Effect of chain architecture on the size, shape, and intrinsic viscosity of chains in polymer solutions: A molecular simulation study

Microscopic Origins of Flow Activation Energy in Biomolecular Condensates

Material properties of biomolecular condensates dictate their form and function, influencing the diffusion of regulatory molecules and the dynamics of biochemical reactions. The increasing quality and quantity of microrheology experiments on biomolecular condensates necessitate a deeper understanding of the molecular grammar that encodes their material properties. Recent reports have identified a characteristic timescale related to network relaxation dynamics in condensates, which governs their temperature-dependent viscoelastic properties. This timescale is intimately connected to an activated process involving the dissociation of sticker regions, with the energetic barrier referred to as flow activation energy. The microscopic origin of activation energy is a complex function of sequence patterns, component stoichiometry, and external conditions. This study elucidates the microscopic origins of flow activation energy in single and multicomponent condensates composed of model peptide sequences with varying sticker and spacer motifs, with RNA as a secondary component. We dissected the effects of condensate density, RNA stoichiometry, and peptide sequence patterning using extensive sequence-resolved coarse-grained simulations. We found that flow activation energy is closely linked to the lifetime of sticker-sticker pairs under certain conditions, though the presence of multiple competing stickers further complicates this relationship. The insights gained in this study should help establish predictive multiscale models for the material properties and serve as a valuable guide for the programmable design of condensates.

Rheological Properties of Small-Molecular Liquids at High Shear Strain Rates

Molecular-scale understanding of rheological properties of small-molecular liquids and polymers is critical to optimizing their performance in practical applications such as lubrication and hydraulic fracking. We combine nonequilibrium molecular dynamics simulations with two unsupervised machine learning methods: principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE), to extract the correlation between the rheological properties and molecular structure of squalane sheared at high strain rates (106-1010s-1) for which substantial shear thinning is observed under pressures P∈0.1-955 MPa at 293 K. Intramolecular atom pair orientation tensors of 435×6 dimensions and the intermolecular atom pair orientation tensors of 61×6 dimensions are reduced and visualized using PCA and t-SNE to assess the changes in the orientation order during the shear thinning of squalane. Dimension reduction of intramolecular orientation tensors at low pressures P=0.1,100 MPa reveals a strong correlation between changes in strain rate and the orientation of the side-backbone atom pairs, end-backbone atom pairs, short backbone-backbone atom pairs, and long backbone-backbone atom pairs associated with a squalane molecule. At high pressures P≥400 MPa, the orientation tensors are better classified by these different pair types rather than strain rate, signaling an overall limited evolution of intramolecular orientation with changes in strain rate. Dimension reduction also finds no clear evidence of the link between shear thinning at high pressures and changes in the intermolecular orientation. The alignment of squalane molecules is found to be saturated over the entire range of rates during which squalane exhibits substantial shear thinning at high pressures.

Effect of Charge Distribution on the Dynamics of Polyampholytic Disordered Proteins

The stability and physiological function of many biomolecular coacervates depend on the structure and dynamics of intrinsically disordered proteins (IDPs) that typically contain a significant fraction of charged residues. Although the effect of relative arrangement of charged residues on IDP conformation is a well-studied problem, the associated changes in dynamics are far less understood. In this work, we systematically interrogate the effects of charge distribution on the chain-level and segmental dynamics of polyampholytic IDPs in dilute solutions. We study a coarse-grained model polyampholyte consisting of an equal fraction of two oppositely charged residues (glutamic acid and lysine) that undergoes a transition from an ideal chain-like conformation for uniformly charge-patterned sequences to a semi-compact conformation for highly charge-segregated sequences. Changes in the chain-level dynamics with increasing charge segregation correlate with changes in conformation. The chain-level and segmental dynamics conform to simple homopolymer models for uniformly charge-patterned sequences but deviate with increasing charge segregation, both in the presence and absence of hydrodynamic interactions. We discuss the significance of these findings, obtained for a model polyampholyte, in the context of a charge-rich intrinsically disordered region of the naturally occurring protein LAF-1. Our findings have important implications for understanding the effects of charge patterning on the dynamics of polyampholytic IDPs in dilute conditions using polymer scaling theories.

Star Polymers vs. Dendrimers: Studies of the Synthesis Based on Computer Simulations

A generic model was developed for studies of the polymerization process of regular branched macromolecules. Monte Carlo simulations were performed employing the Dynamic Lattice Liquid algorithm to study this process. A core-first methodology was used in a living polymerization of stars with up to 32 arms, and dendrimers consisted of 4-functional segments. The kinetics of the synthesis process for stars with different numbers of branches and dendrimers was compared. The size and structure of star-branched polymers and dendrimers during the synthesis were studied. The influence of the functionality of well-defined cores on the structure and on the dispersity of the system was also examined. The differences in the kinetics in the formation of both architectures, as well as changes to their structures, were described and discussed.

State-Of-The-Art Quantification of Polymer Solution Viscosity for Plastic Waste Recycling

Solvent-based recycling is a promising approach for closed-loop recovery of plastic-containing waste. It avoids the energy cost to depolymerize the plastic but still allows to clean the polymer of contaminants and additives. However, viscosity plays an important role in handling the polymer solutions at high concentrations and in the cleaning steps. This Review addresses the viscosity behavior of polymer solutions, available data, and (mostly algebraic) models developed. The non-Newtonian viscosity models, such as the Carreau and Yasuda-Cohen-Armstrong models, pragmatically describe the viscosity of polymer solutions at different concentrations and shear rate ranges. This Review also describes how viscosity influences filtration and centrifugation processes, which are crucial steps in the cleaning of the polymer and includes a polystyrene/styrene case study.

Origin of Rebound Suppression for Dilute Polymer Solution Droplets on Superhydrophobic Substrate

Controlling droplet deposition with a minute amount of polymer additives is of profound practical importance in a wild range of applications. Previous work ascribed the relevant mechanisms to extensional viscosity, normal stress, wetting properties, etc., but the mechanism remains controversial. In this paper, we employ molecular dynamics simulations systematically for the first time to investigate the origin of rebound suppression for dilute polymer solution droplets on a flat superhydrophobic substrate. The results demonstrate that polymer-substrate interactions and impact velocities dominate the antirebound phenomenon. For low impact velocities, the dynamic characteristics of droplets are insensitive to polymer additives. However, large impact velocities will enhance the stretch behavior of polymer chains and make the chains closer to the substrate, increasing the probability of polymer molecules contacting the bottom substrate. With the cooperation of strong polymer-substrate interactions, polymer molecules can be absorbed easily by the bottom substrate, resisting the retraction process and leading to the onset of the antirebound behavior.

Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics

Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.

Collective Motions and Mechanical Response of a Bulk of Single-Chain Nano-Particles Synthesized by Click-Chemistry

We investigate the effect of intra-molecular cross-links on the properties of polymer bulks. To do this, we apply a combination of thermal, rheological, diffraction, and neutron spin echo experiments covering the inter-molecular as well as the intermediate length scales to melts of single-chain nano-particles (SCNPs) obtained through 'click' chemistry. The comparison with the results obtained in a bulk of the corresponding linear precursor chains (prior to intra-molecular reaction) and in a bulk of SCNPs obtained through azide photodecomposition process shows that internal cross-links do not influence the average inter-molecular distances in the melt, but have a profound impact at intermediate length scales. This manifests in the structure, through the emergence of heterogeneities at nanometric scale, and also in the dynamics, leading to a more complex relaxation behavior including processes that allow relaxation of the internal domains. The influence of the nature of the internal bonds is reflected in the structural relaxation that is slowed down if bulky cross-linking agents are used. We also found that any residual amount of cross-links is critical for the rheological behavior, which can vary from an almost entanglement-free polymer bulk to a gel. The presence of such inter-molecular cross-links additionally hinders the decay of density fluctuations at intermediate length scales.

Molecular Dynamics Simulations of Aqueous Nonionic Surfactants on a Carbonate Surface

The interactions and structure of secondary alcohol ethoxylates with 15 and 40 ethoxylate units in water near a calcite surface are studied. It is found that water binds preferentially to the calcite surface. Prediction of the free-energy landscape for surfactant molecules shows that single-surfactant molecules do not adsorb because they cannot get close enough to the surface because of the water layer for attractive ethoxylate-calcite or dispersion interactions to be significant. Micelles can adsorb onto the surface even with the intervening water layer because of the integrative effect of the attractive interactions of all the surfactant molecules. Adsorption is found to increase because of the closer proximity of the micelles to the surface due to a weakened water layer at higher temperatures. The free-energy well and barrier values are used to estimate surface to bulk partition coefficients for different surfactants and temperatures, and qualitative agreement is found with experimental observations. The combined effect of surfactant-water and surfactant-solid interactions is found to be responsible for an increased adsorption for nonionic surfactants as the system approaches the cloud point.

Polymer-functionalized polymer nanoparticles and their behaviour in suspensions

In concentrated suspensions of polymer-functionalized nanoparticles, the softness of the core nanoparticles has a crucial effect on the mechanical behaviour of the resulting colloidal gels.

Multimodal character of shear viscosity response in hydrogen bonded liquids

Non-simple viscosity response of 2E1H alcohol forming supramolecular aggregates.

Synthesis of sequence-determined bottlebrush polymers based on sequence determination in living anionic copolymerization of styrene and dimethyl(4-(1-phenylvinyl)phenyl)silane

Sequence-determined bottlebrush polymers are precisely, efficiently and conveniently synthesized.