Static and dynamic properties of large polymer melts in equilibrium

Evolution Kinetics of Stabilizing Pickering Emulsion by Brush-Modified Janus Particles: DPD Simulation and Experimental Insights

In the present study, we report the evolution of stabilizing Pickering emulsions using brush-modified Janus particles (JPs), utilizing the dissipative particle dynamics (DPD) simulation technique. Our results are subsequently corroborated with experimental findings. Each JP has one-half of the hydrophobic surface, with the other half embedded with hydrophilic polymer brushes grown via atom transfer radical polymerization (ATRP). Our generic simulation model analyzes the chemical kinetics of polymer brush growth on one-half of the initiator-embedded microparticle (MP) surface, resulting in the formation of JP. This involves evaluating monomer conversion and reaction rates. Our results exhibit a substantial influence of the number of JPs, grafted brush density, and brush length on oil-in-water emulsion stability. We studied the evolution kinetics and stability of emulsion formation by analyzing the growth of average domain size and corresponding scaling functions up to a late time limit. This study aims to clarify the connection between the size, quantity, and functionality of JPs and the stability of Pickering emulsions.

Entanglement-Stabilized Nanoporous Polymer Films Made by Mechanical Deformation

We present a new simulation-guided process to create nanoporous materials, which does not require specific chemical treatment and solely relies on mechanical deformation of pure highly entangled homopolymer films. Starting from fully equilibrated freestanding thick polymer melt films, we apply a simple "biaxial expansion" deformation. Upon expansion holes form, which are prevented from growing and coalescing beyond a characteristic size due to the entanglement structure of the melt. We investigate the local morphology, the void formation upon expansion, and their stabilization. The dependence of the average void (pore) size and void fraction (porosity) on the total strain and subsequent relaxation is investigated. Furthermore, the stabilization of the porous structure of the thin expanded films through cooling below the glass transition temperature Tg is discussed.

Unraveling the Glass-like Dynamic Heterogeneity in Ring Polymer Melts: From Semiflexible to Stiff Chain

Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this study, we investigate the effect of chain stiffness and monomer density on the static and dynamic behaviors of ring polymer melts using molecular dynamics simulations. Our first focus is on the non-Gaussian parameter of center-of-mass displacement as a measure of dynamic heterogeneity, which is commonly observed in glass-forming liquids. We find that the non-Gaussianity in the displacement distribution increases with the monomer density and stiffness of the polymer chains, suggesting that excluded volume interactions between centers of mass have a strong effect on the dynamics of ring polymers. We then analyze the relationship between the radius of gyration and monomer density for semiflexible and stiff ring polymers. Our results indicate that the relationship between the two varies with chain stiffness, which can be attributed to the competition between repulsive forces inside the ring and from adjacent rings. Finally, we study the dynamics of bond-breakage virtually connected between the centers of mass of rings to analyze the exchanges of intermolecular networks of bonds. Our results demonstrate that the dynamic heterogeneity of bond-breakage is coupled with the non-Gaussianity in ring polymer melts, highlighting the importance of the bond-breaking method in determining the intermolecular dynamics of ring polymer melts. Overall, our study sheds light on the factors that govern the dynamic behaviors of ring polymers.

Transverse Fluctuations Control the Assembly of Semiflexible Filaments

The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments' ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division.

Effect of amphiphilic polymers on phase separating binary mixtures: A DPD simulation study

We present the phase separation dynamics of a binary (AB), simple fluid (SF), and amphiphilic polymer (AP) mixture using dissipative particle dynamics simulation at d = 3. We study the effect of different AP topologies, including block copolymers, ring block copolymers (RCP), and miktoarm star polymers, on the evolution morphologies, dynamic scaling functions, and length scale of the AB mixture. Our results demonstrate that the presence of APs leads to significantly different evolution morphologies in SF. However, the deviation from dynamical scaling is prominent, mainly for RCP. Typically, the characteristic length scale for SF follows the power law R(t) ∼ tϕ, where ϕ is the growth exponent. In the presence of high AP, we observe diffusive growth (ϕ → 1/3) at early times, followed by saturation in length scale (ϕ → 0) at late times. The extent of saturation varies with constraints imposed on the APs, such as topology, composition ratio, chain length, and stiffness. At lower composition ratios, the system exhibits inertial hydrodynamic growth (ϕ → 2/3) at asymptotic times without clearly exhibiting the viscous hydrodynamic regime (ϕ → 1) at earlier times in our simulations. Our results firmly establish the existence of hydrodynamic growth regimes in low surfactant-influenced phase separation kinetics of binary fluids and settle the related ambiguity in d = 3 systems.

Force transmission during repose of flexible granular chains

We study the mechanics of standing columns formed during the repose of flexible granular chains. It is one of the many intriguing behaviours exhibited by granular materials when links capable of transmitting tension exist between particles. We develop and calibrate a discrete element method contact model to simulate the mechanics of the macroscopic flexible granular chains and conduct simulations of the angle of repose experiments of these chains by extracting a chain-filled cylinder and allowing the material to flow out under gravity and repose. We evaluate various micro-mechanical, topological and macroscopic parameters to elucidate the mechanics of the repose behaviour of chain ensembles. It is the ability of the links connecting the individual particles to transmit tensile forces along the chain backbone that provides lateral stability to the column, enabling them to stand. In particular, the contact force rearrangement inside the columns generates a self-confining radial stress near the base of the columns, which provides an important stabilizing stress.

Non-Rouse behavior of short ring polymers in melts by molecular dynamics simulations

Short ring polymers are expected to behave nearly Rouse-like due to the little effect of topological constraints of non-knot and non-concatenation. However, this notion is questioned because of several simulation and experiment findings in recent times, which requires a further more quantitative study. Therefore, we perform a deep investigation of statics and dynamics of flexible short ring polymers (N < 2Ne) in melts via molecular dynamics simulations by further taking linear analogues as well as all-crossing ring and linear polymers with switched off topological constraints for comparisons and demonstrate the noticeable deviations from the Rouse model in terms of local and global scales. Although the overall size is compact, the subchains are swollen, which is traced back to the deeper "segmental correlation hole" effect. The same scaling relationship of the non-Gaussian deviation of the static structure factor holds, but the deviation magnitude of rings is larger than that of linear analogues. By checking the non-Gaussian parameter and autocorrelation function of center-of-mass velocity, the physical origin of anomalous sub-diffusions of short rings is identified as unscreened viscoelastic hydrodynamic interactions and not correlation hole effects, like linear analogues.

Segregation of fluids with polymer additives at domain interfaces: a dissipative particle dynamics study

This paper investigates the phase separation kinetics of ternary fluid mixtures composed of a polymeric component (C) and two simple fluids (A and B) using dissipative particle dynamics simulations with a system dimensionality of d = 3. We model the affinities between the components to enable the settling of the polymeric component at the interface of fluids A and B. Thus, the system evolves to form polymer coated morphologies, enabling alteration of the fluids' interfacial properties. This manipulation can be utilized across various disciplines, such as the stabilization of emulsions and foams, rheological control, biomimetic design, and surface modification. We probe the effects of various parameters, such as the polymeric concentration, chain stiffness, and length, on the phase separation kinetics of the system. The simulation results show that changes in the concentration of flexible polymers exhibit perfect dynamic scaling for coated morphologies. The growth rate decreases as the polymeric composition is increased due to reduced surface tension and restricted connectivity between A- and B-rich clusters. Variations in the polymer chain rigidity at fixed composition ratios and degrees of polymerization slow the evolution kinetics of AB fluids marginally, although the effect is more pronounced for perfectly rigid chains. Whereas flexible polymer chain lengths at fixed composition ratios slow down the segregation kinetics of AB fluids slightly, varying the chain lengths of perfectly rigid polymers leads to a significant deviation in the length scale and dynamic scaling for the evolved coated morphologies. The characteristic length scale follows a power-law growth with a growth exponent ϕ that shows a crossover from the viscous to the inertial hydrodynamic regime, where the values of ϕ depend on the constraints imposed on the system.

The Role of Polymer Chain Stiffness and Guest Nanoparticle Loading in Improving the Glass Transition Temperature of Polymer Nanocomposites

The impact of polymer chain stiffness characterized by the bending modulus (k_θ) on the glass transition temperature (T_g) of pure polymer systems, as well as polymer nanocomposites (PNCs), is investigated using molecular dynamics simulations. At small k_θ values, the pure polymer system and respective PNCs are in an amorphous state, whereas at large k_θ values, both systems are in a semicrystalline state with a glass transition at low temperature. For the pure polymer system, T_g initially increases with k_θ and does not change obviously at large k_θ. However, the T_g of PNCs shows interesting behaviors with the increasing volume fraction of nanoparticles (f_NP) at different k_θ values. T_g tends to increase with f_NP at small k_θ, whereas it becomes suppressed at large k_θ.

Complex Monte Carlo Light-Driven Dynamics of Monomers in Functionalized Bond Fluctuation Model Polymer Chains

We study Monte Carlo dynamics of the monomers and center of mass of a model polymer chain functionalized with azobenzene molecules in the presence of an inhomogeneous linearly polarized laser light. The simulations use a generalized Bond Fluctuation Model. The mean squared displacements of the monomers and the center of mass are analyzed in a period of Monte Carlo time typical for a build-up of Surface Relief Grating. Approximate scaling laws for mean squared displacements are found and interpreted in terms of sub- and superdiffusive dynamics for the monomers and center of mass. A counterintuitive effect is observed, where the monomers perform subdiffusive motion but the resulting motion of the center of mass is superdiffusive. This result disparages theoretical approaches based on an assumption that the dynamics of single monomers in a chain can be characterized in terms of independent identically distributed random variables.

Simulational Tests of the Rouse Model

An extensive review of literature simulations of quiescent polymer melts is given, considering results that test aspects of the Rouse model in the melt. We focus on Rouse model predictions for the mean-square amplitudes ⟨(Xp(0))2⟩ and time correlation functions ⟨Xp(0)Xp(t)⟩ of the Rouse mode Xp(t). The simulations conclusively demonstrate that the Rouse model is invalid in polymer melts. In particular, and contrary to the Rouse model, (i) mean-square Rouse mode amplitudes ⟨(Xp(0))2⟩ do not scale as sin-2(pπ/2N), N being the number of beads in the polymer. For small p (say, p≤3) ⟨(Xp(0))2⟩ scales with p as p-2; for larger p, it scales as p-3. (ii) Rouse mode time correlation functions ⟨Xp(t)Xp(0)⟩ do not decay with time as exponentials; they instead decay as stretched exponentials exp(-αtβ). β depends on p, typically with a minimum near N/2 or N/4. (iii) Polymer bead displacements are not described by independent Gaussian random processes. (iv) For p≠q, ⟨Xp(t)Xq(0)⟩ is sometimes non-zero. (v) The response of a polymer coil to a shear flow is a rotation, not the affine deformation predicted by Rouse. We also briefly consider the Kirkwood-Riseman polymer model.

Data-Driven Identification and Analysis of the Glass Transition in Polymer Melts

Understanding the nature of glass transition, as well as the precise estimation of the glass transition temperature for polymeric materials, remains open questions in both experimental and theoretical polymer sciences. We propose a data-driven approach, which utilizes the high-resolution details accessible through the molecular dynamics simulation and considers the structural information on individual chains. It clearly identifies the glass transition temperature of polymer melts of weakly semiflexible chains. By combining principal component analysis and clustering, we identify the glass transition temperature in the asymptotic limit even from relatively short time trajectories, which just reach into the Rouse-like monomer displacement regime. We demonstrate that fluctuations captured by the principal component analysis reflect the change in a chain's behavior: from conformational rearrangement above to small fluctuations below the glass transition temperature. Our approach is straightforward to apply and should be applicable to other polymeric glass-forming liquids.

Free Standing Dry and Stable Nanoporous Polymer Films Made through Mechanical Deformation

A new straight forward approach to create nanoporous polymer membranes with well defined average pore diameters is presented. The method is based on fast mechanical deformation of highly entangled polymer films at high temperatures and a subsequent quench far below the glass transition temperature T_g . The process is first designed generally by simulation and then verified for the example of polystyrene films. The methodology does not need any chemical processing, supporting substrate, or self assembly process and is solely based on polymer inherent entanglement effects. Pore diameters are of the order of ten polymer reptation tube diameters. The resulting membranes are stable over months at ambient conditions and display remarkable elastic properties.

Molecular Dynamics Simulation of Entangled Melts at High Rates: Identifying Entanglement Lockup Mechanism Leading to True Strain Hardening

In the present work, molecular dynamics simulations are carried out based on the bead-spring model to indicate how the entanglement lockup manifests in the late stage of fast Rouse-Weissnberg number (Wi_R >>1) uniaxial melt stretching of entangled polymer melts. At high strains, distinct features show up to reveal the emergence of an increasingly tightened entanglement network. Chain tension can build up, peaking at the middle of the chain, to a level for chain scission, through accumulated interchain interactions, as if there is a tug-of-war ongoing for each load-bearing chain. Thanks to the interchain uncrossability, network junctions form by the pairing of two or more hairpins. It is hypothesized that the interchain entanglement at junctions can lockup through prevailing twist-like interchain couplings as long as Wi_R > 9. In this limit, a significant fraction of chains act like cyclic chains to form a network held by interchain uncrossability, and appreciable chain tension emerges.

Entropic Mixing of Ring/Linear Polymer Blends

The topological constraints of nonconcatenated ring polymers force them to form compact loopy globular conformations with much lower entropy than unconstrained ideal rings. The closed-loop structure of ring polymers also enables them to be threaded by linear polymers in ring/linear blends, resulting in less compact ring conformations with higher entropy. This conformational entropy increase promotes mixing rings with linear polymers. Here, using molecular dynamics simulations for bead-spring chains, ring/linear blends are shown to be significantly more miscible than linear/linear blends and that there is an entropic mixing, negative χ, for ring/linear blends compared to linear/linear and ring/ring blends. In analogy with small angle neutron scattering, the static structure function S(q) is measured, and the resulting data are fit to the random phase approximation model to determine χ. In the limit that the two components are the same, χ = 0 for the linear/linear and ring/ring blends as expected, while χ < 0 for the ring/linear blends. With increasing chain stiffness, χ for the ring/linear blends becomes more negative, varying reciprocally with the number of monomers between entanglements. Ring/linear blends are also shown to be more miscible than either ring/ring or linear/linear blends and stay in single phase for a wider range of increasing repulsion between the two components.

Force-driven active dynamics of thin nanorods in unentangled polymer melts

Recent advances in the functional material and biomedical applications of nanorods call for a fundamental understanding of the active motion of nanorods in a viscoelastic medium. Molecular dynamics simulations are performed to investigate a model system consisting of force-driven active thin nanorods in a melt of unentangled polymers. The activeness of a thin nanorod arises from a constant external force applied uniformly along the rod. The simulations demonstrate that the active force overcomes the randomness of the diffusive motion and results in a ballistic motion along the direction of the applied force at long timescales. The constant speed of the force-driven ballistic motion is determined by the balance of the active force and the friction from the coupling of the nanorod with the polymer viscosity. The friction coefficient, which is computed as the ratio of the active force and the speed, decreases as the active force increases. The origin of the reduction in the friction coefficient is the high speed that allows the nanorod to renew its local environment faster than the relaxation time of melt chains. A scaling theory is developed to quantify the dependence of the friction coefficient on the strength of the active force. The simulations also demonstrate that the force-driven ballistic motion suppresses the rotational diffusion of the rod and cuts off the de-correlation of the rod axis with time. On the scaling level, the long-time trajectory of a force-driven active nanorod piercing through unentangled polymers may be described as a stretched array of "active blobs", where the short-time random-walk trajectory within an active blob is unperturbed by the active force.

Screening confinement of entanglements: Role of a self-propelling end inducing ballistic chain reptation

Synthetic and natural nanomaterials with self-propelling mechanisms continue to be explored to boost chain mobility beyond normal reptation in the crowded environments of entangled chains. Here we employ scaling theory and numerical simulations to demonstrate that activating one chain end of a singular or isolated chain boosts entanglement-constrained chain reptation from the one-dimensional diffusive mobility as described by the de Gennes-Edwards-Doi model to ballistic motion along the entanglement tube contour. The active chain is effectively screened from the constraint of entanglements on length scales exceeding the tube size.

Fingerprinting Brownian Motions of Polymers under Flow

We present a quantitative approach to the self-dynamics of polymers under steady flow by employing a set of complementary reference frames and extending the spherical harmonic expansion technique to dynamic density correlations. Application of this method to nonequilibrium molecular dynamics simulations of polymer melts reveals a number of universal features. For both unentangled and entangled melts, the center-of-mass motions in the flow frame are described by superdiffusive, anisotropic Gaussian distributions, whereas the isotropic component of monomer self-dynamics in the center-of-mass frame is strongly suppressed. Spatial correlation analysis shows that the heterogeneity of monomer self-dynamics increases significantly under flow.

Dissipative particle dynamics simulation study on ATRP-brush modification of variably shaped surfaces and biopolymer adsorption

We present a dissipative particle dynamics (DPD) simulation study on the surface modification of initiator embedded microparticles (MPs) of different shapes via atom transfer radical polymerization (ATRP) brush growth. The surface-initiated ATRP-brush growth leads to the formation of a more globular MP shape. We perform the comparative analysis of ATRP-brush growth on three different forms of particle surfaces: cup surface, spherical surface, and flat surface (rectangular/disk-shaped). First, we establish the chemical kinetics of the brush growth: the monomer conversion and the reaction rates. Next, we discuss the structural changes (shape-modification) of brush-modified surfaces by computing the radial distribution function, spatial density distribution, radius of gyration, hydrodynamic radius, and shape factor. The polymer brush-modified particles are well known as the carrier materials for enzyme immobilization. Finally, we study the biopolymer adsorption on ATRP-brush modified particles in a compatible solution. In particular, we explore the effect of ATRP-brush length, biopolymer chain length, and concentration on the adsorption process. Our results illustrate the enhanced biopolymer adsorption with increased brush length, initiator concentration, and biopolymer concentration. Most importantly, when adsorption reaches saturation, the flat surface loads more biopolymers than the other two surfaces. The experimental results verified the same, considering the disk-shaped flat surface particles, cup-shaped particles, and spherical particles.

Decoding polymer self-dynamics using a two-step approach

The self-correlation function and corresponding self-intermediate scattering function in Fourier space are important quantities for describing the molecular motions of liquids. This work draws attention to a largely overlooked issue concerning the analysis of these space-time density-density correlation functions of polymers. We show that the interpretation of non-Gaussian behavior of polymers is generally complicated by intrachain averaging of distinct self-dynamics of different segments. By the very nature of the mathematics involved, the averaging process not only conceals critical dynamical information, but also contributes to the observed non-Gaussian dynamics. To fully expose this issue and provide a thorough benchmark of polymer self-dynamics, we perform analyses of coarse-grained molecular dynamics simulations of linear and ring polymer melts as well as several theoretical models using a "two-step" approach, where interchain and intrachain averagings of segmental self-dynamics are separated. While past investigations primarily focused on the average behavior, our results indicate that a more nuanced approach to polymer self-dynamics is clearly required.

Role of torsional potential in chain conformation, thermodynamics, and glass formation of simulated polybutadiene melts

For polymer chains, the torsional potential is an important intramolecular energy influencing chain flexibility and segmental dynamics. Through molecular dynamics simulations of an atomistic model for melts of cis-trans-1,4-polybutadiene (PBD), we explore the effect of the torsions on conformational properties (bond vector correlations and mean-square internal distances), fundamental thermodynamic quantities (density, compressibility, internal energy, and specific heat), and glass transition temperature T_g. This is achieved by systematically reducing the strength of the torsional potential, starting from the chemically realistic chain (CRC) model with the full potential toward the freely rotating chain (FRC) model without the torsional potential. For the equilibrium liquid, we find that the effect of the torsions on polymer conformations is very weak. Still weaker is the influence on the monomer density ρ and isothermal compressibility κ_T of the polymer liquid, both of which can be considered as independent of the torsional potential. We show that a van der Waals-like model proposed by Long and Lequeux [Eur. Phys. J. E 4, 371 (2001)] allows us to describe very well the temperature (T) dependence of ρ and κ_T. We also find that our data obey the linear relation between 1/k_BTρκ_T and 1/T (with the Boltzmann constant k_B) that has recently been predicted and verified on the experiment by Mirigian and Schweizer [J. Chem. Phys. 140, 194507 (2014)]. For the equilibrium liquid, simulations result in a specific heat, at constant pressure and at constant volume, which increases on cooling. This T dependence is opposite to the one found experimentally for many polymer liquids, including PBD. We suggest that this difference between simulation and experiment may be attributed to quantum effects due to hydrogen atoms and backbone vibrations, which, by construction, are not included in the classical united-atom model employed here. Finally, we also determine T_g from the density-temperature curve monitored in a finite-rate cooling process. While the influence of the torsional potential on ρ(T) is vanishingly small in the equilibrium liquid, the effect of the torsions on T_g is large. We find that T_g decreases by about 150 K when going from the CRC to the FRC model.

Superstretchable Elastomer from Cross-linked Ring Polymers

The stretchability of polymeric materials is critical to many applications such as flexible electronics and soft robotics, yet the stretchability of conventional cross-linked linear polymers is limited by the entanglements between polymer chains. We show using molecular dynamics simulations that cross-linked ring polymers are significantly more stretchable than cross-linked linear polymers. Compared to linear polymers, the entanglements between ring polymers do not act as effective cross-links. As a result, the stretchability of cross-linked ring polymers is determined by the maximum extension of polymer strands between cross-links, rather than between trapped entanglements as in cross-linked linear polymers. The more compact conformation of ring polymers before deformation also contributes to the increase in stretchability.

Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics

Although it is known that RNA undergoes liquid-liquid phase separation, the interplay between the molecular driving forces and the emergent features of the condensates, such as their morphologies and dynamic properties, is not well understood. We introduce a coarse-grained model to simulate phase separation of trinucleotide repeat RNAs, which are implicated in neurological disorders. After establishing that the simulations reproduce key experimental findings, we show that once recruited inside the liquid droplets, the monomers transition from hairpin-like structures to extended states. Interactions between the monomers in the condensates result in the formation of an intricate and dense intermolecular network, which severely restrains the fluctuations and mobilities of the RNAs inside large droplets. In the largest densely packed high-viscosity droplets, the mobility of RNA chains is best characterized by reptation, reminiscent of the dynamics in polymer melts. Our work provides a microscopic framework for understanding liquid-liquid phase separation in RNA, which is not easily discernible in current experiments.

Diffusion of polymer-grafted nanoparticles with dynamical fluctuations in unentangled polymer melts

The dynamics of polymer-grafted nanoparticles (PGNPs) in melts of unentangled linear chains were investigated by means of coarse-grained molecular dynamics simulations. The results demonstrated that the graft monomers closer to the particle surface relax more slowly than those farther away due to the constraint of the grafted surface and the confinement of the neighboring chains. Such heterogeneous relaxations of the surrounding environment would perturb the particle motion, making them fluctuating around their centers before they can diffuse through the melt. During such intermediate-time stage, the dynamics is subdiffusive while the distribution of particle displacements is Gaussian, which can be described by the popular fractional Brownian motion model. For the long-time Fickian diffusion, we found that the diffusivity D decreases with increasing grafting density Σ_g, grafted chain length N_g, and matrix chain length N_m. This is due to the fact that the diffusivity is controlled by the viscous drag of an effective core, consisting of the NP and the non-draining layer of graft segments, and that of the free-draining graft layer outside the "core". With increasing Σ_g, the PGNPs become harder with greater effective size and thinner free draining layer, resulting in a reduction in D. At extremely high Σ_g, the diffusivity can even be estimated by the diameter-renormalized Stokes-Einstein (SE) relation. With increasing N_g, both the effective core size and the thickness of the free-draining layer increase, leading to a reduction in diffusivity by D ∼ N-γg with 0.5 < γ < 1. Increasing N_m would lead to the enlargement of the effective core size but meanwhile result in the reduction of the free-draining layer thickness due to autophobic dewetting. The counteraction between these two opposite effects leads to only a slight reduction in the diffusivity, significantly different from the typical SE behavior where D ∼ N_m^-1. These findings bear significance in unraveling the fundamental physics of the anomalous dynamics of PGNPs in various polymers, including biological and synthetic.

Extracting multi-way chromatin contacts from Hi-C data

There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.

Spatial correlations of entangled polymer dynamics

The spatial correlations of entangled polymer dynamics are examined by molecular dynamics simulations and neutron spin-echo spectroscopy. Due to the soft nature of topological constraints, the initial spatial decays of intermediate scattering functions of entangled chains are, to the first approximation, surprisingly similar to those of an unentangled system in the functional forms. However, entanglements reveal themselves as a long tail in the reciprocal-space correlations, implying a weak but persistent dynamic localization in real space. Comparison with a number of existing theoretical models of entangled polymers suggests that they cannot fully describe the spatial correlations revealed by simulations and experiments. In particular, the strict one-dimensional diffusion idea of the original tube model is shown to be flawed. The dynamic spatial correlation analysis demonstrated in this work provides a useful tool for interrogating the dynamics of entangled polymers. Lastly, the failure of the investigated models to even qualitatively predict the spatial correlations of collective single-chain density fluctuations points to a possible critical role of incompressibility in polymer melt dynamics.

Spatiotemporal mapping of mesoscopic liquid dynamics

The study of liquid dynamics at mesoscopic scales is still strewn with difficulty due to limitations in theory and experiment. Historically, significant attention has been given to the analysis of space-time correlation functions and their frequency-Fourier transforms at a few discrete wave numbers. The massive computing power afforded by modern high performance computing clusters and the advent of a wide-angle neutron spin-echo spectrometer, however, have unlocked a more intuitive and fruitful approach to this problem. Using molecular dynamics simulations, here we demonstrate the benefits of spatiotemporally mapping intermediate scattering functions on a dense grid of correlation times and wave numbers. Four model systems are investigated: a Lennard-Jones liquid, a coarse-grained bead-spring polymer, a molten sodium chloride, and a poly(ethylene oxide) melt. We show that the spatiotemporal mapping approach is particularly useful for elucidating the mesoscopic dynamics in these liquids, where several underlying mechanisms, such as molecular relaxations, hydrodynamic modes, and nonhydrodynamic excitations, are potentially at play. Compared to the traditional method, direct visualization of density space-time correlation functions on two-dimensional color maps permits appraisals of complicated dynamical behavior at mesoscales in a global manner. For example, the scaling relations between space and time for different types of molecular motions can be straightforwardly identified on these plots, without any model-dependent analysis. Additionally, we show how theoretical ideas regarding collective mesoscopic dynamics, such as the classical hydrodynamic theory, the convolution approximation, and a recently proposed phenomenological model, can be discussed in terms of the global features of spatiotemporal maps of intermediate scattering functions. The new perspective offered by the spatiotemporal mapping method should prove useful for the study of liquid dynamics in general.

Photo-induced bond breaking during phase separation kinetics of block copolymer melts: a dissipative particle dynamics study

Using a dissipative particle dynamics (DPD) simulation method, we study the phase separation dynamics in block copolymer (BCP) melts in d = 3, subjected to external stimuli such as light. An initial homogeneous BCP melt is rapidly quenched to a temperature T < T_c, where T_c is the critical temperature. We then allow the system to undergo alternate light "on" and "off" cycles. An on-cycle breaks the stimuli-sensitive bonds connecting both the blocks A and B in the BCP melt, and during the off-cycle, the broken bonds recombine. By simulating the effect of light, we isolate scenarios where phase separation begins with the light off (set 1); the cooperative interactions within the system allow it to undergo microphase separation. When the phase separation starts with the light on (set 2), the system undergoes macrophase separation due to bond breaking. Here, we report the role of alternate cycles on domain morphology by varying the bond-breaking probability for both set 1 and set 2, respectively. We observe that the scaling functions depend upon the conditions mentioned above that change the time scale of the evolving morphologies in various cycles. However, in all the cases, the average domain size respects the power-law growth: R(t) ∼t^φ at late times, where φ is the dynamic growth exponent. After a short-lived diffusive growth (φ∼ 1/3) at early times, φ illustrates a crossover from the viscous hydrodynamic (φ∼ 1) to the inertial hydrodynamic (φ∼ 2/3) regimes at late times.

Assembly of Polymer-Grafted Nanoparticles in Polymer Matrices

Leibler pioneered the idea that long enough matrix polymers of length P will spontaneously dewet a chemically identical polymer layer, comprising chains of length N, densely end-grafted to a flat surface ("brush"). This entropically driven idea is routinely used to explain experiments in which 10-20 nm diameter nanoparticles (NPs) densely grafted with polymer chains are found to phase separate from chemically identical melts for P/N ≳4. At lower grafting densities, these effects are also thought to underpin the self-assembly of grafted NPs into a variety of structures. To explore the validity of this picture, we conducted large-scale molecular dynamics simulations of grafted NPs in a chemically identical polymer melt. For the NPs we consider, in the ≈5 nm diameter range, we find no phase separation even for P/N = 10 in the absence of attractions. Instead, we find behavior that more closely parallels experiments when all of the chain monomers are equally attractive to each other but repel the NPs. Our results thus imply that experimental situations investigated to date are dominated by the surfactancy of the NPs, which is driven by the chemical mismatch between the inorganic core and the organic ligands (the graft and free chains are chemically identical). Entropic effects, that is, the translational entropy of the NPs and the matrix, the entropy of mixing of the grafts and the matrix, and the conformational entropy of the chains appear to thus have a second-order effect even in the context of these model systems.

Efficient equilibration of confined and free-standing films of highly entangled polymer melts

Equilibration of polymer melts containing highly entangled long polymer chains in confinement or with free surfaces is a challenge for computer simulations. We approach this problem by first studying polymer melts based on the soft-sphere coarse-grained model confined between two walls with periodic boundary conditions in two directions parallel to the walls. Then, we insert the microscopic details of the underlying bead-spring model. Tuning the strength of the wall potential, the monomer density of confined polymer melts in equilibrium is kept at the bulk density even near the walls. In a weak confining regime, we observe the same conformational properties of chains as in the bulk melt showing that our confined polymer melts have reached their equilibrated state. Our methodology provides an efficient way of equilibrating large polymer films with different thicknesses and is not confined to a specific underlying microscopic model. Switching off the wall potential in the direction perpendicular to the walls enables to study free-standing highly entangled polymer films or polymer films with one supporting substrate.

Glass Transition of Disentangled and Entangled Polymer Melts: Single-Chain-Nanoparticles Approach

We study the effect of entanglements on the glass transition of high molecular weight polymers, by the comparison of single-chain nanoparticles (SCNPs) and equilibrated melts of high-molecular weight polystyrene of identical molecular weight. SCNPs were prepared by electrospraying technique and characterized using scanning electron microscopy and atomic force microscopy techniques. Differential scanning calorimetry, Brillouin light spectroscopy, and rheological experiments around the glass transition were compared. In parallel, entangled and disentangled polymer melts were also compared under cooling from molecular dynamics simulations based on a bead-spring polymer model. While experiments suggest a small decrease in the glass transition temperature of films of nanoparticles in comparison to entangled melts, simulations do not observe any significant difference, despite rather different chain conformations.

Effects of Tethered Polymers on Dynamics of Nanoparticles in Unentangled Polymer Melts

Polymer-tethered nanoparticles (NPs) are commonly added to a polymer matrix to improve material properties. Critical to the fabrication and processing of such composites is the mobility of the tethered NPs. Here we study the motion of tethered-NPs in unentangled polymer melts using molecular dynamics simulations, which offer a precise control of the grafted chain length N _g and the number z of grafted chains per particle. As N _g increases, there is a crossover from particle-dominated to tethered-chain-dominated terminal diffusion of NPs with the same z. The mean squared displacement of loosely tethered NPs in the case of tethered-chain dominated terminal diffusion exhibits two sub-diffusive regimes at intermediate time scales for small z. The first one at shorter time scales arises from the dynamical coupling of the particle and matrix chains, while the one at longer time scales is due to the participation of the particle in the dynamics of the tethered chains. The friction of loosely grafted chains in unentangled melts scales linearly with the total number of monomers in the chains, as the frictions of individual monomers are additive in the absence of hydrodynamic coupling. As more chains are grafted to a particle, hydrodynamic interactions between grafted chains emerge. As a result, there is a non-draining layer of hydrodynamically coupled chain segments surrounding the bare particle. Outside the non-draining layer is a free-draining layer of grafted chain segments with no hydrodynamic coupling. The boundary of the two layers is the stick surface where the shear stress due to the relative melt flow is balanced by the friction between grafted and melt chains in the interpenetration layer. The stick surface is located further away from the bare surface of the particle with higher grafting density.

Dynamics of poly[n]catenane melts

Inspired by advances in the chemical synthesis of interlocking polymer architectures, extensive molecular dynamics simulations have been conducted to study the dynamical properties of poly[n]catenanes-polymers composed entirely of interlocking rings-in the melt state. Both the degree of polymerization (number of links) and the number of beads per ring are systematically varied, and the results are compared to linear and ring polymers. A simple Rouse-like model is presented, and its analytical solution suggests a decomposition of the dynamics into "ring-like" and "linear-like" regimes at short and long times, respectively. In agreement with this picture, multiple sub-diffusive regimes are observed in the monomer mean-squared-displacements even though interchain entanglement is not prevalent in the system. However, the Rouse-type model does not account for the topological effects of the mechanical bonds, which significantly alter the dynamics at intermediate length scales both within the rings and at the chain segment scales. The stress relaxation in the system is extremely rapid and may be conveniently separated into ring-like and linear-like contributions, again in agreement with the Rouse picture. However, the viscosity has a non-monotonic dependence on the ring size for long chains, which disagrees strongly with theoretical predictions. This unexpected observation cannot be explained in terms of chain disentanglement and is inconsistent with other measures of polymer relaxation. Possible mechanisms for this behavior are proposed and implications for materials design are discussed.

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.

Coarse-grained molecular dynamics simulations of poly(ethylene terephthalate)

We have constructed efficient coarse-grained (CG) models of poly(ethylene terephthalate) (PET), using three mapping schemes, in which a repeat unit is lumped into either three or four beads. The CG potentials are parameterized to reproduce target distributions of an underlying accurate atomistic model [H. Eslami and F. Müller-Plathe, Macromolecules 42, 8241-8250 (2009)]. The CG simulations allow equilibration of long PET chains at all length scales. The CG results on the density of PET in melt and glassy states, chain dimension, local packing, and structure factor are in good agreement with experiment. We have established a link between the glass transition temperature and the local movements including conformational transitions and mean-square displacements of chain segments. Temperature transferabilities of the three proposed models were studied by comparing CG results on the static and thermodynamic properties of a polymer with atomistic and experimental findings. One of the three CG models has a good degree of transferability, following all inter- and intra-structural rearrangements of the atomistic model, over a broad range of temperature. Furthermore, as a distinct point of strength of CG, over atomistic, simulations, we have examined the dynamics of PET long chains, consisting of 100 repeat units, over a regime where entanglements dominate the dynamics. Performing long-time (550 ns) CG simulations, we have noticed the signature of a crossover from Rouse to reptation dynamics. However, a clear separation between the Rouse and the reptation dynamics needs much longer time simulations, confirming the experimental findings that the crossover to full reptation dynamics is very protracted.