new class of materials further such that societally relevant applications will be accessible in the market soon.

Networks of crosslinked biopolymer filaments such as the cytoskeleton are the subject of intense research. Oftentimes, mechanics on the scale of single monomers ( ~ 5 ? n m ) govern the mechanics of the entire network ( ~ 10 ? µ m ). Until now, one either resolved the small scales and lost the big (network) picture or focused on mechanics above the single-filament scale and neglected the molecular architecture. Therefore, the study of network mechanics influenced by the entire spectrum of relevant length scales has been infeasible so far. We propose a method that reconciles both small and large length scales without the otherwise inevitable loss in either numerical efficiency or geometrical (molecular) detail. Both explicitly modeled species, filaments and their crosslinkers, are discretized with geometrically exact beam finite elements of Simo-Reissner type. Through specific coupling conditions between the elements of the two species, mechanical joints can be established anywhere along a beam's centerline, enabling arbitrary densities of chemical binding sites. These binding sites can be oriented to model the monomeric architecture of polymers. First, we carefully discuss the method and then demonstrate its capabilities by means of a series of numerical examples. We model crosslinked biopolymer networks with Brownian dynamics beam finite elements.Decoupling chemical and mechanical resolution, we boost computational efficiency.Our approach allows for network simulations reaching the scale of eukaryotic cells.We account for polar and chiral polymers and filament-linker reaction kinetics.We simulate the evolution, rheology, and effects of chirality of large networks.

In this article we study, through extensions of the generalized Gaussian scheme, the dynamics of semiflexible treelike polymers under the influence of external forces acting on particular (say, charged) monomers. Semiflexibility is introduced following our previous work (Dolgushev and Blumen, 2009 [15]), a procedure which allows one to study treelike structures with arbitrary stiffness and branching. Exemplarily, we illustrate the procedure using linear chains and hyperbranched polymers modeled through Vicsek fractals, and obtain in every case the monomer displacement averaged over the structure. Anomalous behavior manifests itself in the intermediate time region, where the different fractal architectures show distinct scaling behaviors. These behaviors are due to the power law behavior of the spectral density and lead, for arbitrary pulling forces, based on causality and the linear superposition principle, to fractional calculus expressions, in accordance to former phenomenological fractional laws in polymer physics.

Intracellular organelles are either membrane-bound vesicles or membrane-less compartments that are made up of proteins and RNA. These organelles play key biological roles, by compartmentalizing the cell to enable spatiotemporal control of biological reactions. Recent studies suggest that membrane-less intracellular compartments are multicomponent viscous liquid droplets that form via phase separation. Proteins that have an intrinsic tendency for being conformationally heterogeneous seem to be the main drivers of liquid–liquid phase separation in the cell. These findings highlight the relevance of classical concepts from the physics of polymeric phase transitions for understanding the assembly of intracellular membrane-less compartments. However, applying these concepts is challenging, given the heteropolymeric nature of protein sequences, the complex intracellular environment, and non-equilibrium features intrinsic to cells. This provides new opportunities for adapting established theories and for the emergence of new physics. The internal structure of cells is organized into compartments, many of which lack a confining membrane and instead resemble viscous liquid droplets. Evidence is mounting that these compartments form via spontaneous phase transitions. The internal structure of cells is organized into compartments, many of which lack a confining membrane and instead resemble viscous liquid droplets. Evidence is mounting that these compartments form via spontaneous phase transitions.

International audience; The abundance of intrinsic disorder in the protein realm and its role in a variety of physiological and pathological cellular events have strengthened the interest of the scientific community in understanding the structural and dynamical properties of intrinsically disordered proteins (IDPs) and regions (IDRs). Attempts at rationalizing the general principles underlying both conformational properties and transitions of IDPs/IDRs must consider the abundance of charged residues (Asp, Glu, Lys, and Arg) that typifies these proteins, rendering them assimilable to polyampholytes or polyelectrolytes. Their conformation strongly depends on both the charge density and distribution along the sequence (i.e., charge decoration) as highlighted by recent experimental and theoretical studies that have introduced novel descriptors. Published experimental data are revisited herein in the frame of this formalism, in a new and possibly unitary perspective. The physicochemical properties most directly affected by charge density and distribution are compaction and solubility, which can be described in a relatively simplified way by tools of polymer physics. Dissecting factors controlling such properties could contribute to better understanding complex biological phenomena, such as fibrillation and phase separation. Furthermore, this knowledge is expected to have enormous practical implications for the design, synthesis, and exploitation of bio-derived materials and the control of natural biological processes.

Controlling the elastic modulus of simple synthetic hydrogels like polyacrylamide is essential to their use in many areas of biotechnology, including tissue engineering, medical device development, and drug delivery applications. Indentation-based methods for measuring hydrogel elastic moduli are preferred over measurements in shear rheometers or tensile testing instruments when the freedom to choose sample volume and shape are restricted; contact lenses represent such an example. It is often believed that the local application of indentation loads will volumetrically compress hydrogels, increasing the sample's polymer concentration even when the applied pressure is less than the hydrogel's osmotic pressure. Here, we test this idea by volumetrically compressing polyacrylamide hydrogels of different compositions while measuring the degree of compression with increasing applied pressure. Our results reveal that at applied pressures below the hydrogel osmotic pressure, the gels exhibit only marginal compression, while above the osmotic pressure the gels compress as predicted by classical polymer physics theory. Combining measurements of osmotic pressure and polymer mesh size, we determine the scaling relationships between hydrogel composition, mesh size, and osmotic pressure. By demonstrating agreement between experiment and theory, we use our measurements to determine the Kuhn length of the individual polymer chains constituting the hydrogels.

Chromosome motion is an intrinsic feature of all DNA-based metabolic processes and is a particularly well-documented response to both DNA damage and repair. By using both biological and polymer physics approaches, many of the contributing factors of chromatin motility have been elucidated. These include the intrinsic properties of chromatin, such as stiffness, as well as the loop modulators condensin and cohesin. Various biological factors such as external tethering to nuclear domains, ATP-dependent processes, and nucleofilaments further impact chromatin motion. DNA damaging agents that induce double-stranded breaks also cause increased chromatin motion that is modulated by recruitment of repair and checkpoint proteins. Approaches that integrate biological experimentation in conjunction with models from polymer physics provide mechanistic insights into the role of chromatin dynamics in biological function. In this review we discuss the polymer models and the effects of both DNA damage and repair on chromatin motion as well as mechanisms that may underlie these effects.

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.

We present our personal appraisal of a few recent trends in polymer physics and theory. The four main themes discussed are crystallization and melting of polymers, memory in polymer systems, topologically frustrated polymer dynamics, and phase behavior of polyelectrolyte solutions.

Here we present a pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of macromolecules in solution. Using a principle familiar from classic devices based on soft-lithography, the system uses pneumatic pressure to deflect a thin nitride lid into a nanoslit, confining molecules in an array of cavities embedded in the slit. We use this system to quantify the interactions of multiple confined DNA chains, a key problem in polymer physics with important implications for nanofluidic device performance and DNA partitioning/organization in bacteria and the eukaryotes. In particular, we focus on the problem of two-chain confinement, using differential staining of the chains to independently assess the chain conformation, determine the degree of partitioning/mixing in the cavities and assess coupled diffusion of the chain center-of-mass positions. We find that confinement of more than one chain in the cavity can have a drastic impact on the polymer dynamics and conformation.

The notion of three-phase (line) tension remains one of the most disputable notions in surface science. A very broad range of its values has been reported. Experts even do not agree on the sign of line tension. The polymer-chain-like model of three-phase (triple) line enables rough estimation of entropic input into the value of line tension, estimated as &Gamma, e n &cong, k B T d m &cong, 10 &minus, 11 N , where d m is the diameter of the liquid molecule. The introduction of the polymer-chain-like model of the triple line is justified by the &ldquo, water string&rdquo, model of the liquid state, predicting strong orientation effects for liquid molecules located near hydrophobic moieties. The estimated value of the entropic input into the line tension is close to experimental findings, reported by various groups, and seems to be relevant for the understanding of elastic properties of biological membranes.

BackgroundLocalized functional domains within chromosomes, known astopologically associating domains(TADs), have been recently highlighted. InDrosophila, TADs are biochemically defined by epigenetic marks, this suggesting that the 3D arrangement may be the “missing link” between epigenetics and gene activity. Recent observations (Boettiger et al., Nature 2016) provide access to structural features of these domains with unprecedented resolution thanks to super-resolution experiments. In particular, they give access to thedistributionof the radii of gyration for domains of different linear length and associated with different transcriptional activity states: active, inactive or repressed. Intriguingly, the observed scaling laws lack consistent interpretation in polymer physics.ResultsWe develop a new methodology conceived to extract the best information from such super-resolution data by exploiting the whole distribution of gyration radii, and to place these experimental results on a theoretical framework. We show that the experimental data are compatible with thefinite-sizebehavior of aself-attracting polymer. The same generic polymer model leads to quantitative differences between active, inactive and repressed domains. Active domains behave as pure polymer coils, while inactive and repressed domains both lie at the coil-globule crossover. For the first time, the “colo-specificity” of both the persistence length and the mean interaction energy are estimated, leading to important differences between epigenetic states.ConclusionsThese results point toward a crucial role of criticality to enhance the system responsivity, resulting in both energy transitions and structural rearrangements. We get strong indications that epigenetically induced changes in nucleosome-nucleosome interaction can cause chromatin to shift between different activity states.

A brush-like structure emerges from stretching of long polymer chains, densely grafted on to the surface of an impermeable substrate. The structure arises due to the competition between conformational entropic elasticity of polymer chains and excluded volume interactions leading to intra and interchain monomer repulsions. Recently, soft materials based on stimuli responsive polymer brushes have been developed to produce controllable and reversible large bending deformation of the host substrates. To understand such systems and improve their functional properties, we study the stress distribution in a brush, and develop surface stress-curvature relation for an elastic beam of a soft material grafted with a neutral polymer brush. In the strongly stretched brush regime, we combine mean field theory from polymer physics with a continuum mechanics model and show that the residual stress variation in a brush is a quartic function of distance from the grafting surface, with a maximum occurring at the grafting surface. By idealizing a brush as a continuum elastic surface layer with residual stress, we derive a closed form expression for surface stress and surface elasticity of the layer as a function of brush parameters, such as graft density and molecular weight. A generalized continuum beam model accounts for the Young–Laplace and Steigmann–Ogden curvature elasticity correction terms, and yields a surface stress-curvature relation, that contains existing relations in the literature as special cases. Further, we report experiments on a thermoresponsive random copolymer brush, Poly(N- isopropylacrylamide)-co-Poly(N,N-Dimethylacrylamide) (PNIPAm-co-PDMA) brush, grafted on one side of a plasticized poly(vinyl chloride) (pPVC) thin film. Estimated surface stress from measured curvature is on the order of − 10 N/m , and its magnitude decreases gradually, and reversibly, on increasing ambient temperature from 15 °C to 55 °C.

The dynamics of unfolded proteins are important both for the process of protein folding and for the behavior of intrinsically disordered proteins. However, methods for investigating the global chain dynamics of these structurally diverse systems have been limited. A versatile experimental approach is single-molecule spectroscopy in combination with Forster resonance energy transfer and nanosecond fluorescence correlation spectroscopy. The concepts of polymer physics offer a powerful framework both for interpreting the results and for understanding and classifying the properties of unfolded and intrinsically disordered proteins. This information on long-range chain dynamics can be complemented with spectroscopic techniques that probe different length scales and time scales, and integration of these results greatly benefits from recent advances in molecular simulations. This increasing convergence between the experiment, theory, and simulation is thus starting to enable an increasingly detailed view of the dynamics of disordered proteins.

This reactive molecular dynamics study explores the salt concentration dependence of the viscoelastic and mechanical failure properties of a poly(propylene glycol)/LiPF6‐based solid polymer electrolyte (SPE) at a graphitic carbon electrode interface. To account for the finite‐size effect of interface‐confined SPE films, the properties of two distinct film thicknesses are compared with the respective bulk properties. Additionally, the effect of uniaxial compression in the interface‐normal direction on free energy profiles of Li‐ion SPE‐desolvation is studied. © 2018 The Authors. Journal of Polymer Science Part B: Polymer Physics Published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018, 56, 718–730

Conjugated Polymers have attracted a great deal of research interest in recent years due to their optoelectronic properties which makes them suitable for applications in organic light-emitting devices (OLEDs) and organic photovoltaics. Their properties are strongly dependent on the electron-electron and electron-nuclear interactions as well as the disorder which is present in almost all systems at finite temperatures. In this thesis the optical properties of electronically neutral conjugated polymers will be investigated. The results obtained are general and applicable to a wide range of parameters. In order to compare these to experiment the optical properties of poly( paraphenylene), poly(para-phenylene vinylene), and derivatives have been calculated. In these polymers the primary photoexcitations are Frenkel excitons which can be described by the Frenkel-Holstein Hamiltonian, which explicitly takes into account the exciton-nuclear coupling. Disorder can be introduced into this model both as diagonal and off-diagonal disorder within the Hamiltonian. First the optical transitions in ordered, linear conjugated polymers are investigated. It is found that the length of the polymer has a direct spectroscopic signature in the emission spectrum. When off-diagonal disorder is introduced the excitons localise on portions of the chain and the length of these portions, the conjugation length, then shows a clear emission signature. As such, a disordered polymer can be described theoretically as a chain of shorter segments, which define chromophores in a polymer context. Following from these calculations the role of conformation was investigated and effects were observed that greatly determine the optical properties of non-linear polymers. Most notable the Herzberg-Teller effect, which renders symmetrically forbidden transitions weakly allowed and greatly affects the absorption and emission spectra. The signatures observed in these spectra allow the determination of the (coarse grained) conformation of the polymer, something that has been difficult to measure directly.

Compartmentalization of biochemical components, interactions, and reactions is critical for the function of cells. While intracellular partitioning of molecules via membranes has been extensively studied, there has been an expanding focus in recent years on the critical cellular roles and biophysical mechanisms of action of membraneless organelles (MLOs) such as the nucleolus. In this context, a substantial body of recent work has demonstrated that liquid-liquid phase separation (LLPS) plays a key role in MLO formation. However, less is known about MLO dissociation, with phosphorylation being the primary mechanism demonstrated thus far. In this perspective, we focus on another mechanism for MLO dissociation that has been described in recent work, namely a reentrant phase transition (RPT). This concept, which emerges from the polymer physics field, provides a mechanistic basis for both formation and dissolution of MLOs by monotonic tuning of RNA concentration, which is an outcome of cellular processes such as transcription. Furthermore, the RPT model also predicts the formation of dynamic substructures (vacuoles) of the kind that have been observed in cellular MLOs. We end with a discussion of future directions in terms of open questions and methods that can be used to answer them, including further exploration of RPTs in vitro, in cells and in vivo using ensemble and single-molecule methods as well as theory and computation. We anticipate that continued studies will further illuminate the important roles of reentrant phase transitions and associated non-equilibrium dynamics in the spatial patterning of the biochemistry and biology of the cell.

Single-molecule measurements of polymer elasticity are powerful, direct probes of both biomolecular structure and principles of polymer physics. Recent work has revealed low-force regimes in which biopolymer elasticity is understood through blob-based scaling models. However, the small tensions required to observe these regimes have the potential to create measurement biases, particularly due to the increased interactions of the polymer chain with tethering surfaces. Here, we examine one experimentally observed bias, in which fluctuation-based estimates of elasticity report an unexpectedly low chain compliance. We show that the effect is in good agreement with predictions based on quantifying the exclusion effect of the surface through an image-method calculation of available polymer configurations. The analysis indicates that the effect occurs at an external tension inversely proportional to the polymer's zero-tension radius of gyration. We exploit this to demonstrate a self-consistent scheme for estimating the radius of gyration of the tethered polymer. This is shown in measurements of both hyaluronic acid and poly(ethylene glycol) chains.