Charge Transfer Kinetics of Redox-Active Microgels.

Polymer microgel particles decorated with redox-active functional groups are a new and promising object for electrochemical applications. However, the process of charge exchange between an electrode and a microgel particle carrying numerous redox-active centers differs fundamentally from charge exchange involving only molecular species. A single act of contact between the microgel and the electrode surface may not be enough to fully discharge the microgel, and partial charge states are to be expected. Understanding the specifics of this process is crucial for the correct analysis of the data obtained from electrochemical experiments with redox-active microgel solutions. In this study, we employed coarse-grained molecular dynamics to investigate in detail the act of charge transfer from a microgel particle to a flat electrode. The simulations take into account both the mobility of functional groups carrying the charge, which depend on the microgel architecture and the charge exchange between the groups, which can accelerate the propagation of charge within the microgel volume. A set of different microgel systems were simulated in order to reveal the impact of their characteristics: fraction of redox-active groups, microgel molecular mass, cross-linker content, cross-linking topology, and solvent quality. We have found trends in microgel composition leading to the most efficient charge transfer kinetics. The obtained results would be useful for understanding experimental results and for optimizing the design of redox-active microgel particles aimed at faster discharge rates.

Long-range ordering of velocity-aligned active polymers.

In this work, we study the effect of covalent bonding on the behavior of non-equilibrium systems with the active force acting on particles along their velocity. Self-ordering of single particles does not occur in this model. However, starting from some critical polymerization degree, the ordered state is observed. It is homogeneous and exhibits no phase separation. In the ordered state, the chains prefer a near-two-dimensional configuration and all move in one direction. Importantly, the self-ordering is obtained only at intermediate active force magnitudes. At high magnitudes, the transition from the disordered to ordered state is suppressed by the swelling of the chains during the transition, as we show by the transition kinetics analysis. We demonstrate the bistable behavior of the system in a particular range of polymerization degrees, amplitudes of active force, densities, and thermostat temperatures. Overall, we show that covalent bonding greatly aids the self-ordering in this active particle model, in contrast to active Brownian particles.

Double Stimuli-Responsive di- and Triblock Copolymers of Poly(N-isopropylacrylamide) and Poly(1-vinylimidazole): Synthesis and Self-Assembly.

For the first time, double stimuli-responsive properties of poly(N-isopropylacrylamide) (PNIPA) and poly(1-vinylimidazole) (PVIM) block copolymers in aqueous solutions were studied. The synthesis of PNIPA60-b-PVIM90 and PNIPA28-b-PVIM62-b-PNIPA29 was performed using reversible addition-fragmentation chain transfer (RAFT) polymerization. The polymers were characterized by size exclusion chromatography and 1H NMR spectroscopy. The conformational behavior of the polymers was studied using dynamic light scattering (DLS) and fluorescence spectroscopy (FS). It was found that PNIPA and block copolymers conformation and ability for self-assembly in aqueous medium below and above cloud point temperature depend on the locus of hydrophobic groups derived from the RAFT agent within the chain. Additionally, the length of PVIM block, its locus in the chain and charge perform an important role in the stabilization of macromolecular micelles and aggregates below and above cloud point temperature. At 25 °C the average hydrodynamic radius (Rh) of the block copolymer particles at pH 3 is lower than at pH 9 implying the self-assembling of macromolecules in the latter case. Cloud points of PNIPA60-b-PVIM90 are ~43 °C and ~37 °C at a pH of 3 and 9 and of PNIPA28-b-PVIM62-b-PNIPA29 they are ~35 °C and 31 °C at a pH of 3 and 9. Around cloud point independently of pH, the Rh value for triblock copolymer rises sharply, achieves the maximum value, then falls and reaches the constant value, while for diblock copolymer, it steadily grows after reaching cloud point. The information about polarity of microenvironment around polymer obtained by FS accords with DLS data.

Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.

Construction of chromosomes 3D models based on single cell Hi-C data constitute an important challenge. We present a reconstruction approach, DPDchrom, that incorporates basic knowledge whether the reconstructed conformation should be coil-like or globular and spring relaxation at contact sites. In contrast to previously published protocols, DPDchrom can naturally form globular conformation due to the presence of explicit solvent. Benchmarking of this and several other methods on artificial polymer models reveals similar reconstruction accuracy at high contact density and DPDchrom advantage at low contact density. To compare 3D structures insensitively to spatial orientation and scale, we propose the Modified Jaccard Index. We analyzed two sources of the contact dropout: contact radius change and random contact sampling. We found that the reconstruction accuracy exponentially depends on the number of contacts per genomic bin allowing to estimate the reconstruction accuracy in advance. We applied DPDchrom to model chromosome configurations based on single-cell Hi-C data of mouse oocytes and found that these configurations differ significantly from a random one, that is consistent with other studies.

Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface.

Polymer microgels synthesized in silico were studied at a liquid-liquid interface via mesoscopic computer simulations and compared to microgels with ideal (diamond-like) structure. The effect of crosslinkers reactivity ratio on the single particle morphology at the interface and monolayer behavior was examined. It was demonstrated that single particles deform into an explicit core-corona morphology when adsorbed at the interface. An increase in the crosslinker reactivity ratio decreased both the deformation ratio and the ratio between the core and corona sizes. Meanwhile, the compression of microgel monolayers revealed the existence of five distinct interparticle contact regimes, which have been observed experimentally in the literature. The crosslinker reactivity ratio appeared to define the compression range in these regimes and the sharpness of the transition between them. In particular, the higher the crosslinker reactivity ratio, the smaller the corona, and in turn, the narrower the range of the intermediate regime comprising both core-core and corona-corona contacts. The obtained results demonstrate that the more realistic model of microgels synthesized via precipitation polymerization allows for a more accurate prediction of the properties of the microgels at a liquid-liquid interface in comparison to the conventional diamond-like lattice model.

Correction: Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface.

Correction for 'Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface' by Rustam A. Gumerov et al., Soft Matter, 2022, 18, 3738-3747, https://doi.org/10.1039/D2SM00269H.

An exotic microstructured globular state formed by a single multiblock copolymer chain.

In this work, we studied the equilibrium structures formed by a single (AB)k multiblock copolymer chain. Within our model, the interactions between the A-type beads were repulsive and the B-type beads could form pairwise reversible bonds with each other (BB-bonds). Our goal was to investigate how the formation of pairwise reversible bonds between the A-type beads and the B-type beads (AB-bonds) affected the structure of the chain. We observed the formation of well-studied intramolecular micelles when the AB-bonds were absent; however, the chain folding changed dramatically when the formation of the AB-bonds was introduced. In this case, the multiblock copolymer formed a globule, which had a unique heterogeneous checkerboard-like distribution of the contact density. We discovered that contacts of beads of different types (i.e., AB-contacts) occurred much more frequently than contacts of beads of the same type (i.e., AA- and BB-contacts) in these structures. This effect can be explained by a simple model of chemical equilibrium in a two-component fluid of reversibly interacting particles, which can be solved exactly. This novel type of folding can serve as a basic model for any (AB)k multiblock copolymer chain with a non-vanishing attraction between A and B blocks.

Crystallization of semiflexible polymers in melts and solutions.

We studied the crystallization of semiflexible polymer chains in melts and poor-solvent solutions with different concentrations using dissipative particle dynamics (DPD) computer simulation techniques. We used the coarse-grained polymer model to reveal the general principles and microscopic scenario of crystallization in such systems at large time and length scales. It covers both primary and secondary nucleation as well as crystallites' merging. The parameters of the DPD model were chosen appropriately to reproduce the entanglements of polymer chains. We started from an initial homogeneous disordered solution of Gaussian chains and observed the initial stages of crystallization process caused in our model by orientational ordering of polymer chains and polymer-solvent phase separation. We found that the overall crystalline fraction at the end of the crystallization process decreases with the increasing polymer volume fraction while the steady-state crystallization speed at later stages does not depend on the polymer volume fraction. The average crystallite size has a maximal value in the systems with a polymer volume fraction from 0.7 to 0.95. In our model, these polymer concentrations represent an optimal value in the sense of balance between the amount of polymer material available to increase the crystallite size and chain entanglements, that prevent crystallites' growth and merging. On large time scales, our model allows us to observe lamellar thickening linear in logarithmic time scale.

Kinetic mechanisms of crumpled globule formation.

A homopolymer chain with beads forming pairwise reversible bonds is a well-known model in polymer physics. We studied the kinetics of homopolymer chain collapse, which was induced by pairwise reversible bond formation. We compared the kinetic mechanism of this coil-globule transition with the mechanism of collapse in a poor solvent. We discovered that if collapse of a spatially confined chain is induced by formation of long-living pairwise reversible bonds, the transient structures do not resemble classical pearl-necklace conformations formed during collapse in a poor solvent. However, both types of collapse lead to formation of a metastable state of a crumpled globule, which is one of the well-known models of interphase chromatin structure in different organisms. Moreover, we found that the stability and dynamics of this state can be controlled by the fraction of reversible bonds and bond lifetime.

Simulation of interpenetrating networks microgel synthesis.

In this paper, we have implemented the sequential template synthesis of interpenetrating network (IPN) microgels in computer simulations and studied the behavior of such particles. We explored the influence of the interaction between the components of primary and secondary networks on the polymerization process and determined the necessary conditions for IPN particle formation. The interconnection between the parameters of synthesis and topological properties of the resulting microgels was investigated. We studied the morphologies of microgels in "good", "poor" and "selective" solvents. For the first time, we demonstrated the possibility of the formation of shell-corona structures in IPN microgels obtained by in silico synthesis from monomers and exposed to a selective solvent. These results allow for the better understanding of the required experimental conditions and data interpretation such as static structure factors.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.

Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)(+) RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.

Micellar polymerization: Computer simulations by dissipative particle dynamics.

Nowadays, micellar polymerization is widely used in different fields of industry and research, including modern living polymerization technique. However, this process has many variables and there is no comprehensive model to describe all features. This research presents simulation methodology which describes key properties of such reactions to take a guide through a variety of their modifications. Dissipative particle dynamics is used in addition to Monte Carlo scheme to simulate initiation, propagation, and termination events. Influence of initiation probability and different termination processes on final conversion and molecular-weight distribution are presented. We demonstrate that prolonged initiation leads to increasing in polymer average molecular weight, and surface termination events play major role in conversion limitation, in comparison with recombination. © 2018 Wiley Periodicals, Inc.

Shell-corona microgels from double interpenetrating networks.

Polymer microgels with a dense outer shell offer outstanding features as universal carriers for different guest molecules. In this paper, microgels formed by an interpenetrating network comprised of collapsed and swollen subnetworks are investigated using dissipative particle dynamics (DPD) computer simulations, and it is found that such systems can form classical core-corona structures, shell-corona structures, and core-shell-corona structures, depending on the subchain length and molecular mass of the system. The core-corona structures consisting of a dense core and soft corona are formed at small microgel sizes when the subnetworks are able to effectively separate in space. The most interesting shell-corona structures consist of a soft cavity in a dense shell surrounded with a loose corona, and are found at intermediate gel sizes; the area of their existence depends on the subchain length and the corresponding mesh size. At larger molecular masses the collapsing network forms additional cores inside the soft cavity, leading to the core-shell-corona structure.

Copolymerization on Selective Substrates: Experimental Test and Computer Simulations.

We explore the influence of a selective substrate on the composition and sequence statistics during the free radical copolymerization. In particular, we study the radical copolymerization of styrene and acrylic acid in bulk and in silica pores of different sizes. We show that the substrate affects both polymer composition and sequence statistics. We use dissipative particle dynamics simulations to study the polymerization process in detail, trying to pinpoint the parameters responsible for the observed differences in the polymer chain composition and sequences. The magnitude of the observed effect depends on the fraction of adsorbed monomer units, which cannot be described in the framework of the copolymerization theories based on the terminal unit model.

Phase diagrams of block copolymer melts by dissipative particle dynamics simulations.

Phase diagrams for monodisperse and polydisperse diblock copolymer melts and a random multiblock copolymer melt are constructed using dissipative particle dynamics simulations. A thorough visual analysis and calculation of the static structure factor in several hundreds of points at each of the diagrams prove the ability of mesoscopic molecular dynamics to predict the phase behavior of polymer systems as effectively as the self-consistent field-theory and Monte Carlo simulations do. It is demonstrated that the order-disorder transition (ODT) curve for monodisperse diblocks can be precisely located by a spike in the dependence of the mean square pressure fluctuation on χN, where χ is the Flory-Huggins parameter and N is the chain length. For two other copolymer types, the continuous ODTs are observed. Large polydispersity of both blocks obeying the Flory distribution in length does not shift the ODT curve but considerably narrows the domains of the cylindrical and lamellar phases partially replacing them with the wormlike micelle and perforated lamellar phases, respectively. Instead of the pure 3d-bicontinuous phase in monodisperse diblocks, which could be identified as the gyroid, a coexistence of the 3d phase and cylindrical micelles is detected in polydisperse diblocks. The lamellar domain spacing D in monodisperse diblocks follows the strong-segregation theory prediction, D∕N(1∕2) ~ (χN)(1∕6), whereas in polydisperse diblocks it is almost independent of χN at χN < 100. Completely random multiblock copolymers cannot form ordered microstructures other than lamellas at any composition.

Phase Diagrams of Polymerization-Induced Self-Assembly Are Largely Determined by Polymer Recombination.

In the current work, atom transfer radical polymerization-induced self-assembly (ATRP PISA) phase diagrams were obtained by the means of dissipative particle dynamics simulations. A fast algorithm for determining the equilibrium morphology of block copolymer aggregates was developed. Our goal was to assess how the chemical nature of ATRP affects the self-assembly of diblock copolymers in the course of PISA. We discovered that the chain growth termination via recombination played a key role in determining the ATRP PISA phase diagrams. In particular, ATRP with turned off recombination yielded a PISA phase diagram very similar to that obtained for a simple ideal living polymerization process. However, an increase in the recombination probability led to a significant change of the phase diagram: the transition between cylindrical micelles and vesicles was strongly shifted, and a dependence of the aggregate morphology on the concentration was observed. We speculate that this effect occurred due to the simultaneous action of two factors: the triblock copolymer architecture of the terminated chains and the dispersity of the solvophobic blocks. We showed that these two factors affected the phase diagram weakly if they acted separately; however, their combination, which naturally occurs during ATRP, affected the ATRP PISA phase diagram strongly. We suggest that the recombination reaction is a key factor leading to the complexity of experimental PISA phase diagrams.

Microphase separation of stimuli-responsive interpenetrating network microgels investigated by scattering methods.

Polymer stimuli-responsive microgels find their use in various applications. The knowledge of its internal structure is of importance for further improvement and expanding the scope. Interpenetrating network (IPN) microgels may possess a remarkable feature of strongly non-uniform inner architecture, even microphase separation, in conditions of a selective solvent. In this research, we, for the first time, use a combination of static light scattering (SLS) and small-angle X-ray scattering (SAXS) techniques to collect the structure factors of aqueous dispersions of poly(N-isopropylacrylamide)-polyacrylic acid IPN microgels on the broad scale ofqvalues. We study the influence of solvent quality on microgel conformations and show that in a selective solvent, such a system undergoes microphase separation: the sub-network in a poor solvent conditions forms dense small aggregates inside the large swollen sub-network in a good solvent. We propose the microstructured sphere model for the IPN microgel structure factor interpretation and perform additional analysis and verification through coarse-grained molecular dynamics computer simulations.

Order and stochasticity in the folding of individual Drosophila genomes.

Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.

Polymerization-Induced Microphase Separation with Long-Range Order in Melts of Gradient Copolymers.

In this work, we studied the question of whether it is possible to develop a one-step approach for the creation of microphase-separated materials with long-range order with the help of spontaneous gradient copolymers, i.e., formed during controlled copolymerization solely due to the large difference in the reactivity ratios. To that end, we studied the polymerization-induced microphase separation in bulk on the example of a monomer pair with realistic parameters based on styrene (S) and vinylpirrolydone (VP) by means of computer simulation. We showed that for experimentally reasonable chain lengths, the structures with long-range order start to appear at the conversion degree as low as 76%; a full phase diagram in coordinates (fraction of VP-conversion degree) was constructed. Rather rich phase behavior was obtained; moreover, at some VP fractions, order-order transitions were observed. Finally, we studied how the conversion degree at which the order-disorder transition occurs changes upon varying the maximum average chain length in the system.

Phase Diagram for Ideal Diblock-Copolymer Micelles Compared to Polymerization-Induced Self Assembly.

In this work we constructed a detailed phase diagram for the solutions of ideal diblock-copolymers and compared such diagram with that obtained during polymerization-induced self-assembly (PISA); a wide range of polymer concentrations as well as chain compositions was studied. As the length of the solvophobic block nB increases (the length of the solvophilic block nA was fixed), the transition from spherical micelles to cylinders and further to vesicles (lamellae) occurs. We observed a rather wide transition region between the spherical and cylindrical morphology in which the system contains a mixture of spheres and short cylinders, which appear to be in dynamic equilibrium; the transition between the cylinders and vesicles was found to be rather sharp. Next, upon increasing the polymer concentration in the system, the transition region between the spheres and cylinders shifts towards lower nB/nA values; a similar shift but with less magnitude was observed for the transition between the cylinders and vesicles. Such behavior was attributed to the increased number of contacts between the micelles at higher polymer volume concentrations. We also found that the width of the stability region of the cylindrical micelles for small polymer volume concentrations is in good quantitative agreement with the predictions of analytical theory. The obtained phase diagram for PISA was similar to the case of presynthesized diblock copolymer; however, the positions of the transition lines for PISA are slightly shifted towards higher nB/nA values in comparison to the presynthesized diblock copolymers, which is more pronounced for the case of the cylinders-to-vesicles transition. We believe that the reason for such behavior is the polydispersity of the core-forming blocks: The presence of the short and long blocks being located at the micelle interface and in its center, respectively, helps to reduce the entropy losses due to the insoluble block stretching, which leads to the increased stability of more curved micelles.