Single Chain Dynamics Research Articles

Exploring the Growth Dynamics of Size-Selected Carbon Atomic Wires with In Situ UV Resonance Raman Spectroscopy.

Short carbon atomic wires, the prototypes of the lacking carbon allotrope carbyne, represent the fundamental 1D system and the first stage in carbon nanostructure growth, which still exhibits many open points regarding their growth and stability. An in situ UV resonance Raman approach is introduced for real-time monitoring of the growth of carbon atomic wires during pulsed laser ablation in liquid without perturbing the synthesis environment. Single-chain species' growth dynamics are tracked, achieving size selectivity by exploiting the peculiar optoelectronic properties of carbon wires and the tunability of synchrotron radiation. Diverse solvents are systematically explored, finding size- and solvent-dependent production rates linked to the solvent's C/H ratio and carbonization tendency. Carbon atomic wires' growth dynamics reveal a complex interplay between formation and degradation, leading to an equilibrium. Water, lacking in carbon atoms and reduced polyynes solubility, yields fewer wires with rapid saturation. Organic solvents exhibit enhanced productivity and near-linear growth, attributed to additional carbon from solvent dissociation and low relative polarity. Exploring the dynamics of the saturation regime provides new insights into advancing carbon atomic wires synthesis via PLAL. Understanding carbon atomic wires' growth dynamics can contribute to optimizing PLAL processes for nanomaterial synthesis.

Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning

Conformational dynamics of RNA plays important roles in a variety of cellular functions such as transcriptional regulation, catalysis, scaffolding, and sensing. Recently, RNAs with low-complexity sequences have been shown to phase separate and form condensate phases similar to lowcomplexity protein domains. The affinity for phase separation and the material characteristics of RNA condensates are strongly dependent on sequence composition and patterning. We hypothesize that differences in the affinities for RNA phase separation can be uncovered by studying sequence-dependent conformational dynamics of single RNA chains. To this end, we have employed atomistic simulations and deep dimensionality reduction techniques to map temperature-dependent conformational free energy landscapes for 20 base-long homopolymeric RNA sequences: poly(U), poly(G), poly(C), and poly(A). The energy landscapes of homopolymeric RNAs reveal a plethora of metastable states with qualitatively different populations stemming from differences in base chemistry. Through detailed analysis of base, phosphate, and sugar interactions, we show that experimentally observed temperature-driven shifts in metastable state populations align with experiments on RNA phase transitions. Specifically, we find that the thermodynamics of unfolding of homopolymeric RNA follows the poly(G) > poly(A) > poly(C) > poly(U) order of stability, mirroring the propensity of RNA to form condensates. To conclude, this work shows that at least for homopolymeric RNA sequences the single-chain conformational dynamics contains sufficient information for predicting and quantifying condensate forming affinities of RNAs. Thus, we anticipate that atomically detailed studies of temeprature -dependent energy landscapes of RNAs will be a useful guide for understanding the propensity of various RNA molecules to form condensates.

Dynamics of Acrylamide Hydrogels, Polymers, and Monomers in Water Measured with Optical Heterodyne-Detected Optical Kerr Effect Spectroscopy.

The ultrafast dynamics of acrylamide monomers (AAm), polyacrylamide (PAAm), and polyacrylamide hydrogels (PAAm-HG) in water were studied using optical heterodyne-detected optical Kerr effect (OHD-OKE) spectroscopy. Previous ultrafast infrared (IR) measurements of the water dynamics showed that at the same concentration of the acrylamide moiety, AAm, PAAm, and PAAm-HG exhibited identical water dynamics and that these dynamics slowed with increasing concentration. In contrast to the IR measurements, OHD-OKE experiments measure the dynamics of both the water and the acrylamide species, which occur on different time scales. In this study, the dynamics of all the acrylamide systems slowed with increasing concentration. We found that AAm exhibits tetraexponential decays, the longest component of which followed Debye-Stokes-Einstein behavior except for the highest concentration, 40% (w/v). Low concentrations of PAAm followed a single power law decay, while high concentrations of PAAm and all concentrations of PAAm-HG decayed with two power laws. The highest concentrations, 25% and 40%, of PAAm and PAAm-HG showed nearly identical dynamics. We interpreted this result as reflecting a similar extent of chain-chain interactions. At low concentrations, PAAm displays non-Markovian, single-chain dynamics (single power law), but PAAm displays entangled chain-chain interactions at high concentrations (two power laws). PAAm-HG has chain-chain interactions at all concentrations that arise from the cross-linking. At high concentrations, the dynamics of the entangled of PAAm become identical within error as those of the cross-linked PAAm-HG.

Microrheological study of single chain dynamics in semidilute entangled flexible polymer solutions: Crossover from Rouse to Zimm modes

The dynamics of polymer chains in entangled semidilute solution have been of theoretical and experimental interest. Among a number of characteristic lengths and times of the polymer in solution, those of the correlation blob are the key to understand the applicability of the Rouse and Zimm models to rheology of the semidilute solution. Direct rheological measurements of Rouse and Zimm modes are limited as the corresponding time scale is out of the range of classical rheological techniques. We investigated the single chain dynamics of entangled poly(ethylene oxide) in semidilute aqueous solutions by high-frequency micro-rheology based on diffusing-wave spectroscopy compared to classical shear macro-rheology. Concentration dependence of the three characteristic times of the entangled polymer chains, reptation time, entanglement time, and correlation time, was studied with the help of the time-concentration superposition. At the low frequency range, dynamic moduli measured by macro-rheology and micro-rheology showed a good agreement without adjustable parameters. At the higher frequency range, we found the Rouse regime in the mean square displacement of the probe particles and in the magnitude of the complex specific viscosity of the solution. We propose a simple method to estimate the boundary of the Rouse regime. Finally, at the high frequency range, we demonstrate that the contribution of the solvent to the solution viscosity needs to be subtracted to observe the power-law behavior of the Zimm mode.

Simulation of Solvent Evaporation from a Diblock Copolymer Film: Orientation of the Cylindrical Mesophase

Using particle-based Monte Carlo simulations and continuum modeling, we study the self-assembly of asymmetric diblock copolymers in the course of solvent evaporation. We examine the effects of evaporation rate and solvent selectivity on the structure formation, especially the alignment of the cylindrical domains of the minority block. The comparison of the two simulation techniques facilitates identifying general trends upon parameter variation, while their inherent differences help us to understand the role of single-chain dynamics, fluctuations, and additional model details. In both cases, the simulation models feature a liquid and a gas phase with an explicit surface, across which solvent evaporates. We propose a “layer evolution model” that links processing parameters to the final morphology via the time dependence of layers, in which characteristic microphases, for example, spherical or cylindrical, can form. The evolution of these layers varies with the processing conditions and determines the morphology. This allows us to discuss the interplay of various experimentally accessible parameters, which we support by respective simulations. Our results single out two main factors to ensure the formation of minority-block cylinders, perpendicular to the film surface: (i) Fast evaporation rates induce a steep gradient in the polymer-density profile; that is, the polymer density immediately beneath the gas–liquid surface rapidly exceeds the critical value for cylinder formation. This confines cylinder formation into a layer that is thinner than the actual cylinder diameter, forcing a perpendicular alignment. (ii) A certain selectivity of the gas phase for the matrix-forming, majority block is necessary to disrupt an otherwise entropically favored surface layer of the minority block that would lead to parallel cylinder alignment.

Single-chain polymerization dynamics and conformational mechanics of conjugated polymers

<h2>Summary</h2> Conjugated polymers possess unique optoelectrical properties. Characterizing their synthesis and mechanical processability is crucial for tailored applications. Their poor solubility presents a universal challenge, however. Here, we report a single-molecule study, which circumvents the solubility challenge, of the polymerization kinetics and conformational mechanics of polyacetylene, a prototypical conjugated polymer. We monitor the growth of individual long-chain polyacetylenes during ring-opening metathesis polymerization of cyclooctatetraene. We discover that polyacetylene forms nonequilibrium conformational entanglements, whose kinetic instability and structural looseness appear to render its polymerization more facile than that of polycyclooctene, a nonconjugated analog. This relative kinetics is contrary to monomer reactivity predictions. Moreover, even under identical solvent conditions, individual polyacetylenes show diverse extension-versus-force scaling behaviors; many span multiple scaling regimes predicted previously but never observed. The extracted persistence and Kuhn length of polyacetylene are also significantly shorter than its wavefunction delocalization length, indicating that polyacetylene can maintain backbone conjugation while staying flexible.

Modeling of Nonlinear Optical Phenomena in Host-Guest Systems Using Bond Fluctuation Monte Carlo Model: A Review.

We review the results of Monte Carlo studies of chosen nonlinear optical effects in host-guest systems, using methods based on the bond-fluctuation model (BFM) for a polymer matrix. In particular, we simulate the inscription of various types of diffraction gratings in degenerate two wave mixing (DTWM) experiments (surface relief gratings (SRG), gratings in polymers doped with azo-dye molecules and gratings in biopolymers), poling effects (electric field poling of dipolar molecules and all-optical poling) and photomechanical effect. All these processes are characterized in terms of parameters measured in experiments, such as diffraction efficiency, nonlinear susceptibilities, density profiles or loading parameters. Local free volume in the BFM matrix, characterized by probabilistic distributions and correlation functions, displays a complex mosaic-like structure of scale-free clusters, which are thought to be responsible for heterogeneous dynamics of nonlinear optical processes. The photoinduced dynamics of single azopolymer chains, studied in two and three dimensions, displays complex sub-diffusive, diffusive and super-diffusive dynamical regimes. A directly related mathematical model of SRG inscription, based on the continuous time random walk (CTRW) formalism, is formulated and studied. Theoretical part of the review is devoted to the justification of the a priori assumptions made in the BFM modeling of photoinduced motion of the azo-polymer chains.

Dynamics and rheology of a suspension of super-paramagnetic chains under the combined effect of a shear flow and a rotating magnetic field.

This study presents an analysis of the dynamics of single and multiple chains of spherical super-paramagnetic beads suspended in a Newtonian fluid under the combined effect of an external rotating magnetic field and a shear flow. Viscosity results depend on two main non-dimensional numbers: the ratio between the shear rate and the magnetic rotation frequency and the ratio between the hydrodynamic and magnetostatic interactions (the Mason number). When the shear rate is smaller than the magnetic field frequency, the chain rotation accelerates the surrounding fluid, reducing the value of the measured suspension viscosity even below that of the solvent. In this regime, shear-thickening is observed. For values of the shear rates comparable to the rotation magnetic frequency, the viscosity reaches a maximum and non-linear coupling effects come up. If the shear rate is increased to values above the rotation frequency, the viscosity decreases and a mild shear-thinning is observed. In terms of the Mason number, the suspension viscosity reduces in line with the literature results reported for fixed magnetic fields, whereas the shear-rate/magnetic-frequency ratio parameters induce a shift of the viscosity curve towards larger values. Results at larger concentrations and multiple chains amplify the observed effects.

Photoinduced Mass Transport in Azo-Polymers in 2D: Monte Carlo Study of Polarization Effects.

We studied the impact of light polarization on photoinduced dynamics of model azo-polymer chains in two dimensions, using bond-fluctuation Monte Carlo simulations. For two limiting models—sensitive to and independent of light polarization—their dynamics driven by photoisomerization of azo-dyes as well as by thermal effects was studied, including characterization of mass transport and chain reorientations. The corresponding schemes of light–matter interaction promote qualitatively different dynamics of photoinduced motion of azo-polymer chains. In particular, they can inhibit or trigger off a directed mass transport along a gradient of light illumination. The generic dynamics of single chains is superdiffusive and is promoted by breaking a symmetry present in the polarization independent model.

Entangled Polymer Dynamics in Attractive Nanocomposite Melts

We investigate single chain dynamics of an entangled linear poly(ethylene oxide) melt in the presence of well-dispersed attractive nanoparticles using high-resolution neutron spectroscopy at partic...

Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model.

Intrinsically disordered proteins (IDPs) play an important role in an array of biological processes but present a number of fundamental challenges for computational modeling. Recently, simple polymer models have regained popularity for interpreting the experimental characterization of IDPs. Homopolymer theory provides a strong foundation for understanding generic features of phenomena ranging from single-chain conformational dynamics to the properties of entangled polymer melts, but is difficult to extend to the copolymer context. This challenge is magnified for proteins due to the variety of competing interactions and large deviations in side-chain properties. In this work, we apply a simple physics-based coarse-grained model for describing largely disordered conformational ensembles of peptides, based on the premise that sampling sterically forbidden conformations can compromise the faithful description of both static and dynamical properties. The Hamiltonian of the employed model can be easily adjusted to investigate the impact of distinct interactions and sequence specificity on the randomness of the resulting conformational ensemble. In particular, starting with a bead–spring-like model and then adding more detailed interactions one by one, we construct a hierarchical set of models and perform a detailed comparison of their properties. Our analysis clarifies the role of generic attractions, electrostatics, and side-chain sterics, while providing a foundation for developing efficient models for IDPs that retain an accurate description of the hierarchy of conformational dynamics, which is nontrivially influenced by interactions with surrounding proteins and solvent molecules.

Dynamical self-consistent field theory captures multi-scale physics during spinodal decomposition in a symmetric binary homopolymer blend.

We study the spinodal decomposition in a symmetric, binary homopolymer blend using our recently developed dynamical self-consistent field theory. By taking the extremal solution of a dynamical functional integral, the theory reduces the interacting, multi-chain dynamics to a Smoluchowski equation describing the statistical dynamics of a single, unentangled chain in a self-consistent, time-dependent, mean force-field. We numerically solve this equation by evaluating averages over a large ensemble of replica chains, each one of which obeys single-chain Langevin dynamics, subject to the mean field. Following a quench from the disordered state, an early time spinodal instability in the blend composition develops, before even one Rouse time elapses. The dominant, unstable, growing wavelength is on the order of the coil size. The blend then enters a late-time, t, scaling regime with a growing domain size that follows the expected Lifshitz-Slyozov-Wagner t1/3 power law, a characteristic of a diffusion-driven coarsening process. These results provide a satisfying test of this new method, which correctly captures both the early and late time physics in the blend. Our simulation spans five orders-of-magnitude in time as the domains coarsen to 20 times the coil size, while remaining faithful to the dynamics of the microscopic chain model.

Complex Dynamics of Photoinduced Mass Transport and Surface Relief Gratings Formation.

The microscopic and semi-macroscopic mechanisms responsible for photoinduced mass transport in functionalized azo-polymers are far from deeply understood. To get some insight into those mechanisms on “microscopic” scale, we studied the directed photoinduced motion of single functionalized polymer chains under various types of polarized light illumination using Monte Carlo bond fluctuation model and our kinetic Monte Carlo model for photoinduced mass transport. We found sub-diffusive, diffusive and super-diffusive regimes of the dynamics of single chains at constant illumination and mostly super-diffusive regime for directed motion in the presence of the gradient of light intensity. This regime is more enhanced for long than for short chains and it approaches the ballistic limit for very long chains. We propose a physical picture of light-driven inscription of Surface Relief Gratings (SRG) as corresponding to a dynamical coexistence of normal and anomalous diffusion in various parts of the system. A simple continuous time random walk model of SRG inscription based on this physical picture reproduced the light-driven mass transport found in experiments as well as the fine structure of SRG.

Random Co(II)-Ni(II) Ferromagnetic Chains Showing Coexistent Antiferromagnetism, Metamagnetism, and Single-Chain Magnetism.

A series of isomorphous compounds of general formula [Co1- xNi x(tzpo)(N3)(H2O)2] n· nH2O ( x = 0, 0.19, 0.38, 0.53, 0.68, 0.84, and 1; tzpo = 4-(5-tetrazolate)pyridine- N-oxide) was prepared. The compounds consist of homometallic or heterometallic chains with simultaneous azide-tetrazolate bridges. The heterometallic systems feature random distribution of metal ions. All compounds across the series exhibit intrachain ferromagnetic coupling, interchain antiferromagnetic (AF) ordering, field-induced metamagnetic transition, and, except the Ni-only compound, single-chain magnetic dynamics. The AF ordering temperature, the metamagnetic critical field, and the relaxation parameters show different composition dependence. Notably, the blocking temperature for the Co-rich materials is higher than the Co-only compound, suggesting synergy between the randomly distributed Co(II) and Ni(II) ions in promoting slow relaxation. The results imply rich physics in the random mixed-metal systems and demonstrate the possibility of improving single-chain relaxation properties by blending metal ions.

Small Particle Driven Chain Disentanglements in Polymer Nanocomposites.

Using neutron spin-echo spectroscopy, x-ray photon correlation spectroscopy, and bulk rheology, we studied the effect of particle size on the single-chain dynamics, particle mobility, and bulk viscosity in athermal polyethylene oxide-gold nanoparticle composites. The results reveal a ≈25% increase in the reptation tube diameter with the addition of nanoparticles smaller than the entanglement mesh size (≈5 nm), at a volume fraction of 20%. The tube diameter remains unchanged in the composite with larger (20nm) nanoparticles at the same loading. In both cases, the Rouse dynamics is insensitive to particle size. These results provide a direct experimental observation of particle-size-driven disentanglements that can cause non-Einstein-like viscosity trends often observed in polymer nanocomposites.

Elucidating the flow-microstructure coupling in the entangled polymer melts. Part I: Single chain dynamics in shear flow

Tube-based theories have accurately predicted the rheological properties of entangled, linear, monodisperse polymer melts for slow flows since reptation is the dominant chain relaxation mechanism in this flow regime. However, at higher strain rates, the continuum level theories fail to describe the nonlinear properties precisely since all the relevant physical processes have not been incorporated self-consistently into the constitutive equation expression. Therefore, we have utilized dissipative particle dynamics (DPD) simulations to examine the flow microstructure coupling of moderately entangled polymer melts (13 ≤ 〈Zk〉 ≤ 27, 〈Zk〉: average entanglement density at equilibrium) undergoing simple shear flow. In so doing, not only do we gauge the fidelity of DPD simulations of flow of entangled polymeric fluids via a direct comparison with nonequilibrium molecular dynamics results, but also, we elucidate the intricate relationship between single chain dynamics and relaxation mechanisms in moderately entangled polymeric melts. Specifically, it is shown that at small shear rates, γ̇ ≤ τd−1, chains reptate and flow align and as shear rate increases, at τd−1 ≤ γ̇ ≤ τR−1, significant chain orientation and onset of chain extension lead to flow-induced chain disentanglement and a commensurate dilation of the “tubes” allowing chain rotation/retraction to occur. Ultimately, at very high shear rates, τR−1 ≤ γ̇, the chains become significantly aligned with the flow leading to destruction of the entanglement network where the chain motion resembles that of dilute/semi-dilute polymer solutions under theta condition.

Ring Polymer Dynamics Are Governed by a Coupling between Architecture and Hydrodynamic Interactions

The behavior of linear polymer chains in dilute solution flows has an established history. Polymers often possess more complex architectures, however, such as branched, dendritic, or ring structures. A major challenge lies in understanding how these nonlinear chain topologies affect the dynamic properties in nonequilibrium conditions, in both dilute and entangled solutions. In this work, we interrogate the single-chain dynamics of ring polymers using a combination of simulation, theory, and experiment. Inspired by recent experimental results by Li et al., we demonstrate that the presence of architectural constraints has surprising and pronounced effects on the dynamic properties of polymers as they are driven out of equilibrium. Ring constraints lead to two behaviors that contrast from linear chains. First, the coil–stretch transition occurs at larger values of the dimensionless flow strength (Weissenberg number) compared to linear chains, which is driven by coupling between intramolecular hydrodynamic in...

Complex Interactions with the Surroundings Dictate a Tagged Chain’s Dynamics in Unentangled Polymer Melts

For more than half a century the theoretical landscape for single chain dynamics for dense polymeric solutions and melts below the entanglement threshold has been dominated by the Rouse model for independent phantom chains, supported by ideas of hydrodynamic screening. There exists, however, a large body of literature from experiments, Monte Carlo, and molecular dynamics simulations on the deviations from the Rouse behavior for unentangled homopolymer melts, showcased mostly in the subdiffusive behavior of center-of-mass of tagged chains at intermediate times, with the subdiffusion exponent reported in the range 0.75–0.85. The influence of the surrounding chains of length Ns on the motion of a single tagged chain of length N is a key test, by which, through high-precision numerical simulation of unentangled melts, we show that the Rouse model fails. Our central results are that at intermediate times the tagged chain’s center-of-mass moves subdiffusively, ⟨Δr2cm⟩ ∝ tα with subdiffusion exponent α = 0.87 ± ...

Dynamics of single polyelectrolyte chains in salt-free dilute solutions investigated by analytical ultracentrifugation

The dynamics of polyelectrolytes in salt-free solution is an unsolved problem. We have investigated the sedimentation and diffusion of xanthan and poly(N-methyl 4-vinyl pyridine iodide) (P4VPI) in salt-free dilute solutions by analytical ultracentrifugation (AUC) using sedimentation velocity (SV) as a function of polyelectrolyte concentration (Cp). Our study reveals two concentration regimes distinguished in either polyanion (xanthan) or polycation (P4VPI) dilute aqueous solution. When Cp is below the Debye concentration (Cd) at which the chain separation (d) is close to the debye length (lD), the interchain electrostatic repulsion is negligible, and the reciprocal apparent sedimentation coefficient (1/s), apparent diffusion coefficient (D) or reciprocal apparent molecular weight (1/Mw) is linearly related to Cp. In the range Cp > Cd with d < lD, the interchain electrostatic repulsion is present, and the dynamics of polyelectrolytes becomes complex. The real sedimentation coefficient (s0), the diffusion coefficient (D0) and the molecular weight (Mw,0) of the single polyelectrolyte chain in salt-free dilute solution can be obtained by extrapolating the concentration to zero. The present study reveals that the complex dynamics of polyelectrolytes in salt-free dilute solutions arises due to the interchain electrostatic repulsion.

Macromolecular motions and hydrodynamic radius variation in dilute solutions under shear action

Understanding the dynamics of single polymer chains and rheological mechanism in dilute polymer solutions under shear stress is essential for fields such as the petroleum and food industries, biomedical materials and drug delivery. Here we present an experimental method for measuring the viscosity of polymer solutions and studying the variation of single polymer chain conformation and the mechanism of molecular motions according to the relationship between the intrinsic viscosity, [η], and the shear rate. Of striking interest is that we find that [η] changing with the shear rate presents three stages which may explain the nature of the viscoelastic performance of polymer solutions and the isolated molecular motions. The significance of these results is the finding of the polymer chain deformation to match the pore throat which has enormous potential implications in drug delivery, genetics and biomedicine © 2014 Society of Chemical Industry.