We use simple analytic arguments and lattice-based computer simulations to study the growth of structures made from a large number of distinct component types. Components possess 'designed' interactions, chosen to stabilize an equilibrium target structure in which each component type has a defined spatial position, and 'undesigned' interactions that allow components to bind in a compositionally-disordered way. We find that high-fidelity growth of the equilibrium target structure can happen in the presence of substantial attractive undesigned interactions, as long as the energy scale of the set of designed interactions is chosen appropriately. This observation may help explain why equilibrium DNA 'brick' structures self-assemble even if undesigned interactions are not suppressed [Ke et al. Science 338, 1177 (2012)]. We also find that high-fidelity growth of the target structure is most probable when designed interactions are drawn from a distribution that is as narrow as possible. We use this result to suggest how to choose complementary DNA sequences in order to maximize the fidelity of multicomponent self-assembly mediated by complementary DNA interactions. We also comment on the prospect of growing macroscopic structures in this manner
We use computer simulation to study the layer-by-layer growth of particle structures in a lattice gas, taking the number of incorporated vacancies as a measure of the quality of the grown structure. By exploiting a dynamic scaling relation between structure quality in and out of equilibrium, we determine that the best quality of structure is obtained, for fixed observation time, with strong interactions and far-from-equilibrium growth conditions. This result contrasts with the usual assumption that weak interactions and mild nonequilibrium conditions are the best way to minimize errors during …
The roughening behavior of a one-dimensional interface fluctuating under quenched disorder growth is examined while keeping an anchored boundary. The latter introduces detailed balance conditions which allows for a thorough analysis of equilibrium aspects at both macroscopic and microscopic scales. It is found that the interface roughens linearly with the substrate size only in the vicinity of special disorder realizations. Otherwise, it remains stiff and tilted.
The static and dynamic roughenings of a growing crystalline facet is studied where the growth mechanism is controlled by a restricted-curvature (RC) geometry. A continuum equation, in analogy with the Kardar-Parisi-Zhang (KPZ) equation is considered for the purpose. It is shown here that although the growth process begins with a RC geometry, a structural phase transition occurs from the restricted-curvature phase to the KPZ phase. An estimation of the corresponding critical temperature is given here. Calculations on the static phase transition give results along the same line as existing predi…
Using kinetic Monte Carlo simulations, we show that molecular morphologies found in non-equilibrium growth can be strongly different from those at equilibrium. We study the prototypical hybrid inorganic-organic system 6P on ZnO(10-10) during thin film adsorption, and find a wealth of phenomena including re-entrant growth, a critical adsorption rate and observables that are non-monotonous with the adsorption rate. We identify the transition from lying to standing molecules with a critical cluster size and discuss the competition of time scales during growth in terms of a rate equation approach.…
We discuss the growth process of a crystalline phase out of a metastable over-compressed liquid that is brought into contact with a crystalline substrate. The process is modeled by means of molecular dynamics. The particles interact via the Lennard-Jones potential and their motion is locally thermalized by Langevin dynamics. We characterize the relaxation process of the solid-liquid interface, showing that the growth speed is maximal for liquid densities above the solid coexistence density, and that the structural properties of the interface rapidly converge to equilibrium-like properties. In …
A continuum growth equation in 1+1 dimensions is obtained by considering the contributions to the underlying current from kinetics of adatoms on the surface. These considerations reproduce the slope dependent term that represents a stable or an unstable growth depending on the sign of the associated coefficient. In addition an h to -h symmetry breaking nonlinear term is obtained. Implications of this term on stable to unstable transition are discussed. This term is tilt independent and is expected to be present independent of the source of the current in the conserved growth. Computer simulati…
The growth of multicomponent structures in simulations and experiments often results in kinetically trapped, nonequilibrium objects. In such cases we have no general theoretical framework for predicting the outcome of the growth process. Here we use computer simulations to study the growth of two-component structures within a simple lattice model. We show that kinetic trapping happens for many choices of growth rate and inter-component interaction energies, and that qualitatively distinct kinds of kinetic trapping are found in different regions of parameter space. In a region in which the low-…
Models of bacterial growth tend to be `irreversible', allowing for the number of bacteria in a colony to increase but not to decrease. By contrast, models of molecular self-assembly are usually `reversible', allowing for addition and removal of particles to a structure. Such processes differ in a fundamental way because only reversible processes possess an equilibrium. Here we show at mean-field level that dynamic trajectories of reversible and irreversible growth processes are similar in that both feel the influence of attractors, at which growth proceeds without limit but the intensive prope…
Unlike atoms, colloidal particles are not identical, but can only be synthesised within a finite size tolerance. Colloids are therefore polydisperse, i.e. mixtures of infinitely many components with sizes drawn from a continuous distribution. We model the crystallisation of hard-sphere colloids (with/without attractions) from an initially amorphous phase. Though the polydisperse hard-sphere phase diagram has been widely studied, it is not straightforwardly applicable to real colloidal crystals, since they are inevitably out of equilibrium. The process by which colloidal crystals form determine…
Stochastic thermodynamics provides a useful set of tools to analyze and constrain the behavior of far from equilibrium systems. In this paper, we report an application of ideas from stochastic thermodynamics to the problem of membrane growth. Non-equilibrium forcing of the membrane can cause it to buckle and undergo a morphological transformation. We show how ideas from stochastic thermodynamics, in particular the recently derived thermodynamic uncertainty relations, can be used to phenomenologically describe and constrain the parameters required to excite morphological changes during a non-eq…
Results from the state-of-the-art molecular dynamics simulations are presented for both equilibrium and nonequilibrium dynamics following vapor-liquid transition in a single component Lennard-Jones system. We have fixed the overall density close to the vapor-branch of the coexistence curve so that the liquid phase forms droplet structure in the background of vapor phase. In the equilibrium case, the motion of a single droplet is studied in both microcanonical and canonical ensembles, in the latter case a hydrodynamics preserving Nosé-Hoover thermostat was used to control the temperature. The d…
Diffusion processes are widespread in biological and chemical systems, where they play a fundamental role in the exchange of substances at the cellular level and in determining the rate of chemical reactions. Recently, the classical picture that portrays diffusion as random uncorrelated motion of molecules has been revised, when it was shown that giant non-equilibrium fluctuations develop during diffusion processes. Under microgravity conditions and at steady-state, non-equilibrium fluctuations exhibit scale invariance and their size is only limited by the boundaries of the system. In this wor…
We study the formation and growth of equilibrium clusters in a suspension of weakly-charged colloidal particles and small non-adsorbing polymers. The effective potential is characterised by a short-range attraction and a long-range repulsion. The size, shape and local structure of the clusters are studied using three-dimensional particle microscopy. We observe a rapid growth in the mean cluster size and the average number of nearest neighbours approaching the gel boundary.
We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can be driven out of equilibrium to ensure protocell growth and replication. This coupling allows us to derive the equations of evolution and to rigorously demonstrate how growth and replication life-cycle can be understood as a non-equilibrium thermodynamic cycle. The process does not appeal to genetic information or inheritance, and is based only on non-equil…
A continuum field theory approach is presented for modeling elastic and plastic deformation, free surfaces and multiple crystal orientations in non-equilibrium processing phenomena. Many basic properties of the model are calculated analytically and numerical simulations are presented for a number of important applications including, epitaxial growth, material hardness, grain growth, reconstructive phase transitions and crack propagation.
Colonies of bacteria endowed with a pili-based self-propulsion machinery are ideal models for investigating the structure and dynamics of active many-particle systems. We study Neisseria gonorrhoeae colonies with a molecular-dynamics-based approach. A generic, adaptable simulation method for particle systems with fluctuating bond-like interactions is devised. The simulations are employed to investigate growth of bacterial colonies and the dependence of the colony structure on cell-cell interactions. In colonies, pilus retraction enhances local ordering. For colonies consisting of different typ…
Using event-driven kinetic Monte-Carlo simulations we investigate the early stage of non-equilibrium surface growth in a generic model with anisotropic interactions among the adsorbed particles. Specifically, we consider a two-dimensional lattice model of spherical particles where the interaction anisotropy is characterized by a control parameter $η$ measuring the ratio of interaction energy along the two lattice directions. The simplicity of the model allows us to study systematically the effect and interplay between $η$, the nearest-neighbor interaction energy $E_{n}$, and the flux rate $F$,…
We study the equilibrium configurations related to the growth of an elastic fibre in a confining flexible ring. This system represents a paradigm for a variety of biological, medical, and engineering problems. We consider a simplified geometry in which initially the container is a circular ring of radius $R$. Quasi-static growth is then studied by solving the equilibrium equations as the fibre length $l$ increases, starting from $l = 2R$. Considering both the fibre and the ring as inextensible and unshearable, we find that beyond a critical length, which depends on the relative bending stiffne…
Roughness and orientational order in thin films of anisotropic particles are investigated using kinetic Monte Carlo simulations on a cubic lattice. Anisotropic next-neighbor interactions between the lattice particles were chosen to mimic the effects of shape anisotropy in the interactions of disc- or rod-like molecules with van-der-Waals attractions. Increasing anisotropy leads first to a preferred orientation in the film (which is close to the corresponding equilibrium transition) while the qualitative mode of roughness evolution (known from isotropic systems) does not change. At strong aniso…
We determine the non-equilibrium grain size distribution during the crystallization of a solid in $d$ dimensions at fixed thermodynamic conditions, for the random nucleation and growth model, and in absence of grain coalescence. Two distinct generalizations of the theory established earlier are considered. A closed analytic expression of the grain size distribution useful for experimental studies is derived for anisotropic growth rates. The main difference from the isotropic growth case is the appearance of a constant prefactor in the distribution. The second generalization considers a Gaussia…
