Bulk Chain Research Articles

What geometrically constrained models can tell us about real-world protein contact maps

The mechanisms by which a protein’s 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture bulk real-world 3D protein-protein properties well. One approach is using protein contact maps (PCMs) to better understand proteins’ properties. In this study, we explore the emergent behaviour of contact maps for different geometrically constrained models and compare them to real-world protein systems. Specifically, we derive an analytical approximation for the distribution of amino acid distances, denoted as P(s), using a mean-field approach based on a geometric constraint model. This approximation is then validated for amino acid distance distributions generated from a 2D and 3D version of the geometrically constrained random interaction model. For real protein data, we show how the analytical approximation can be used to fit amino acid distance distributions of protein chain lengths of L ≈ 100, L ≈ 200, and L ≈ 300 generated from two different methods of evaluating a PCM, a simple cutoff based method and a shadow map based method. We present evidence that geometric constraints are sufficient to model the amino acid distance distributions of protein chains in bulk and amino acid sequences only play a secondary role, regardless of the definition of the PCM.

Role of long-chain backbone in side-chain crystallization of densely grafted comb-like polymers

Crystallization behaviors of alkane side-chains in densely grafted comb-like vinyl or acrylate polymers are influenced by their long-chain backbones as observed in experiments. By means of dynamic Monte Carlo simulations of the lattice polymer model, we compared cooling and isothermal crystallization behaviors of side chains in bulk alternatingly grafted polymers separately holding crystallizable and non-crystallizable long-chain backbones. The results of a series of side-chain lengths showed that both non-crystallizable backbones and very short side chains suppress side-chain crystallization in agreement with experiments, demonstrating the constraint effects of the backbone on side-chain crystallization. However, both crystallizable and non-crystallizable long-chain backbones maintain their nearly random-coil conformation over side-chain crystallization, not adopting the expected bottle-brush shapes. We discussed the related experimental observations on crystal morphologies that derived the bottle-brush assumption. Our observations facilitate a better understanding of structure-property relationships for side-chain crystallization in densely grafted comb-like polymers holding relatively long backbones.

Skyrmion clusters and chains in bulk and thin-layered cubic helimagnets

Here, the author overviews the properties and the internal structure of isolated skyrmions within a cone phase of cubic helimagnets and chiral liquid crystals. The nascent conical state is shown to substantiate the attracting skyrmion-skyrmion interaction, which leads to the formation of skyrmion clusters and/or skyrmions chains. Whereas in bulk helimagnets skyrmion clusters exhibit the hexagonal arrangement of constituent skyrmions, in thin layers skyrmions align into polar skyrmion chains. Such behavior is thickness dependent and depends on the characteristic energy profiles.

Combinations of dual-function azide-containing crosslinkers with C-H insertion capabilities for polymeric elastomers with improved adhesion properties

The utilization of the noncatalytic C-H insertion capability of the nitrene intermediate of azide-containing compounds is proposed in this study for the clean fabrication of polymer-inorganic functional hybrid materials with elasticity and adhesion capabilities. For this purpose, a combination of dual-function azide-based crosslinkers composed of azidosilane (6-azidosulfonylhexyltriethoxysilane, AS) and diazide-based crosslinkers [tri(ethylene glycol)diazidoformate, GDAF] is attempted. AS affords good adhesion capability of polymer materials to OH-containing inorganic substrate/fillers, while GDAF undergoes a simultaneous C-H insertion reaction with polymer chains in bulk, affording enough crosslinking sites to improve elasticity. Through adjustments of the compositions and curing conditions, the styrene butadiene rubber compound with the proposed combination of crosslinkers exhibits good mechanical properties and excellent elasticity, as demonstrated by the low tension set value. The compound also exhibits improved adhesion capability on OH-containing silica, quartz and polyimide films, providing functional hybrid materials with an ideal combination of elasticity and adhesion capabilities suitable possibly for cutting-edge applications.

Rheology, Sticky Chain, and Sticker Dynamics of Supramolecular Elastomers Based on Cluster-Forming Telechelic Linear and Star Polymers

We elucidate the properties of unentangled telechelic poly(isobutylene) (PIB) chains in bulk forming dynamic micellar networks mediated by endgroups capable of hydrogen-bonding and π–π interactions. The effects of the molecular architecture and type of endgroup on the properties of networks are studied by a combination of small-angle X-ray scattering (SAXS), rheology, low-resolution NMR, and dielectric spectroscopy (DS). It is found that star-shaped molecules form more time-stable networks with larger and somewhat more distantly arranged aggregates compared to their linear counterparts. Using stickers providing less hydrogen bonds speeds up terminal flow significantly, yet surprisingly, the nanoscale morphology, apparent activation energies, and the timescale of endgroup fluctuations probed by DS are very similar across the two sample series. The correlation of results from the three dynamic methods (rheology, NMR, and DS) thus fortifies previous findings for linear chains: (i) even for star molecules, terminal stress relaxation is governed by single-chain relaxation rather than the reorganization of whole micelles, and (ii) the cluster-related relaxation time accessed by DS has no trivial relation to the actual sticky bond lifetime, the determination of which is concluded to be an open problem.

Sequence-Engineering Polyethylene-Polypropylene Copolymers with High Thermal Conductivity Using a Molecular-Dynamics-Based Genetic Algorithm.

Polymer sequence engineering is emerging as a potential tool to modulate material properties. Here, we employ a combination of a genetic algorithm (GA) and atomistic molecular dynamics (MD) simulation to design polyethylene-polypropylene (PE-PP) copolymers with the aim of identifying a specific sequence with high thermal conductivity. PE-PP copolymers with various sequences at the same monomer ratio are found to have a broad distribution of thermal conductivities. This indicates that the monomer sequence has a crucial effect on thermal energy transport of the copolymers. A non-periodic and non-intuitive optimal sequence is indeed identified by the GA, which gives the highest thermal conductivity compared with any regular block copolymers, for example, diblock, triblock, and hexablock. In comparison to the bulk density, chain conformations, and vibrational density of states, the monomer sequence has the strongest impact on the efficiency of thermal energy transport via inter- and intra-molecular interactions. Our work highlights polymer sequence engineering as a promising approach for tuning the thermal conductivity of copolymers, and it provides an example application of integrating atomistic MD modeling with the GA for computational material design.

Viscoelastic Properties of Dumbbell-Shaped Polystyrenes in Bulk and Solution

This study examined viscoeslastic properties of two flexible dumbbell-shaped polystyrene (PS) samples, D-30/120/30 and D-30/240/30, which possess the same ring size (MR ∼ 30 kg/mol) and different lengths of central linear chains (ML ∼ 120 and 240 kg/mol) in bulk and solution. In bulk, both dumbbell PS samples exhibited an extremely long entanglement plateau in dynamic oscillatory measurements, and their terminal relaxation behavior was not observed in our experimental window. In stress relaxation measurements, dumbbell samples in bulk exhibited considerably slower terminal relaxation than high-molecular-weight linear PS samples (M ∼ 10⁶ g/mol), and a clear difference between two dumbbell PS samples was observed in the long time regime, i.e., terminal relaxation of D-30/240/30 is much slower than that of D-30/120/30. These results suggest that (i) the dumbbell polymer forms a characteristic “network” where two rings on both ends in a molecule spontaneously thread the ring part of other dumbbell chains and (ii) this type of interchain interaction resulting in network formation becomes more dominant than usual entanglements similar to linear chains. The network of dumbbell chains starts to relax their stress when the intermolecular threading is released, and this release process tends to occur more frequently for the dumbbell with a shorter central chain, D-30/120/30, than that with a longer one, D-30/240/30. In dioctyl phthalate (DOP) solutions of D-30/240/30, where DOP is known as a θ-solvent for PS at 22 °C, in a relatively high concentration regime (i.e., 20–30 wt %), the solutions exhibited an entanglement plateau and higher viscosity than the corresponding linear PS solutions, suggesting that the characteristic entanglement originating from intermolecular threading of dumbbell chains is still dominant in the solution. On the contrary, in a lower-concentration regime (≤8 wt %), the D-30/240/30 solutions exhibited similar viscosities to the linear PS ones, wherein the dumbbell molecules behave like unentangled/isolated chains.

Compression and Stretching of Single DNA Molecules under Channel Confinement.

We study the compression and extension response of single dsDNA (double-stranded DNA) molecules confined in cylindrical channels by means of Monte Carlo simulations. The elastic response of micrometer-sized DNA to the external force acting through the chain ends or through the piston is markedly affected by the size of the channel. The interpretation of the force (f)-displacement (R) functions under quasi-one-dimensional confinement is facilitated by resolving the overall change of displacement ΔR into the confinement contribution ΔRD and the force contribution ΔRf. The external stretching of confined DNA results in a characteristic pattern of f-R functions involving their shift to the larger extensions due to the channel-induced pre-stretching ΔRD. A smooth end-chain compression into loop-like conformations observed in moderately confined DNA can be accounted for by the relationship valid for a Gaussian chain in bulk. In narrow channels, the considerably pre-stretched DNA molecules abruptly buckle on compression by the backfolding into hairpins. On the contrary, the piston compression of DNA is characterized by a gradual reduction of the chain span S and by smooth f-S functions in the whole spatial range from the 3d near to 1d limits. The observed discrepancy between the shape of the f-R and f-S functions from two compression methods can be important for designing nanopiston experiments of compaction and knotting of single DNA in nanochannels.

RETRACTED ARTICLE: Core–mantle–shell novel nanostructures for efficacy escalating in poly(3-hexylthiophene):phenyl-C71-butyric acid methyl ester photovoltaics

Core–mantle nanohybrids were prepared via grafting the multi-walled carbon nanotubes (MWCNTs) with polyaniline (PANI). Core–mantle–shell supramolecules were then designed by crystallization of poly(3-hexylthiophene) (P3HT) and poly[benzodithiophene-bis(decyltetradecyl-thien) naphthothiadiazole] (PBDT-DTNT) conductive polymers onto core (CNT)–mantle (PANI) nanostructures. Supramolecules were thoroughly investigated and applied in active layers of P3HT:phenyl-C71-butyric acid methyl ester (PC71BM) solar cells. Efficacies of 5.71% and 6.02% were acquired for photovoltaics based on nanostructures having PBDT-DTNT and P3HT shells, respectively. Diameters of core(CNT)–mantle(PANI), core(CNT)–mantle(PANI)–shell(P3HT), and core(CNT)–mantle(PANI)–shell(PBDT-DTNT) supramolecules ranged in 75–90 nm, 145–160 nm, and 120–130 nm, respectively. The highest efficiency (= 6.02%) was achieved for P3HT:PC71BM:CNT-graft-PANI/P3HT systems without any post-treatment (13.42 mA/cm2, 0.68 V, and 66%). Charge mobilities were also very high for corresponding electron-only (µe = 9.8 × 10−3 cm2/V s) and hole-only (µh = 5.0 × 10−3 cm2/V s) devices. PANI mantle may act as both acceptor and donor in core–mantle–shell supramolecules. Core(CNT)–mantle(PANI)–shell(PBDT-DTNT) nanostructures also elevated photovoltaic efficiency up to 5.71% (13.12 mA/cm2, 0.67 V, 65%, 4.7 × 10−3 cm2/V s, and 9.0 × 10−3 cm2/V s). Results acquired for core(CNT)–mantle(PANI)–shell(P3HT)-based systems were somehow higher than those recorded for core(CNT)–mantle(PANI)–shell(PBDT-DTNT)-based ones. It could be assigned to consistency of P3HT shells and P3HT host chains in bulk of P3HT:PC71BM active layer. P3HT backbones owing to their simpler chemical structures were also capable of arranging more ordered shells, leading to larger charge mobilities and currents.

Spatial distribution of entanglements and dynamics in polymer films confined by smooth walls

Using Monte Carlo simulations combined with a geometric analysis method (Z1), we investigate the spatial distribution of entanglements and dynamics in polymer films confined by smooth walls, where the chain length spans a range from the unentangled to the entangled region. Our results demonstrate a supersaturated region of entanglements as the distance of chains from the wall approaching 2Rg,e, where Rg,e represents the coil size of chain segment of the entanglement length. As the distance is further increased, the entanglements become well-distributed as in the bulk. Moreover, when the film thickness is smaller than the bulk chain dimension, the variations of the dynamics of polymers with the film thickness can be divided into three cases: for the unentangled short chains, the diffusion coefficient is a slowly decreasing function with the decrease of the film thickness; for the chains with a few entanglement points, the diffusion coefficient is almost independent of the film thickness; for the chains with considerable entanglement points, the diffusion coefficient becomes a rapidly increasing function with the decrease of the film thickness, which can be attributed to the competition between the spatial confinement and the disentanglement. Our work can provide an understanding of the microscopic distribution of entanglements and dynamics of polymer films deviating from what we know from the bulk.

Entanglement dynamics at flat surfaces: Investigations using multi-chain molecular dynamics and a single-chain slip-spring model.

The dynamics of an entangled polymer melt confined in a channel by parallel plates is investigated by Molecular Dynamics (MD) simulations of a detailed, multi-chain model. A primitive path analysis predicts that the density of entanglements remains approximately constant throughout the gap and drops to lower values only in the immediate vicinity of the surface. Based on these observations, we propose a coarse-grained, single-chain slip-spring model with a uniform density of slip-spring anchors and slip-links. The slip-spring model is compared to the Kremer-Grest MD bead-spring model via equilibrium correlation functions of chain orientations. Reasonably good agreement between the single-chain model and the detailed multi-chain model is obtained for chain relaxation dynamics, both away from the surface and for chains whose center of mass positions are at a distance from the surface that is less than the bulk chain radius of gyration, without introducing any additional model parameters. Our results suggest that there is no considerable drop in topological interactions for chains in the vicinity of a single flat surface. We infer from the slip-spring model that the experimental plateau modulus of a confined polymer melt may be different to a corresponding unconfined system even if there is no drop in topological interactions for the confined case.

Rubber-Filler Interactions in Polyisoprene Filled with In Situ Generated Silica: A Solid State NMR Study.

In this paper we used high- and low-resolution solid state Nuclear Magnetic Resonance (NMR) techniques to investigate a series of polyisoprene samples filled with silica generated in situ from tetraethoxysilane by sol-gel process. In particular, 1H spin-lattice and spin-spin relaxation times allowed us to get insights into the dynamic properties of both the polymer bulk and the bound rubber, and to obtain a comparative estimate of the amount of bound rubber in samples prepared with different compositions and sol-gel reaction times. In all samples, three fractions with different mobility could be distinguished by 1H T2 and ascribed to loosely bound rubber, polymer bulk, and free chain ends. The amount of bound rubber was found to be dependent on sample preparation, and it resulted maximum in the sample showing the best dispersion of silica domains in the rubber matrix. The interpretation of the loosely bound rubber in terms of “glassy” behaviour was discussed, also on the basis of 1H T1 and T1ρ data.

Inelastic and quasi-elastic neutron scattering. Application to soft-matter

Microscopic dynamical events control many of the physical processes at play in condensed matter: transport, magnetism, catalysis and even function of biological assemblies. Inelastic (INS) and Quasi-Elastic Neutron Scattering (QENS) are irreplaceable probes of these phenomena. These experimental techniques reveal the displacements of atoms and molecules over distances spanning from angstroms to a few tens of nanometers, on time scales ranging from a fraction of picoseconds to microseconds. In this context, the different INS and QENS machines (Time-of-Flight (ToF), Backscattering (BS) and Neutron spin-echo (NSE)) stand at a central position. After introducing an underlying basic theoretical toolbox for neutron scattering, the principles and key elements of a ToF measurement are described. While, here, we mainly focus on disk choppers spectrometers, all the INS/QENS instruments share a common ground: they directly and simultaneously probe correlation functions in both time and space, so that the scattering vector (Q) dependence of the systems characteristic time(s) can be measured. To illustrate, the potentialities of the technique in the field of soft-matter, we show a multiscale approach of the dynamics of a polymer melt. The system is probed from the molecular to the mesoscopic scale (1 ps to 0.6 μs and 0.1 to 40 nm), in bulk and under nanometric confinement. We address the different dynamical modes of a high mass entangled polymer chain: local monomer dynamics, Rouse modes up to the reptation process. This study exemplifies that, used in conjunction with hydrogen/deuterium isotopic effects, high resolution QENS can be bridged to the Zero Average Contrast (ZAC) method to probe, in a non destructive way, the dynamics of a single polymer chain in bulk but also under severe nanometric confinement. Connection and complementarity of the neutron derived analysis with Pulsed-Field Gradient and Relaxation NMR techniques are discussed.

Ultrastretchable, Tough, and Notch-Insensitive Hydrogels Formed with Spherical Polymer Brush Crosslinker.

Spherical polymer brushes, poly(acrylic acid) (PAA)-grafted polystyrene nanoparticle (PAA@PS), are employed as the macro-crosslinker to prepare PAA hydrogels. Benefitting from the innumerable hydrogen bonds between highly entangled PAA chains both in bulk and on the polymer brush, the PAA/PAA@PS hydrogels combine desirable stretchability, toughness, and notch-insensitivity. The uniaxial tensile tests show a very high fracture elongation up to 9.1 × 103 % while the fracture toughness reaches 3.0 MJ m-3 and the maximum swelling ratio of the hydrogel can be 2.0 × 103 as well. After being loaded with silver nanoparticles, the PAA/PAA@PS hydrogels are employed as a recyclable catalyst successfully.

Molecular dynamics for linear polymer melts in bulk and confined systems under shear flow

In this work, we analyzed the individual chain dynamics for linear polymer melts under shear flow for bulk and confined systems using atomistic nonequilibrium molecular dynamics simulations of unentangled (C50H102) and slightly entangled (C178H358) polyethylene melts. While a certain similarity appears for the bulk and confined systems for the dynamic mechanisms of polymer chains in response to the imposed flow field, the interfacial chain dynamics near the boundary solid walls in the confined system are significantly different from the corresponding bulk chain dynamics. Detailed molecular-level analysis of the individual chain motions in a wide range of flow strengths are carried out to characterize the intrinsic molecular mechanisms of the bulk and interfacial chains in three flow regimes (weak, intermediate, and strong). These mechanisms essentially underlie various macroscopic structural and rheological properties of polymer systems, such as the mean-square chain end-to-end distance, probability distribution of the chain end-to-end distance, viscosity, and the first normal stress coefficient. Further analysis based on the mesoscopic Brightness method provides additional structural information about the polymer chains in association with their molecular mechanisms.

Tg-confinement effects in strongly miscible blends of poly(2,6-dimethyl-1,4-phenylene oxide) and polystyrene: Roles of bulk fragility and chain segregation

The glass transition temperature (Tg)-confinement effects in single-layer, supported films of strongly miscible poly(2,6-dimethyl-1,4-phenylene oxide)/polystyrene (PPO/PS) blends are characterized using ellipsometry and fluorescence, both of which report a single, reduced blend Tg upon confinement. These results indicate that PPO/PS blends exhibit strong miscibility under conditions of nanoscale confinement and that there is a lack of strong attractive polymer-substrate interactions in PPO/PS films supported on Si/SiOx. The strength of the Tg-confinement effect obtained via ellipsometry scales with bulk blend fragility in PPO/PS blends and exhibits a weaker dependence on bulk fragility than that observed previously [Evans et al. Macromolecules 2013, 46, 6091] in supported films of linear homopolymers lacking attractive polymer-substrate interactions. We further compare Tg results obtained from fluorescence of both pyrenyl labels (covalently attached to PS) and dopants (freely dispersed in PPO/PS blends) along with those from ellipsometry. In the confined state, pyrenyl dopant fluorescence reports blend Tg values that agree relatively well with Tg values reported by ellipsometry; in contrast, pyrenyl label fluorescence reports blend Tg values that are significantly lower than those reported by both ellipsometry and pyrenyl dopant fluorescence. We attribute this difference to the combined effects of the distribution of pyrenyl dye across the film and underlying surface segregation. Our results indicate that the combination of ellipsometry and fluorescence provides a powerful methodology to study interface-induced chain segregation in nanoconfined miscible polymer blends, whether in film geometry or in nanocomposites.

Effects of Polymer-Wall Interactions on Entanglements and Dynamics of Confined Polymer Films.

Using Monte Carlo simulations combined with a geometric primitive path analysis method (Z1 algorithm), we investigate the effects of polymer-wall interactions on the entanglements and dynamics of the polymer films capped between two walls. We introduce a new parameter, the average number of near-neighboring particles of each monomer, to understand the effects of the polymer-wall interactions on the entanglements and dynamics of these confined systems. Our results show that the number of entanglements increases from the attractive polymer-wall interactions to the repulsive polymer-wall interactions. When the film thickness is greater than the bulk chain dimensions, the diffusion coefficient is a slowly decreasing function of the film thickness; however, when the film thickness is smaller than the bulk chain dimensions, the diffusion coefficient is an increasing function of the film thickness. However, for stronger polymer-wall interactions, although the number of entanglements decreases, the average number of the near-neighboring particles rapidly increases, which screens the effect of the disentanglements and thus limits the diffusivity of the polymers. Moreover, our simulations demonstrate that a critical attractive energy exists in the polymer-wall systems, where the diffusion coefficient reaches a maximum value and decreases toward stronger attractions or stronger repulsions. Our simulations provide new insights into the molecular mechanisms of the effects of polymer-wall interactions on the confined polymer films.

An Update on the Pivotal Role of Kinetic Modeling for the Mechanistic Understanding and Design of Bulk and Solution RAFT Polymerization

The importance of the development of kinetic modeling tools to mechanistically understand and design bulk and solution reversible addition fragmentation chain transfer (RAFT) polymerization is highlighted. Both deterministic and stochastic kinetic modeling methods are covered, considering a detailed reaction scheme and accounting for the impact of diffusional limitations on the reaction rates. A novel strategy is introduced to fundamentally calculate the diffusional contributions for the apparent RAFT addition and fragmentation rate coefficients. Next to literature examples, case studies are included to demonstrate that detailed theoretical studies are indispensable to completely map the effect of the polymerization conditions and RAFT agent reactivity on the control over microstructural properties and the overall polymerization time. Guidelines for future kinetic modeling activities are formulated to enhance joined theoretical and experimental research.image

Spatial distribution of entanglements in thin free-standing films.

We simulate entangled linear polymers in free-standing thin film geometries where the confining dimension is on the same scale as or smaller than the bulk chain dimensions. We compare both film-averaged and layer-resolved, spatially inhomogeneous measures of the polymer structure and entanglement network with theoretical models. We find that these properties are controlled by the ratio of both chain- and entanglement-strand length scales to the film thickness. While the film-averaged entanglement properties can be accurately predicted, we identify outstanding challenges in understanding the spatially resolved character of the heterogeneities in the entanglement network, particularly when the scale of both the entanglement strand and the chain end-to-end vector is comparable to or smaller than the film thickness.

Protein Composition Determines the Effect of Crowding on the Properties of Disordered Proteins

Unlike dilute experimental conditions under which biological molecules are typically characterized, the cell interior is crowded by macromolecules, which affects both the thermodynamics and kinetics of in vivo processes. Although the excluded-volume effects of macromolecular crowding are expected to cause compaction of unfolded and disordered proteins, the extent of this effect is uncertain. We use a coarse-grained model to represent proteins with varying sequence content and directly observe changes in chain dimensions in the presence of purely repulsive spherical crowders. We find that the extent of crowding-induced compaction is dependent not only on crowder size and concentration, but also on the properties of the protein itself. In fact, we observe a nonmonotonic trend between the dimensions of the polypeptide chain in bulk and the degree of compaction: the most extended chains experience up to 24% compaction, the most compact chains show virtually no change, and intermediate chains compress by up to 40% in size at a 40% crowder volume fraction. Free-volume theory combined with an impenetrable ellipsoidal representation of the chains predicts the crowding effects only for collapsed protein chains. An additional scaling factor, which can be easily computed from protein-crowder potential of mean force, corrects for the penetrability of extended chains and is sufficient to capture the observed nonmonotonic trend in compaction.