Polymer Physics Research Articles

Fluctuating Chromatin Facilitates Enhancer-Promoter Communication by Regulating Transcriptional Clustering Dynamics.

Enhancers regulate gene expression by forming contacts with distant promoters. Phase-separated condensates or clusters formed by transcription factors (TFs) and cofactors are thought to facilitate these enhancer-promoter (E-P) interactions. Using polymer physics, we developed distinct coarse-grained chromatin models that produce similar ensemble-averaged Hi-C maps but with "stable" and "dynamic" characteristics. Our findings, consistent with recent experiments, reveal a multistep E-P communication process. The dynamic model facilitates E-P proximity by enhancing TF clustering and subsequently promotes direct E-P interactions by destabilizing the TF clusters through chain flexibility. Our study promotes physical understanding of the molecular mechanisms governing E-P communication in transcriptional regulation.

Study of the Skin-Resorptive Properties of Chitosan

The Aim of the Work: study of the skin-resorptive and sensitizing effects of various chitosan de-rivatives. Material and Methods: To study the skin-resorptive and allegnizing effects of chitosan sulfate and chitosan with furacilin according to the recommendations for the study of the toxicological proper-ties of drugs. Results: For the first time, a complex of preclinical experimental studies of various chitosan deriva-tives developed at the nstitute of Polymer Chemistry and Physics of the Academy of Sciences of the Republic of Uzbekistan was carried out. It was revealed that they do not have a resorptive and irritating effect on the skin and mucous membranes of the eyes, does not cause sensitization of the body of guinea pigs. The drugs do not have a cumulative effect and sensitizing effect. Conclusions: • Chitosan sulfate and chitosan preparations with furacilin do not have a skin-resorptive effect and a locally irritating effect. • Chitosan sulfate and chitosan preparations with furacilin do not have an allergenic effect.

Topological comparison of flexible and semiflexible chains in polymer melts with θ-chains.

A central paradigm of polymer physics states that chains in melts behave like random walks as intra- and interchain interactions effectively cancel each other out. Likewise, θ-chains, i.e., chains at the transition from a swollen coil to a globular phase, are also thought to behave like ideal chains, as attractive forces are counterbalanced by repulsive entropic contributions. While the simple mapping to an equivalent Kuhn chain works rather well in most scenarios with corrections to scaling, random walks do not accurately capture the topology and knots, particularly for flexible chains. In this paper, we demonstrate with Monte Carlo and molecular dynamics simulations that chains in polymer melts and θ-chains not only agree on a structural level for a range of stiffnesses but also topologically. They exhibit similar knotting probabilities and knot sizes, both of which are not captured by ideal chain representations. This discrepancy comes from the suppression of small knots in real chains, which is strongest for very flexible chains because excluded volume effects are still active locally and become weaker with increasing semiflexibility. Our findings suggest that corrections to ideal behavior are indeed similar for the two scenarios of real chains and that the structure and topology of a chain in a melt can be approximately reproduced by a corresponding θ-chain.

A Gram-Charlier Analysis of Scattering to Describe Nonideal Polymer Conformations.

Theories of interpreting polymer physics and rheology at the molecular level from experiments, including small-angle scattering, typically rely on the assumption that polymer chains possess a Gaussian configuration distribution. This assumption frequently fails to describe features of real polymer molecules both at equilibrium (when polymers have nonlinear topology or heterogeneous chemistry) and out of equilibrium (when they are subjected to nonlinear deformations). To better describe non-Gaussian polymer conformation distributions, we propose a moments analysis based on the Gram-Charlier expansion as a natural framework for describing structure and scattering from non-Gaussian polymers. The expansion describes the conformation distribution in terms of cumulants (equivalent to moments of the distribution) of the underlying segment density distribution function, providing low-dimensional descriptors that can be inferred directly from measured scattering in a way that is agnostic to a polymer's topology, chemistry, or state of deformation. We use this framework to show that cumulants can be used to "fingerprint" non-Gaussian conformation distributions of polymers either at equilibrium (applied to sequence-defined heteropolymers) or out of equilibrium (applied to polymers experiencing nonlinear deformation due to flow). We anticipate that this new analysis method will provide a general framework for examining nonideal polymer configurations and the properties that arise from them.

Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.

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.

Modeling of Dissolving Microneedle-Based Transdermal Drug Delivery: Effects of Dynamics of Polymers in Solution.

Dissolving microneedle (DMN)-assisted transdermal drug delivery (TDD) has received attention from the scientific community in recent years due to its ability to control the rate of drug delivery through its design, the choice of polymers, and its composition. The dissolution of the polymer depends strongly on the polymer-solvent interaction and polymer physics. Here, we developed a mathematical model based on the physicochemical parameters of DMNs and polymer physics to determine the drug release profiles. An annular gap width is defined when the MN is inserted in the skin, accumulating interstitial fluid (ISF) from the surrounding skin and acting as a boundary layer between the skin and the MN. Poly(vinylpyrrolidone) (PVP) is used as a model dissolving polymer, and ceftriaxone is used as a representative drug. The model agrees well with the literature data for ex vivo permeation studies, along with the percent height reduction of the MN. Based on the suggested mathematical model, when loading 0.39 mg of ceftriaxone, the prediction indicates that approximately 93% of the drug will be cleared from the bloodstream within 24 h. The proposed modeling strategy can be utilized to optimize drug transport behavior using DMNs.

Free energy and extension of stiff polymer chains confined in nanotubes with diverse cross-sectional shapes

The statistical mechanics of stiff polymer chains confined within narrow tubes is a foundational topic in polymer physics, extensively analyzed in prior research. For cylindrical, rectangular, and slit-like confinements, the chains’ free energy and extension adhere to a scaling law consistent with the Odijk theory. While this scaling law may not apply to tubes with different cross-sectional geometries, there is a lack of research examining the behavior of stiff chains in tubes with intricate cross-sectional shapes. In this study, we investigate the partition function of a stiff chain confined within an elliptic tube using the path integral approach, deriving a deflection length in a concise closed form through dimensional analysis. This length scale facilitates straightforward expressions for the chain's free energy and extension. Notably, we discover a shape-independent property of these expressions applicable to tubes with a wide variety of cross-sectional geometries. Extensive numerical simulations are conducted using a biased chain-growth Monte Carlo method, incorporating the Pruned and Enriched Rosenbluth algorithm, to validate the theoretical predictions on the confinement free energy and extension of chains in tubes with differing shapes.

Longitudinal ultrasound measurements of polyethylene oxide across dilute to concentrated aqueous solutions

Measuring the properties of polymer solutions is crucial for understanding fundamental polymer physics. The longitudinal ultrasound measurement method offers a promising technique for characterizing these properties. In this study, we develop a mathematical model to correlate longitudinal ultrasonic signals with the material properties of polyethylene oxide (PEO) from dilute to concentrated aqueous solutions. After applying reflection and diffraction corrections, the accuracy of the measurement results improves to over 97 %. Our findings reveal a positive correlation between the speed of sound, density, and longitudinal modulus with the mass concentration of PEO. Additionally, ultrasonic relaxation analysis reveals that PEO solutions exhibit at least one relaxation process in the frequency range of 3–7 MHz, independent of concentration and molecular weight. Compared to dilute solutions, the relaxation amplitude in concentrated solutions is larger and accompanied by strong nonlinearity, attributed to conformational changes caused by molecular entanglement in concentrated solutions.

Experimental teaching reform of polymer molar mass determination using gel permeation chromatography coupled with light scattering

Gel permeation chromatography coupled with light scattering (GPC-LS) is among the most common methods for determining the molar masses of polymers. GPC-LS is widely used in polymer science research and has been adopted for many industrial applications owing to its high sensitivity, accuracy, and precision. The determination of polymer molar masses using GPC-LS is an important experimental component of the "Polymer Physics Experiments" course. However, the present GPC-LS experimental teaching content tends to be overly simplistic and lacking in depth. Herein, the original experimental content is expanded and multiple sets of experiments are redesigned: (1) Using commercial polystyrene as an experimental sample, the molar mass, molar mass distribution, radius of gyration, and other molecular structure parameters are determined using GPC-LS; (2) Using two polyacrylonitriles with similar molecular structure parameters, subtle differences in the molar mass distributions of the samples are explored using differential mass distribution curves; (3) By comparing the chromatograms of a series of polyethylene glycols with different molar masses, the effect of molar mass on chromatographic peaks is investigated; and (4) For three different polymers (polyacrylonitrile, poly(methyl methacrylate), and poly(β-cyclodextrin)), the polymer chain conformations are analyzed using conformation plots (i.e., radius of gyration vs. molar mass). In addition, the experimental teaching method is modified to convert passive learning into active learning, thereby improving the students' self-directed learning ability. This experimental teaching reform will help students obtain a more comprehensive understanding of GPC-LS principles and applications, stimulate their enthusiasm for learning, and improve the teaching quality of the experimental course.

Polymer Physics Experiment Teaching Design - Taking the Preparation and Performance Research of Conductive Ion Gel as an Example

Polymer physics is a required course for materials majors. Promoting teaching with scientific research is an important way to improve the quality of teaching in colleges and universities. In this paper, ionic liquid was used as multifunctional components to prepare ion gels by photoinitiated polymerization of acrylamide and acrylic acid monomers, and the effect of the content of ionic liquids on the mechanical properties and ionic conductivity of ion gels was further investigated. This experiment can cultivate students comprehensive experimental ability and in-depth understanding of the influence of polymer structure on performance. Through this experimental teaching reform, students can master knowledge principles and experimental skills, stimulate their enthusiasm for learning, and cultivate scientific thinking and scientific research innovation capabilities.

Dialysis Monitoring of Ionic Strength and Denaturant Effects, and Their Reversibility, for Various Classes of Macromolecules.

Monitoring membrane-mediated dialysis in real time with static and dynamic light scattering revealed distinctive differences, including reversibility/irreversibility, in the effects of ionic strength (NaCl) and the denaturant guanidine-HCl (Gd) on a synthetic polyelectrolyte and several types of biomacromolecules: protein, polysaccharide, and polyampholyte. Dialysis cycles against aqueous NaCl and Gd, and reverse back to the original aqueous solution, were monitored. The behavior of Na-polystyrenesulfonate was reversible and yielded a detailed polymer physics description. The biomacromolecules additionally showed hydrogen-bonding/hydrophobic (HP) interactions. An interpretive model was developed that considers the interplay among polyelectrolyte, polyampholyte, and HP potential energies in determining the different associative, aggregative, and dissociative behaviors. NaCl isolated purely electrostatic effects, whereas Gd combined electrostatic and HP effects. Some macromolecules showed partially reversible behavior, and others were completely irreversible. The dialysis monitoring method should prove useful for investigating fundamental macromolecular and colloid properties and for drug formulation and stability optimization.

Exact analytical solution of the Flory-Huggins model and extensions to multicomponent systems.

The Flory-Huggins theory describes the phase separation of solutions containing polymers. Although it finds widespread application from polymer physics to materials science to biology, the concentrations that coexist in separate phases at equilibrium have not been determined analytically, and numerical techniques are required that restrict the theory's ease of application. In this work, we derive an implicit analytical solution to the Flory-Huggins theory of one polymer in a solvent by applying a procedure that we call the implicit substitution method. While the solutions are implicit and in the form of composite variables, they can be mapped explicitly to a phase diagram in composition space. We apply the same formalism to multicomponent polymeric systems, where we find analytical solutions for polydisperse mixtures of polymers of one type. Finally, while complete analytical solutions are not possible for arbitrary mixtures, we propose computationally efficient strategies to map out coexistence curves for systems with many components of different polymer types.

Passive and active field theories for disease spreading

The worldwide COVID-19 pandemic has led to a significant growth of interest in the development of mathematical models that allow to describe effects such as social distancing measures, the development of vaccines, and mutations. Several of these models are based on concepts from soft matter theory. Considerably less well investigated is the reverse direction, i.e. how results from epidemiological research can be of interest for the physics of colloids and polymers. In this work, we consider the susceptible-infected-recovered (SIR)-dynamical density functional theory (DDFT) model, a combination of the SIR model from epidemiology with DDFT from nonequilibrium soft matter physics, which allows for an explicit modeling of social distancing. We extend the SIR-DDFT model both from an epidemiological perspective by incorporating vaccines, asymptomaticity, reinfections, and mutations, and from a soft matter perspective by incorporating noise and self-propulsion and by deriving a phase field crystal (PFC) model that allows for a simplified description. On this basis, we investigate via computer simulations how epidemiological models are affected by the presence of non-reciprocal interactions. This is done in a numerical study of a zombie outbreak.

Synthesis of isotope‐substituted conjugated ladder polymers

AbstractConjugated ladder polymers (cLPs) represent an intriguing class of macromolecules, characterized by their multi‐stranded structure, with continuous fused π‐conjugated rings forming the backbone. Isotope substitution, such as deuteration and carbon‐13 labeling, offers unique approaches to address the significant challenges associated with elucidating the structure and solution phase dynamics of these polymers. For instance, selective deuteration can highlight parts of the polymer by controlling the scattering length density of specific molecular sections, thereby enhancing the contrast for neutron scattering experiments. In this context, deuteration of side‐chains in cLPs represents a promising approach to uncover the elusive polymer physics properties of their backbone. The synthesis of two distinct types of cLPs with perdeuterated side‐chains are reported here. During the synthesis, 13C isotope labeling was also employed to verify the low levels of defects in the synthesized polymers. Demonstrating these synthetic successes lays the foundation for rigorous characterization of the defects, conformation, and dynamics of cLPs.

Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.

Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2Mb 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.

Separation of sticker-spacer energetics governs the coalescence of metastable biomolecular condensates.

Biological condensates often emerge as a multi-droplet state and never coalesce into one large droplet within the experimental timespan. Previous work revealed that the sticker-spacer architecture of biopolymers may dynamically stabilize the multi-droplet state. Here, we simulate the condensate coalescence using metadynamics approach and reveal two distinct physical mechanisms underlying the fusion of droplets. Condensates made of sticker-spacer polymers readily undergo a kinetic arrest when stickers exhibit slow exchange while fast exchanging stickers at similar levels of saturation allow merger to equilibrium states. On the other hand, condensates composed of homopolymers fuse readily until they reach a threshold density. Increase in entropy upon inter-condensate mixing of chains drives the fusion of sticker-spacer chains. We map the range of mechanisms of kinetic arrest from slow sticker exchange dynamics to density mediated in terms of energetic separation of stickers and spacers. Our predictions appear to be in excellent agreement with recent experiments probing dynamic nature of protein-RNA condensates.

From Bioreactor to Bulk Rheology: Achieving Scalable Production of Highly Concentrated Circular DNA.

DNA serves as a model system in polymer physics due to its ability to be obtained as a uniform polymer with controllable topology and nonequilibrium behavior. Currently, a major obstacle in the widespread adoption of DNA is obtaining it on a scale and cost basis that accommodates bulk rheology and high-throughput screening. To address this, recent advancements in bioreactor-based plasmid DNA production is coupled with anion exchange chromatography producing a unified approach to generating gram-scale quantities of monodisperse DNA. With this method, 1.1 grams of DNA is obtained per batch to generate solutions with concentrations up to 116mg mL-1. This solution of uniform supercoiled and relaxed circular plasmid DNA, is roughly 69 times greater than the overlap concentration. The utility of this method is demonstrated by performing bulk rheology measurements at sample volumes up to 1 mL on DNA of different lengths, topologies, and concentrations. The measured elastic moduli are orders of magnitude larger than those previously reported for DNA and allowed for the construction of a time-concentration superposition curve that spans 12 decades of frequency. Ultimately, these results can provide important insights into the dynamics of ring polymers and the nature of highly condensed DNA dynamics.

Storage Life of Particle-Filled Polymer Composites Considering Aging Effects.

This study investigates the storage life of particle-filled polymer composites (PFPCs) under the influence of aging effects. High-temperature accelerated aging tests were conducted at 60 °C, 70 °C, and 80 °C for various days to analyze the impact of aging time and temperature on the mechanical behavior of the materials. A predictive model for crosslink density was established using the Arrhenius equation, and the relationship between crosslink density and relaxation modulus was determined based on polymer physics theory. On this basis, a viscoelastic constitutive model that incorporates aging effects was developed. Structural analyses of a PFPC column with a length of 2.3 m and outer diameter of 1.8 m were performed using the UMAT subroutine in ABAQUS. Subsequently, a safety margin assessment method based on dewetting strain was employed to predict the storage life of the PFPC column. The results indicate that the aging viscoelastic constitutive model effectively characterizes the hardening effects caused by aging in the composites during storage. The storage life for the PFPC column considering aging effects decreases from 22 years to 19 years compared to models that ignore such effects. This approach provides a reference for estimating the storage life of PFPC columns considering aging effects.

Interfacial Engineering of Soft Matter Substrates by Solid-State Polymer Adsorption.

Polymer coating to substrates alters surface chemistry and imparts bulk material functionalities with a minute thickness, even in nanoscale. Specific surface modification of a substate usually requires an active substrate that, e.g., undergoes a chemical reaction with the modifying species. Here, we present a generic method for surface modification, namely, solid-state adsorption, occurring purely by entropic strive. Formed by heating above the melting point or glass transition and subsequent rinsing of the excess polymer, the emerging ultrathin (<10 nm) layers are known in fundamental polymer physics but have never been utilized as building blocks for materials and they have never been explored on soft matter substrates. We show with model surfaces as well as bulk substrates, how solid-state adsorption of common polymers, such as polystyrene and poly(lactic acid), can be applied on soft, cellulose-based substrates. Our study showcases the versatility of solid-state adsorption across various polymer/substrate systems. Specifically, we achieve proof-of-concept hydrophobization on flexible cellulosic substrates, maintaining irreversible and miniscule adsorption yet with nearly 100% coverage without compromising the bulk material properties. The method can be considered generic for all polymers whose Tg and Tm are below those of the to-be-coated adsorbed layer, and whose integrity can withstand the solvent leaching conditions. Its full potential has broad implications for diverse materials systems where surface coatings play an important role, such as packaging, foldable electronics, or membrane technology.

Correlation between synthesis parameters and hyperelasticity of hydrogels: Experimental investigation and theoretical modeling

The mechanical properties of hydrogels are significantly influenced by synthesis parameters. Although the mapping from the space of synthesis parameters to the space of properties has been investigated experimentally, a quantitative theoretical framework is still lacking. In this work, the effect of synthesis parameters on the hyperelastic behaviors of hydrogels was experimentally studied. Subsequently, we conducted theoretical analysis by combining the constitutive model and polymer physics to quantify the correlation between synthesis parameters (the initial water content, current water content, and degree of cross-linking) and hyperelasticity (the elastic modulus, degree of entanglement, and stress-stretch ratio curve) of hydrogels. The internal relation between critical polymer content for entanglement and both the initial water content and degree of cross-linking arises from the scaling laws. By analyzing the critical polymer content for entanglement and comparing it with the current polymer content, hydrogels are categorized as either cross-linking-dominated or entanglement-dominated. The current study indicates that a low degree of cross-linking, i.e., a long-chain structure, is an important prerequisite for plenty of entanglements. Hydrogels with low cross-linking are highly entangled, whether they possess high initial water content/low current water content or low initial water content/high current water content. This work paves the way for the systematic design of synthesis parameters, thereby guiding the modulation and optimization of the overall mechanical properties and the application of hydrogels.