Search

In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a gel-like state. In the present work, we formulate a thermodynamically consistent kinetic framework to study the interplay between phase separation, chemical reaction and aging in spatially inhomogeneous macromolecular mixtures. A numerical algorithm is also proposed to simulate domain growth from collisions of liquid and gel domains via passive Brownian motion in both two and three spatial dimensions. Our results show that the coarsening behavior is significantly influenced by the degree of gelation and Brownian motion. The presence of a gel phase inside condensates strongly limits the diffusive transport processes, and Brownian motion coalescence controls the coarsening process in systems with high area/volume fractions of gel-like condensates, leading to formation of interconnected domains with atypical domain growth rates controlled by size-dependent translational and rotational diffusivities., Comment: 14 pages, 9 figures

Mixtures of several macromolecular species can lead to the formation of higher-order structures that often display non-ideal mixing behavior. In this work, we propose a minimal model of a quaternary system which considers the formation of a complex via a chemical reaction involving two macromolecular species; the complex may then phase separate from the buffer and undergo a further transition into a gel-like state over time. First, a ternary phase diagram that captures the volume fraction of each species and phases at equilibrium is constructed. Specifically, we investigate how physical parameters such as stoichiometric coefficients, molecular sizes and interaction parameters affect LLPS and aging. Finally, we analyze the thermodynamic stability of the two-phase system and identify the spinodal regions, and outline the generalization of our approach to reactive biomolecular systems with an arbitrary number of components., Comment: 8 pages, 5 figures

Demixing of multicomponent biomolecular systems via liquid-liquid phase separation (LLPS) has emerged as a potentially unifying mechanism governing the formation of several membrane-less intracellular organelles ("condensates"), both in the cytoplasm (e.g., stress granules) and in the nucleoplasm (e.g., nucleoli). While both in vivo experiments and studies of synthetic systems demonstrate that LLPS is strongly affected by the presence of a macromolecular elastic network, a fundamental understanding of the role of such networks on LLPS is still lacking. Here we show that, upon accounting for capillary forces responsible for network expulsion, small-scale heterogeneity of the network, and its nonlinear mechanical properties, an intriguing picture of LLPS emerges. Specifically, we predict that, in addition to the experimentally observed cavitated droplets which fully exclude the network, two other phases are thermodynamically possible: elastically arrested, size-limited droplets at the network pore scale, and network-including macroscopic droplets. In particular, pore size-limited droplets may emerge in chromatin networks, with implications for structure and function of nucleoplasmic condensates., Comment: 6 pages, 7 pages SI

Multicomponent systems are ubiquitous in nature and industry. While the physics of few-component liquid mixtures (i.e., binary and ternary ones) is well-understood and routinely taught in undergraduate courses, the thermodynamic and kinetic properties of $N$-component mixtures with $N>3$ have remained relatively unexplored. An example of such a mixture is provided by the intracellular fluid, in which protein-rich droplets phase separate into distinct membraneless organelles. In this work, we investigate equilibrium phase behavior and morphology of $N$-component liquid mixtures within the Flory-Huggins theory of regular solutions. In order to determine the number of coexisting phases and their compositions, we developed a new algorithm for constructing complete phase diagrams, based on numerical convexification of the discretized free energy landscape. Together with a Cahn-Hilliard approach for kinetics, we employ this method to study mixtures with $N=4$ and $5$ components. We report on both the coarsening behavior of such systems, as well as the resulting morphologies in three spatial dimensions. We discuss how the number of coexisting phases and their compositions can be extracted with Principal Component Analysis (PCA) and K-Means clustering algorithms. Finally, we discuss how one can reverse engineer the interaction parameters and volume fractions of components in order to achieve a range of desired packing structures, such as nested `Russian dolls' and encapsulated Janus droplets., Comment: 16 pages, 11 figures + hyperlinks to 7 videos

Helical ribbons arise in many biological and engineered systems, often driven by anisotropic surface stress, residual strain, and geometric or elastic mismatch between layers of a laminated composite. A full mathematical analysis is developed to analytically predict the equilibrium deformed helical shape of an initially flat, straight ribbon, with prescribed magnitudes and orientations of the principal curvatures when subjected to arbitrary surface stress and/or internal residual strain distribution. The helix angle, radius, axis and chirality of the deformed helical ribbons are predicted with a comprehensive, three-dimensional model that incorporates elasticity, differential geometry, and variational principles. In general, the mechanical anisotropy (e.g., in surface/external stress, residual strain or elastic modulus) will lead to spontaneous, three-dimensional helical deformations. Ring shapes are formed when the principle axes of deformation coincide with the geometric axes of the ribbon. The transition from cylindrical helical ribbons to purely twisted ribbons, or tubular structures is controlled by tuning relevant geometric parameters. Analytic, closed-form predictions of the ribbon shapes are validated with simple, table-top experiments. This theoretical approach represent a tool to inform the design of materials and systems in order to achieve desired helical geometries on demand.

Bistable structures associated with non-linear deformation behavior, exemplified by the Venus flytrap and slap bracelet, can switch between different functional shapes upon actuation. Despite numerous efforts in modeling such large deformation behavior of shells, the roles of mechanical and nonlinear geometric effects on bistability remain elusive. We demonstrate, through both theoretical analysis and table-top experiments, that two dimensionless parameters control bistability. Our work classifies the conditions for bistability, and extends the large deformation theory of plates and shells., Comment: 3 figures

Developing effective descriptions of the microscopic dynamics of many physical phenomena can both dramatically enhance their computational exploration and lead to a more fundamental understanding of the underlying physics. Previously, an effective description of a driven interface in the presence of mobile impurities, based on an Ising variant model and a single empirical coarse variable, was partially successful; yet it underlined the necessity of selecting additional coarse variables in certain parameter regimes. In this paper we use a data mining approach to help identify the coarse variables required. We discuss the implementation of this diffusion map approach, the selection of a similarity measure between system snapshots required in the approach, and the correspondence between empirically selected and automatically detected coarse variables. We conclude by illustrating the use of the diffusion map variables in assisting the atomistic simulations, and we discuss the translation of information between fine and coarse descriptions using lifting and restriction operators., Comment: 28 pages, 10 figures

We report on a novel extension of the recent phase-field crystal (PFC) method introduced in [Elder et al., Phys. Rev. Lett., Vol. 88, 245701:1-4 (2002)], which incorporates elastic interactions as well as crystal plasticity and diffusive dynamics. In our model, elastic interactions are mediated through wave modes that propagate on time scales many orders of magnitude slower than atomic vibrations but still much faster than diffusive times scales. This allows us to preserve the quintessential advantage of the PFC model: the ability to simulate atomic-scale interactions and dynamics on time scales many orders of magnitude longer than characteristic vibrational time scales. We demonstrate the two different modes of propagation in our model and show that simulations of grain growth and elasto-plastic deformation are consistent with the microstructural properties of nanocrystals., Comment: 4 pages, 6 figures

We simulate dendritic growth in directional solidification in dilute binary alloys using a phase-field model solved with an adaptive-mesh refinement. The spacing of primary branches is examined for a range of thermal gradients and alloy compositions and is found to undergo a maximum as a function of pulling velocity, in agreement with experimental observations. We demonstrate that wavelength selection is unambiguously described by a non-trivial crossover scaling function from the emergence of cellular growth to the onset of dendritic fingers, a result validated using published experimental data., Comment: 4 pages, four figures, submitted to Physical Review Letters

Interaction between extended defects and impurities lies at the heart of many physical phenomena in materials science. Here we revisit the ubiquitous problem of the driven motion of an extended defect in a field of mobile impurities, which self-organize to cause drag on the defect. Under a wide range of external conditions (e.g. drive), the defect undergoes a transition from slow to fast motion. This transition is commonly hysteretic: the defect either moves slow or fast, depending on the initial condition. We explore such hysteresis via a kinetic Monte Carlo spin simulation combined with computational coarse-graining. Obtaining bifurcation diagrams (stable and unstable branches), we map behavior regimes in parameter space. Estimating fast-slow switching times, we determine whether a simulation or experiment will exhibit hysteresis depending on observation conditions. We believe our approach is applicable to quantifying hysteresis in a wide range of physical contexts., Comment: 11 pages (preprint format), 4 color figures in separate files

A new model of crystal growth is presented that describes the phenomena on atomic length and diffusive time scales. The former incorporates elastic and plastic deformation in a natural manner, and the latter enables access to times scales much larger than conventional atomic methods. The model is shown to be consistent with the predictions of Read and Shockley for grain boundary energy, and Matthews and Blakeslee for misfit dislocations in epitaxial growth., Comment: 4 pages, 10 figures

We model driven two-dimensional charge-density waves in random media via a modified Swift-Hohenberg equation, which includes both amplitude and phase fluctuations of the condensate. As the driving force is increased, we find that the defect density first increases and then decreases. Furthermore, we find switching phenomena, due to the formation of channels of dislocations. These results are in qualitative accord with recent dynamical x-ray scattering experiments by Ringlandet al. and transport experiments by Lemay et al., Comment: Accepted to Phys. Rev. Lett. Click here for "http://www-theory.mpip-mainz.mpg.de/~karttune/CDW/", movies of driven CDWs