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Chromatin structures from integrated AI and polymer physics model
The physical organization of the genome in three-dimensional space regulates many biological processes, including gene expression and cell differentiation. Three-dimensional characterization of genome structure is critical to understanding these biological processes. Direct experimental measurements of genome structure are challenging; computational models of chromatin structure are therefore necessary. We develop an approach that combines a particle-based chromatin polymer model, molecular simulation, and machine learning to efficiently and accurately estimate chromatin structure fromindirectmeasures of genome structure. More specifically, we introduce a new approach where the interaction parameters of the polymer model are extracted from experimental Hi-C data using a graph neural network (GNN). We train the GNN on simulated data from the underlying polymer model, avoiding the need for large quantities of experimental data. The resulting approach accurately estimates chromatin structures across all chromosomes and across several experimental cell lines despite being trained almost exclusively on simulated data. The proposed approach can be viewed as a general framework for combining physical modeling with machine learning, and it could be extended to integrate additional biological data modalities. Ultimately, we achieve accurate and high-throughput estimations of chromatin structure from Hi-C data, which will be necessary as experimental methodologies, such as single-cell Hi-C, improve.
Composites of functional polymers: Toward physical intelligence using flexible and soft materials
Abstract Materials that can assist with perception and responsivity of an engineered machine are said to promote physical intelligence. Physical intelligence may be important for flexible and soft materials that will be used in applications like soft robotics, wearable computers, and healthcare. These applications require stimuli responsivity, sensing, and actuation that allow a machine to perceive and react to its environment. The development of materials that exhibit some form of physical intelligence has relied on functional polymers and composites that contain these polymers. This review will focus on composites of functional polymers that display physical intelligence by assisting with perception, responsivity, or by off-loading computation. Composites of liquid crystal elastomers, shape-memory polymers, hydrogels, self-healing materials, and transient materials and their functionalities are examined with a viewpoint that considers physical intelligence. Graphic Abstract
The role of free volume, hydrogen bonds, and crosslinks on physical aging in polymers of intrinsic microporosity (PIMs)
Physical aging rates strongly correlate with the initial free volume of microporous polymers. Introducing hydrogen bonds and crosslinks can reduce the initial free volume and significantly impact gas separation selectivity over time.
From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture
Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.
Time–Concentration Superposition for Linear Viscoelasticity of Polymer Solutions
The concentration dependence of linear viscoelastic properties of polymer solutions is a well-studied topic in polymer physics. Dynamic scaling theories allow qualitative predictions of polymer solution rheology, but quantitative predictions are still limited to model polymers. Meanwhile, the scaling properties of non-model polymer solutions must be determined experimentally. In present paper, the time–concentration superposition (TCS) of experimental data is shown to be a robust procedure for studying the concentration scaling properties of binary and ternary polymer solutions. TCS can not only identify whether power law scaling may exist or not, and over which concentration range, but also unambiguously estimate the concentration scaling exponents of linear viscoelastic properties for a range of non-model polymer solutions.
Stretching of immersed polyelectrolyte brushes in shear flow
In this article, the way that polymer brushes respond to shear flow has important implications in various applications, including antifouling, corrosion protection, and stimuli-responsive materials. However, there is still much to learn about the behaviours and mechanisms that govern these responses. To address this gap in knowledge, our study uses in situ X-ray reflectivity to investigate how poly(styrene sulfonate) (PSS) brushes stretch and change in different environments, such as isopropanol (a poor solvent), water (a good solvent), and aqueous solutions containing various cations (Cs + , Ba 2+ , La 3+ , and Y 3+ ). We have designed a custom apparatus that exposes the PSS brushes to both tangential shear forces from the primary flow and upward drag forces from a secondary flow. Our experimental findings clearly show that shear forces have a significant impact on how the chains in PSS brushes are arranged. At low shear rates, the tangential shear force causes the chains to tilt, leading to brush contraction. In contrast, higher shear rates generate an upward shear force that stretches and expands the chains. By analysing electron density profiles obtained from X-ray reflectivity, we gain valuable insights into how the PSS brushes respond structurally, especially the role of the diffuse layer in this dynamic behaviour. Our results highlight the importance of the initial chain configuration, which is influenced by the solvent and cations present, in shaping how polymer brushes respond to shear flow. The strength of the salt bridge network also plays a crucial role in determining how easily the brushes can stretch, with stronger networks offering more resistance to stretching. Ultimately, our study aims to enhance our understanding of polymer physics at interfaces, with a particular focus on practical applications involving polymer brushes.
Extreme Nanoconfinement Dramatically Enhances Small Molecule Solubility in Nonpolar Polymers
Elucidating gas solubility in confined polymer systems addresses a fundamental gap in polymer physics and has important implications for gas barrier and separation technologies and polymer upcycling reactions. In this study, we examine the solubility of methanol and n-hexane in polystyrene and low-density polyethylene confined within the interstitial pores of disordered silica nanoparticle packings. Using capillary rise infiltration, these polymers are infiltrated into the nanoparticle packings. Gas solubility in these confined polymers is measured using a quartz crystal microbalance. Remarkably, confinement leads to a 10- to ∼100-fold increase in gas solubility. Systematic experiments reveal that pore size plays a dominant role in increasing solubility. In contrast, the molecular weight of the polymer and the surface wetting characteristics of the nanoparticles, achieved by hydrophobically modifying the nanoparticles, have minimal effects. By systematically varying penetrant polarity, polymer crystallinity, pore size, and nanopore surface chemistry, this study isolates geometric nanoconfinement as the dominant factor governing solubility enhancement in confined polymers. Atomistic simulations revealed that confinement and surface−polymer interactions both contribute to enhanced solubility, with polymer packing playing a significant role in modulating gas uptake. Here, these results suggest that the changes in the molecular arrangements of polymer segments underlie the observed trends. This study highlights the potential of confined polymers in engineering the separation performance of membranes and heterogeneously catalyzed polymer upcycling reactions.
Glassy polymers: Historical findings, membrane applications, and unresolved questions regarding physical aging
Polymers below their glass transition temperature (Tg) are non-equilibrium glasses because excess free volume “frozen” between kinetically-restricted polymer chains slowly relaxes over time towards equilibrium via local, segmental chain motion. This process, known as physical aging, is observed through time-dependent decreases in a polymer's specific volume, enthalpy, etc. This article focuses on the history of glassy polymers in membrane separation applications. Open questions regarding the influence of thickness (e.g., membrane geometry) and temperature on physical aging in glassy polymers are highlighted.
A solvent-targeted recovery and precipitation scheme for the recycling of up to ten polymers from post-industrial mixed plastic waste
Solvent-Targeted Recovery and Precipitation (STRAP TM ) separates polymers within a plastic waste stream by selective dissolution. In this work, the STRAP framework, which combines computational modeling and experiments, was applied to develop a series of steps to separate up to 10 polymers from post-industrial mixed plastic waste (MPW) and the main components recovered were LDPE, HDPE, and PET. The STRAP steps were initially demonstrated with a physical polymer mixture containing LDPE, HDPE, PS, PVC, EVOH, PET, PP, PA6, PA66, and PA66/6, in which recoveries of 89% or higher were achieved for each polymer. Furthermore, this paper demonstrates a solvent selection approach that can be applied to separate unknown plastics materials into purer components.
Synthesis of Poly(Ester-Ether) Polymers via Hydroesterificative Polymerization of α,ω-Enol Ethers
The Pd-catalyzed carbonylative polymerization of α,ω-enol ethers derived from etherification of 10-undecenol with diols is reported, extending the scope of this relatively new polymerization strategy beyond simple 10-undecenol. Here, by varying the length of the aliphatic diol fragment in the α,ω-enol ether monomers the T m and T d of the polymers could be modified, ranging from 53 to 62 °C and 247 to 277 °C. Additionally, polymerization of α,ω-enol ethers containing rigid and bioderived diol moieties has been achieved, expanding the range of structures and polymer properties accessible via hydroesterificative polymerization. These more rigid α,ω-enol ether monomers resulted in further tuning of the polymer physical properties, with T m values ranging from 54 to 68 °C and T g values increasing up to –17 °C.
Rheology and Gelation of Hyaluronic Acid/Chitosan Coacervates
Hyaluronic acid (HA) and chitosan (CHI) are biopolyelectrolytes which are interesting for both the medical and polymer physics communities due to their biocompatibility and semi-flexibility, respectively. In this work, we demonstrate by rheology experiments that the linear viscoelasticity of HA/CHI coacervates depends strongly on the molecular weight of the polymers. Moduli for coacervates were found significantly higher than those of individual HA and CHI physical gels. A remarkable 1.5-fold increase in moduli was noted when catechol-conjugated HA and CHI were used instead. This was attributed to the conversion of coacervates to chemical gels by oxidation of 3,4-dihydroxyphenylalanine (DOPA) groups in HA and CHI to di-DOPA crosslinks. These rheological results put HA/CHI coacervates in the category of strong candidates as injectable tissue scaffolds or medical adhesives.
Molecular insights into the complex mechanics of plant epidermal cell walls
Computational analysis of cell walls Layers of intertwined fibers make up plant cell walls. The various types of fibers respond differently to deformation. Cellulose microfibrils, for example, can stretch or curve, changing their end-to-end length, and can also slide past each other, reorient relative directions, and bundle with neighboring microfibrils. Zhang et al. developed a computational model based on observations of onion skin epidermis that describes how these complex changes in space govern cell wall mechanics. The results inform ways to engineer multifunctional fibrous materials. Science , this issue p. 706
Device and methods for determination of molecular weight distributions of polymers and distributions of other polymer properties without physical separation
Devices and methods for determining the cumulative distribution of a polymer property in a reactor without physical separation of reaction subcomponents. The device includes a means of measuring an instantaneous property of the polymers being produced in a reaction vessel a plurality of times during a polymerization reaction as well as a means of determining the corresponding change in polymer concentration in the reaction vessel between measurements of the instantaneous polymer property The device also includes a means of computing a statistical distribution appropriate to the polymer characteristic and applying the statistical distribution to a recently measured instantaneous value of the polymer property so as to have an instantaneous distribution of the polymer property and a means of adding together the instantaneous distributions of the polymer property in order to obtain the cumulative distribution of the polymer property in the reactor.
Device and methods for determination of molecular weight distributions of polymers and distributions of other polymer properties without physical separation
Devices and methods for determining the cumulative distribution of a polymer property in a reactor without physical separation of reaction subcomponents. The device includes a means of measuring an instantaneous property of the polymers being produced in a reaction vessel a plurality of times during a polymerization reaction as well as a means of determining the corresponding change in polymer concentration in the reaction vessel between measurements of the instantaneous polymer property. The device also includes a means of computing a statistical distribution appropriate to the polymer characteristic and applying the statistical distribution to a recently measured instantaneous value of the polymer property so as to have an instantaneous distribution of the polymer property and a means of adding together the instantaneous distributions of the polymer property in order to obtain the cumulative distribution of the polymer property in the reactor.
Simulating sticky particles: A Monte Carlo method to sample a stratification
Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their equilibrium distribution, and there are several methods to sample probability distributions subject to fixed constraints. We introduce a Monte Carlo method to handle the case when constraints can break and form. More generally, the method samples a probability distribution on a stratification: a collection of manifolds of different dimensions, where the lower-dimensional manifolds lie on the boundaries of the higher-dimensional manifolds. We show several applications of the method in polymer physics, self-assembly of colloids, and volume calculation in high dimensions.
Molecular dynamics studies of knotted polymers
Molecular dynamics calculations have been used to explore the influence of knots on the strength of a polymer strand. In particular, the mechanism of breaking 31, 41, 51, and 52 prime knots has been studied using two very different models to represent the polymer: (1) the generic coarse-grained (CG) bead model of polymer physics and (2) a state-of-the-art machine learned atomistic neural network (NN) potential for polyethylene derived from electronic structure calculations. While there is a broad overall agreement between the results on the influence of the pulling rate on chain rupture based on the CG and atomistic NN models, for the simple 31 and 41 knots, significant differences are found for the more complex 51 and 52 knots. Notably, in the latter case, the NN model more frequently predicts that these knots can break not only at the crossings at the entrance/exit but also at one of the central crossing points. The relative smoothness of the CG potential energy surface also leads to stabilization of tighter knots compared to the more realistic NN model.