A Review of Multiscale Computational Methods in Polymeric Materials

Atomistic to continuum model for studying mechanical properties of RNA nanotubes

With rapid advancements in the emerging field of RNA nanotechnology, its current and potential applications, new important problems arise in our quest to better understand properties of RNA nanocomplexes. In this paper, our focus is on the modeling of RNA nanotubes which are important for many biological processes. These RNA complexes are also important for human beings, with their theurapeutical and biomedical applications discussed vigorously in the literature over the recent years. Here, we develop a continuum model of RNA nanotubes, originally obtained from self assembly of RNA building blocks in the molecular dynamics simulation. Based on the finite element method, we calculate the elastic properties of these nanostructures and provide a relationship between stress and strain induced in the RNA nanotube. We also analyze the variations in the displacement vector along the assembly axis for RNA nanotubes of different sizes. In particular, we show that oscillations in the amplitudes of strains and displacements significantly differ for such RNA nanotubes. These findings are discussed in the context of atomistic simulations and experimental results in this field.

A polyesteramide library from dicarboxylic acids and 2,2′-bis(2-oxazoline): synthesis, characterization, nanoparticle formulation and molecular dynamics simulations

A combined experimental and in silico approach enabled tailoring of polyesteramides with respect to formation of aqueous nanoparticle dispersions.

Implicit-solvent coarse-grained modeling for polymer solutions via Mori-Zwanzig formalism

We present a bottom-up coarse-graining (CG) method to establish implicit-solvent CG modeling for polymers in solution, which conserves the dynamic properties of the reference microscopic system. In particular, tens to hundreds of bonded polymer atoms (or Lennard-Jones beads) are coarse-grained as one CG particle, and the solvent degrees of freedom are eliminated. The dynamics of the CG system is governed by the generalized Langevin equation (GLE) derived via the Mori-Zwanzig formalism, by which the CG variables can be directly and rigorously linked to the microscopic dynamics generated by molecular dynamics (MD) simulations. The solvent-mediated dynamics of polymers is modeled by the non-Markovian stochastic dynamics in GLE, where the memory kernel can be computed from the MD trajectories. To circumvent the difficulty in direct evaluation of the memory term and generation of colored noise, we exploit the equivalence between the non-Markovian dynamics and Markovian dynamics in an extended space. To this end, the CG system is supplemented with auxiliary variables that are coupled linearly to the momentum and among themselves, subject to uncorrelated Gaussian white noise. A high-order time-integration scheme is used to solve the extended dynamics to further accelerate the CG simulations. To assess, validate, and demonstrate the established implicit-solvent CG modeling, we have applied it to study four different types of polymers in solution. The dynamic properties of polymers characterized by the velocity autocorrelation function, diffusion coefficient, and mean square displacement as functions of time are evaluated in both CG and MD simulations. Results show that the extended dynamics with auxiliary variables can construct arbitrarily high-order CG models to reproduce dynamic properties of the reference microscopic system and to characterize long-time dynamics of polymers in solution.

X-ray data from a cyclic tensile study of melt-spun poly(3-hydroxybutyrate) P3HB fibers: A reversible mesophase

Wide-angle x-ray diffraction (WAXD) patterns that show mesophases in core-sheath bicomponent fibers and amorphous fibers are presented in section 1.1 of the article. Section 1.2 presents molecular dynamics simulations and scattered intensity calculations of stretched P3HB chains. Sections 1.3–1.6 summarize WAXD and small-angle x-ray scattering (SAXS) data analysis from a tensile study of melt-spun P3HB fibers. Azimuthal profiles are extracted from 2D WAXD patterns at various angular regions and the positions of equatorial reflections and corresponding d-spacings are summarized. Additionally, the extracted structural parameters from SAXS images are summarized. The tensile stress calculations, crystal orientation calculations, applied intensity corrections, calculations of long spacings, coherence lengths and lamellar diameters are explained in the methods subsections 2.3.1–2.3.7. WAXD and SAXS measurements of P3HB fibers were recorded on a Bruker Nanostar U diffractometer (Bruker AXS, Karlsruhe, Germany). The recorded WAXD/SAXS patterns were analyzed with the evaluation software DIFFRAC.EVA (version 4.2., Bruker AXS, Karlsruhe, Germany) and python codes. For more information see ‘Tensile study of melt-spun poly(3-hydroxybutyrate) P3HB fibers: Reversible transformation of a highly oriented phase’ (Perret et al., 2019).

Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers

With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.

From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field

Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.

Morphology Development of Polymer Blend Fibers along Spinning Line

Melt spinning is an efficient platform to continuously produce fiber materials with multifunctional and novel properties at a large scale. This paper briefly reviews research works that reveal the morphology development of immiscible polymer blend fibers during melt spinning. The better understanding of the formation and development of morphology of polymer blend fibers during melt spinning could help us to generate desired morphologies and precisely control the final properties of fiber materials via the melt spinning process.

The heterogeneous multiscale method applied to inelastic polymer mechanics

Mechanisms emerging across multiple scales are ubiquitous in physics and methods designed to investigate them are becoming essential. The heterogeneous multiscale method (HMM) is one of these, concurrently simulating the different scales while keeping them separate. Owing to the significant computational expense, developments of HMM remain mostly theoretical and applications to physical problems are scarce. However, HMM is highly scalable and is well suited for high performance computing. With the wide availability of multi-petaflop infrastructures, HMM applications are becoming practical. Rare applications to mechanics of materials at low loading amplitudes exist, but are generally confined to the elastic regime. Beyond that, where history-dependent, irreversible or nonlinear mechanisms occur, not only computational cost but also data management issues arise. The micro-scale description loses generality, developing a specific microstructure based on the deformation history, which implies inter alia that as many microscopic models as discrete locations in the macroscopic description must be simulated and stored. Here, we present a detailed description of the application of HMM to inelastic mechanics of materials, with emphasis on the efficiency and accuracy of the scale-bridging methodology. The method is well suited to the estimation of macroscopic properties of polymers (and derived nanocomposites) starting from knowledge of their atomistic chemical structure. Through application of the resulting workflow to polymer fracture mechanics, we demonstrate deviation in the predicted fracture toughness relative to a single-scale molecular dynamics approach, thus illustrating the need for such concurrent multiscale methods in the predictive estimation of macroscopic properties. This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'.

Entropic Effects in Polymer Nanocomposites

Polymer nanocomposite materials, consisting of a polymer matrix embedded with nanoscale fillers or additives that reinforce the inherent properties of the matrix polymer, play a key role in many industrial applications. Understanding of the relation between thermodynamic interactions and macroscopic morphologies of the composites allow for the optimization of design and mechanical processing. This review article summarizes the recent advancement in various aspects of entropic effects in polymer nanocomposites, and highlights molecular methods used to perform numerical simulations, morphologies and phase behaviors of polymer matrices and fillers, and characteristic parameters that significantly correlate with entropic interactions in polymer nanocomposites. Experimental findings and insight obtained from theories and simulations are combined to understand how the entropic effects are turned into effective interparticle interactions that can be harnessed for tailoring nanostructures of polymer nanocomposites.

Assessing the transferability of common top-down and bottom-up coarse-grained molecular models for molecular mixtures

Assessing the performance of top-down and bottom-up coarse-graining approaches.

Limitations of Viscoelastic Constitutive Models for Carbon-Black Reinforced Rubber in Medium Dynamic Strains and Medium Strain Rates

Modelling the viscoelastic behavior of rubber for use in component design remains a challenge. Most of the literature does not consider the typical regimes encountered by anti-vibration devices that are deformed to medium dynamic strains (0.5 to 3.5) at medium strain rates (0.5/s to 10/s). Previous studies have either focused on the behaviour at small strains and small strain rates or in fast loading conditions that result in low cycle fatigue or tearing phenomena. There is a lack of understanding of the dynamic response of natural rubber suspension components when used in real vehicle applications. This paper presents a review of popular viscoelastic nonlinear constitutive models and their ability to model the mechanical behaviour of typical elastomer materials such as Natural Rubber (NR) incorporating different PHR (Parts per Hundred Rubber, XX) of carbon black. The range of strain and strain rate are typical for the materials used in rubber suspensions when operating in severe service operating conditions, such as over rough terrain or over pot-holes. The cyclic strain is applied at different amplitudes and different strain rates in this medium strain range. Despite the availability of many models in the literature, our study reports that none of the existing models can fit the data satisfactorily over a wide range of conditions.

Thermodynamics of star polymer solutions: A coarse-grained study

We consider a coarse-grained (CG) model with pairwise interactions, suitable to describe low-density solutions of star-branched polymers of functionality f. Each macromolecule is represented by a CG molecule with (f + 1) interaction sites, which captures the star topology. Potentials are obtained by requiring the CG model to reproduce a set of distribution functions computed in the microscopic model in the zero-density limit. Explicit results are given for f = 6, 12, and 40. We use the CG model to compute the osmotic equation of state of the solution for concentrations c such that Φ_p=c∕c^*≲1, where c^* is the overlap concentration. We also investigate in detail the phase diagram for f = 40, identifying the boundaries of the solid intermediate phase. Finally, we investigate how the polymer size changes with c. For Φ_p≲0.3, polymers become harder as f increases at fixed reduced concentration c∕c^*. On the other hand, for Φ_p≳0.3, polymers show the opposite behavior: At fixed Φ_p, the larger the value of f, the larger their size reduction is.

Exploring the Molecular Distributions in Dilute Polymer Solutions Using a Multi-Scale Numerical Solver

Simulating the rheological behaviors of polymer solutions is intrinsically a multi-scale problem. To study the macroscopic and microscopic characteristics in the fluid flow of dilute polymer solutions, we designed a multi-scale solver, which couples the Brownian Configuration Fields with the macroscopic hydrodynamic governing equations. Numerical simulation results using the multi-scale solver exhibited good accordance with the macroscopic only approach. Through a scalar field D we also quantitatively studied the flow behaviours in 2D planar channels, and analyzed the correlation between the molecular distribution and the macroscopic fluid flow in polymer solutions. Our results verified the correctness of the solver, which could provide valuable guidance for multi-scale simulations of complex fluids based on OpenFOAM.

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

Assessing numerical methods for molecular and particle simulation

We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss the characteristics of different algorithms, including their essential conservation properties, the convergence of averages, and the accuracy of numerical discretizations. Formulations of the equations of motion which are suited to both equilibrium and nonequilibrium simulation include Langevin dynamics, dissipative particle dynamics (DPD), and the more recently proposed "pairwise adaptive Langevin" (PAdL) method, which, like DPD but unlike Langevin dynamics, conserves momentum and better matches the relaxation rate of orientational degrees of freedom. PAdL is easy to code and suitable for a variety of problems in nonequilibrium soft matter modeling; our simulations of polymer melts indicate that this method can also provide dramatic improvements in computational efficiency. Moreover we show that PAdL gives excellent control of the relaxation rate to equilibrium. In the nonequilibrium setting, we further demonstrate that while PAdL allows the recovery of accurate shear viscosities at higher shear rates than are possible using the DPD method at identical timestep, it also outperforms Langevin dynamics in terms of stability and accuracy at higher shear rates.

The Effect of Heat Transfer and Polymer Concentration on Non-Newtonian Fluid from Pore-Scale Simulation of Rock X-ray Micro-CT

Most of the pore-scale imaging and simulations of non-Newtonian fluid are based on the simplifying geometry of network modeling and overlook the fluid rheology and heat transfer. In the present paper, we developed a non-isothermal and non-Newtonian numerical model of the flow properties at pore-scale by simulation of the 3D micro-CT images using a Finite Volume Method (FVM). The numerical model is based on the resolution of the momentum and energy conservation equations. Owing to an adaptive mesh generation technique and appropriate boundary conditions, rock permeability and mobility are accurately computed. A temperature and concentration-dependent power-law viscosity model in line with the experimental measurement of the fluid rheology is adopted. The model is first applied at isothermal condition to 2 benchmark samples, namely Fontainebleau sandstone and Grosmont carbonate, and is found to be in good agreement with the Lattice Boltzmann method (LBM). Finally, at non-isothermal conditions, an effective mobility is introduced that enables to perform a numerical sensitivity study to fluid rheology, heat transfer, and operating conditions. While the mobility seems to evolve linearly with polymer concentration in agreement with a derived theoretical model, the effect of the temperature seems negligible by comparison. However, a sharp contrast is found between carbonate and sandstone under the effect of a constant temperature gradient. Besides concerning the flow index and consistency factor, a master curve is derived when normalizing the mobility for both the carbonate and the sandstone.

Molecular Structuring and Percolation Transition in Hydrated Sulfonated Poly(ether ether ketone) Membranes

The extent of phase separation and water percolation in sulfonated membranes are the key to their performance in fuel cells. Toward this, the effect of hydration on the morphology and transport characteristics of sulfonated poly(ether ether ketone), sPEEK, membrane is investigated using atomistic molecular dynamics simulation at various hydration levels(λ: number of water molecules per sulfonate group). The evolution of local morphology is investigated using structural correlations and minimum pair distances. Transport properties are probed using mean squared displacements and diffusion coefficients. The water-sulfonate interaction in sPEEK is found to be stronger than that in Nafion, as observed in experiments. Analyses indicate the presence of narrow connected path of water and hydronium at λ = 4 and large domains, spanning half the simulation box, at λ = 15. The behavior of membrane water remains far from bulk as indicated by its diffusion coefficient. The persistence of small isolated water clusters demonstrates the extent of phase separation in sPEEK to be lesser than that in Nafion. Analyses at molecular and collective levels suggest the occurrence of a percolation transition between λ = 8 and 10, which leads to a connected network of water channels in the membrane, thereby boosting the hydronium mobility.