Phase separation and ripening in a viscoelastic gel.

The process of phase separation in elastic solids and viscous fluids is of fundamental importance to the stability and function of soft materials. We explore the dynamics of phase separation and domain growth in a viscoelastic material such as a polymer gel. Using analytical theory and Monte Carlo simulations, we report a domain growth regime in which the domain size increases algebraically with a ripening exponent [Formula: see text] that depends on the viscoelastic properties of the material. For a prototypical Maxwell material, we obtain [Formula: see text], which is markedly different from the well-known Ostwald ripening process with [Formula: see text]. We generalize our theory to systems with arbitrary power-law relaxation behavior and discuss our findings in the context of the long-term stability of materials as well as recent experimental results on phase separation in cross-linked networks and cytoskeleton.

Two Mesoporous Domains Are Better Than One for Catalytic Deconstruction of Polyolefins.

Catalytic hydrogenolysis of polyolefins into valuable liquid, oil, or wax-like hydrocarbon chains for second-life applications is typically accompanied by the hydrogen-wasting co-formation of low value volatiles, notably methane, that increase greenhouse gas emissions. Catalytic sites confined at the bottom of mesoporous wells, under conditions in which the pore exerts the greatest influence over the mechanism, are capable of producing less gases than unconfined sites. A new architecture was designed to emphasize this pore effect, with the active platinum nanoparticles embedded between linear, hexagonal mesoporous silica and gyroidal cubic MCM-48 silica (mSiO2/Pt/MCM-48). This catalyst deconstructs polyolefins selectively into ∼C20-C40 paraffins and cleaves C-C bonds at a rate (TOF = 4.2 ± 0.3 s-1) exceeding that of materials lacking these combined features while generating negligible volatile side products including methane. The time-independent product distribution is consistent with a processive mechanism for polymer deconstruction. In contrast to time- and polymer length-dependent products obtained from non-porous catalysts, mSiO2/Pt/MCM-48 yields a C28-centered Gaussian distribution of waxy hydrocarbons from polyolefins of varying molecular weight, composition, and physical properties, including low-density polyethylene, isotactic polypropylene, ultrahigh-molecular-weight polyethylene, and mixtures of multiple, post-industrial polyolefins. Coarse-grained simulation reveals that the porous-core architecture enables the paraffins to diffuse away from the active platinum site, preventing secondary reactions that produce gases.

Hydrodynamically Controlled Self-Organization in Mixtures of Active and Passive Colloids.

Active particles are known to exhibit collective behavior and induce structure in a variety of soft-matter systems. However, many naturally occurring complex fluids are mixtures of active and passive components. The authors examine how activity induces organization in such multi-component systems. Mixtures of passive colloids and colloidal micromotors are investigated and it is observed that even a small fraction of active particles induces reorganization of the passive components in an intriguing series of phenomena. Experimental observations are combined with large-scale simulations that explicitly resolve the near- and far-field effects of the hydrodynamic flow and simultaneously accurately treat the fluid-colloid interfaces. It is demonstrated that neither conventional molecular dynamics simulations nor the reduction of hydrodynamic effects to phoretic attractions can explain the observed phenomena, which originate from the flow field that is generated by the active colloids and subsequently modified by the aggregating passive units. These findings not only offer insight into the organization of biological or synthetic active-passive mixtures, but also open avenues to controlling the behavior of passive building blocks by means of small amounts of active particles.

From predictive modelling to machine learning and reverse engineering of colloidal self-assembly.

An overwhelming diversity of colloidal building blocks with distinct sizes, materials and tunable interaction potentials are now available for colloidal self-assembly. The application space for materials composed of these building blocks is vast. To make progress in the rational design of new self-assembled materials, it is desirable to guide the experimental synthesis efforts by computational modelling. Here, we discuss computer simulation methods and strategies used for the design of soft materials created through bottom-up self-assembly of colloids and nanoparticles. We describe simulation techniques for investigating the self-assembly behaviour of colloidal suspensions, including crystal structure prediction methods, phase diagram calculations and enhanced sampling techniques, as well as their limitations. We also discuss the recent surge of interest in machine learning and reverse-engineering methods. Although their implementation in the colloidal realm is still in its infancy, we anticipate that these data-science tools offer new paradigms in understanding, predicting and (inverse) design of novel colloidal materials.

Accelerated simulation method for charge regulation effects.

The net charge of solvated entities, ranging from polyelectrolytes and biomolecules to charged nanoparticles and membranes, depends on the local dissociation equilibrium of individual ionizable groups. Incorporation of this phenomenon, charge regulation (CR), in theoretical and computational models requires dynamic, configuration-dependent recalculation of surface charges and is therefore typically approximated by assuming constant net charge on particles. Various computational methods exist that address this. We present an alternative, particularly efficient CR Monte Carlo method (CR-MC), which explicitly models the redistribution of individual charges and accurately samples the correct grand-canonical charge distribution. In addition, we provide an open-source implementation in the large-scale Atomic/Molecular Massively Parallel Simulator molecular dynamics (MD) simulation package, resulting in a hybrid MD/CR-MC simulation method. This implementation is designed to handle a wide range of implicit-solvent systems that model discreet ionizable groups or surface sites. The computational cost of the method scales linearly with the number of ionizable groups, thereby allowing accurate simulations of systems containing thousands of individual ionizable sites. By matter of illustration, we use the CR-MC method to quantify the effects of CR on the nature of the polyelectrolyte coil-globule transition and on the effective interaction between oppositely charged nanoparticles.

Kinetic pathways of crystallization at the nanoscale.

Nucleation and growth are universally important in systems from the atomic to the micrometre scale as they dictate structural and functional attributes of crystals. However, at the nanoscale, the pathways towards crystallization have been largely unexplored owing to the challenge of resolving the motion of individual building blocks in a liquid medium. Here we address this gap by directly imaging the full transition of dispersed gold nanoprisms to a superlattice at the single-particle level. We utilize liquid-phase transmission electron microscopy at low dose rates to control nanoparticle interactions without affecting their motions. Combining particle tracking with Monte Carlo simulations, we reveal that positional ordering of the superlattice emerges from orientational disorder. This method allows us to measure parameters such as line tension and phase coordinates, charting the nonclassical nucleation pathway involving a dense, amorphous intermediate. We demonstrate the versatility of our approach via crystallization of different nanoparticles, pointing the way to more general applications.

Charge Regulation Effects in Nanoparticle Self-Assembly.

Nanoparticles in solution acquire charge through the dissociation or association of surface groups. Thus, a proper description of their electrostatic interactions requires the use of charge-regulating boundary conditions rather than the commonly employed constant-charge approximation. We implement a hybrid Monte Carlo/molecular dynamics scheme that dynamically adjusts the charges of individual surface groups of objects while evolving their trajectories. Charge regulation effects are shown to qualitatively change self-assembled structures due to global charge redistribution, stabilizing asymmetric constructs. We delineate under which conditions the conventional constant-charge approximation may be employed and clarify the interplay between charge regulation and dielectric polarization.

Particle-particle particle-mesh algorithm for electrolytes between charged dielectric interfaces.

Ionic distributions near charged interfaces control processes from colloidal aggregation to solvent flow in nanodevices. Such interfaces are often characterized by a jump in the permittivity, which gives rise to the surface polarization charge. This induced charge may significantly affect the ionic distributions so that efficient methods for modeling spatially varying dielectrics are needed. We formulate a method with O(N⁡log⁡N) scaling for electrolytes between charged planar interfaces with asymmetric dielectric contrasts. Our approach, which builds on earlier work, is based on combining image charges with the particle-particle particle-mesh algorithm and representing uniform surface charges via an electric field. This enables simulations of complex dielectric interactions that outperform most alternative methods in speed and accuracy. To make the method practically useful, we provide guidelines-based upon careful tests-for choosing optimal simulation parameters. Explicit expressions for the electrostatic forces are given to facilitate the implementation of our algorithm in standard molecular dynamics packages.

Harmonic surface mapping algorithm for molecular dynamics simulations of particle systems with planar dielectric interfaces.

We have developed an accurate and efficient method for molecular dynamics simulations of charged particles confined by planar dielectric interfaces. The algorithm combines the image-charge method for near field with the harmonic surface mapping, which converts the contribution of infinite far-field charges into a finite number of charges on an auxiliary spherical surface. We approximate the electrostatic potential of far-field charges via spherical harmonic expansion and determine the coefficients by fitting the Dirichlet-to-Neumann boundary condition, which only requires the potential within the simulation cell. Instead of performing the direct evaluation of spherical harmonic series expansion, we use Green's second identity to transform the series expansion into a spherical integral, which can be accurately represented by discrete charges on the sphere. Therefore, the fast multipole method can be readily employed to sum over all charges within and on the sphere, achieving truly linear O(N) complexity. Our algorithm can be applied to a broad range of charged complex fluids under dielectric confinement.

Effective temperature concept evaluated in an active colloid mixture.

Thermal energy agitates all matter, and its competition with ordering tendencies is a fundamental organizing principle in the physical world; this observation suggests that an effective temperature might emerge when external energy input enhances agitation. However, despite the repeated proposal of this concept based on kinetics for various nonequilibrium systems, the value of an effective temperature as a thermodynamic control parameter has been unclear. Here, we introduce a two-component system of driven Janus colloids, such that collisions induced by external energy sources agitate the system, and we demonstrate quantitative agreement with hallmarks of statistical thermodynamics for binary phase behavior: the archetypal phase diagram with equilibrium critical exponents, Gaussian displacement distributions, and even capillarity. The significance is to demonstrate a class of dynamical conditions under which thermodynamic analysis extends quantitatively to systems that are decidedly nonequilibrium except that the effective temperature differs from the physical temperature.

Dielectric Modulation of Two-Dimensional Dipolar Materials.

Spontaneous pattern formation plays an important role in a wide variety of natural phenomena and materials systems. A key ingredient for the occurrence of modulated phases is the presence of competing interactions, generally of different physical origins. We demonstrate that in dipolar films, a prototypical system for pattern formation, patterns can be induced by dielectric effects alone. A rich phase diagram arises, where striped and circular morphologies emerge with geometric properties that can be controlled through variation of particle shape and substrate permittivity or permeability. These effects are particularly enhanced by metamaterial substrates.

Dynamics and structure of colloidal aggregates under microchannel flow.

The kinetics of colloidal gels under narrow confinement are of widespread practical relevance, with applications ranging from flow in biological systems to 3D printing. Although the properties of such gels under uniform shear have received considerable attention, the effects of strongly nonuniform shear are far less understood. Motivated by the possibilities offered by recent advances in nano- and microfluidics, we explore the generic phase behavior and dynamics of attractive colloids subject to microchannel flow, using mesoscale particle-based hydrodynamic simulations. Whereas moderate shear strengths result in shear-assisted crystallization, high shear strengths overwhelm the attractions and lead to melting of the clusters. Within the transition region between these two regimes, we discover remarkable dynamics of the colloidal aggregates. Shear-induced surface melting of the aggregates, in conjunction with the Plateau-Rayleigh instability and size-dependent cluster velocities, leads to a cyclic process in which elongated threads of colloidal aggregates break up and reform, resulting in large crystallites. These insights offer new possibilities for the control of colloidal dynamics and aggregation under confinement.

Psl trails guide exploration and microcolony formation in Pseudomonas aeruginosa biofilms.

Bacterial biofilms are surface-associated, multicellular, morphologically complex microbial communities. Biofilm-forming bacteria such as the opportunistic pathogen Pseudomonas aeruginosa are phenotypically distinct from their free-swimming, planktonic counterparts. Much work has focused on factors affecting surface adhesion, and it is known that P. aeruginosa secretes the Psl exopolysaccharide, which promotes surface attachment by acting as 'molecular glue'. However, how individual surface-attached bacteria self-organize into microcolonies, the first step in communal biofilm organization, is not well understood. Here we identify a new role for Psl in early biofilm development using a massively parallel cell-tracking algorithm to extract the motility history of every cell on a newly colonized surface. By combining this technique with fluorescent Psl staining and computer simulations, we show that P. aeruginosa deposits a trail of Psl as it moves on a surface, which influences the surface motility of subsequent cells that encounter these trails and thus generates positive feedback. Both experiments and simulations indicate that the web of secreted Psl controls the distribution of surface visit frequencies, which can be approximated by a power law. This Pareto-type behaviour indicates that the bacterial community self-organizes in a manner analogous to a capitalist economic system, a 'rich-get-richer' mechanism of Psl accumulation that results in a small number of 'elite' cells becoming extremely enriched in communally produced Psl. Using engineered strains with inducible Psl production, we show that local Psl concentrations determine post-division cell fates and that high local Psl concentrations ultimately allow elite cells to serve as the founding population for initial microcolony development.

Efficient dynamic simulations of charged dielectric colloids through a novel hybrid method.

Modern particle-based simulations increasingly incorporate polarization charges arising from spatially nonuniform permittivity. For complex dielectric geometries, calculation of these induced many-body effects typically requires numerical solvers based upon boundary-element methods, which very significantly increase the required computational effort. For the special case of dielectric spheres, such as colloids or nanoparticles, we recently proposed a semianalytical spectrally accurate hybrid method that combines the method of moments, the image-charge method, and the fast multipole method. The hybrid method is efficient and accurate even when dielectric spheres are closely packed. Here, we extend the method to the evaluation of direct and induced electrostatic forces and demonstrate how this can be incorporated in molecular dynamics simulations. The choice of the relevant numerical parameters for molecular dynamics simulations is discussed in detail, as well as comparisons to the boundary-element method. As a concrete example, we examine the challenging case of binary crystal structures composed of close-packed dielectric colloidal spheres.

Subtle changes in surface-tethered groups on PEGylated DNA nanoparticles significantly influence gene transfection and cellular uptake.

PEGylation strategy has been widely used to enhance colloidal stability of polycation/DNA nanoparticles (NPs) for gene delivery. To investigate the effect of polyethylene glycol (PEG) terminal groups on the transfection properties of these NPs, we synthesized DNA NPs using PEG-g-linear polyethyleneimine (lPEI) with PEG terminal groups containing alkyl chains of various lengths with or without a hydroxyl terminal group. For both alkyl- and hydroxyalkyl-decorated NPs with PEG grafting densities of 1.5, 3, or 5% on lPEI, the highest levels of transfection and uptake were consistently achieved at intermediate alkyl chain lengths of 3 to 6 carbons, where the transfection efficiency is significantly higher than that of nonfunctionalized lPEI/DNA NPs. Molecular dynamics simulations revealed that both alkyl- and hydroxyalkyl-decorated NPs with intermediate alkyl chain length exhibited more rapid engulfment than NPs with shorter or longer alkyl chains. This study identifies a new parameter for the engineering design of PEGylated DNA NPs.

The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization.

DNA hybridization onto DNA-functionalized nanoparticle surfaces (e.g., in the form of a spherical nucleic acid (SNA)) is known to be enhanced relative to hybridization free in solution. Surprisingly, via isothermal titration calorimetry, we reveal that this enhancement is enthalpically, as opposed to entropically, dominated by ∼20 kcal/mol. Coarse-grained molecular dynamics simulations suggest that the observed enthalpic enhancement results from structurally confining the DNA on the nanoparticle surface and preventing it from adopting enthalpically unfavorable conformations like those observed in the solution case. The idea that structural confinement leads to the formation of energetically more stable duplexes is evaluated by decreasing the degree of confinement a duplex experiences on the nanoparticle surface. Both experiment and simulation confirm that when the surface-bound duplex is less confined, i.e., at lower DNA surface density or at greater distance from the nanoparticle surface, its enthalpy of formation approaches the less favorable enthalpy of duplex formation for the linear strand in solution. This work provides insight into one of the most important and enabling properties of SNAs and will inform the design of materials that rely on the thermodynamics of hybridization onto DNA-functionalized surfaces, including diagnostic probes and therapeutic agents.

Dielectric Modulation of Ion Transport near Interfaces.

Ion mobility and ionic conductance in nanodevices are known to deviate from bulk behavior, a phenomenon often attributed to surface effects. We demonstrate that dielectric mismatch between the electrolyte and the surface can qualitatively alter ionic transport in a counterintuitive manner. Instead of following the polarization-induced modulation of the concentration profile, mobility is enhanced or reduced by changes in the ionic atmosphere near the interface and affected by a polarization force parallel to the surface. In addition to revealing this mechanism, we explore the effect of salt concentration and electrostatic coupling.

Optothermally Reversible Carbon Nanotube-DNA Supramolecular Hybrid Hydrogels.

Supramolecular hydrogels (SMHs) are three-dimensional constructs wherein the majority of the volume is occupied by water. Since the bonding forces between the components of SMHs are noncovalent, SMH properties are often tunable, stimuli-responsive, and reversible, which enables applications including triggered drug release, sensing, and tissue engineering. Meanwhile, single-walled carbon nanotubes (SWCNTs) possess superlative electrical and thermal conductivities, high mechanical strength, and strong optical absorption at near-infrared wavelengths that have the potential to add unique functionality to SMHs. However, SWCNT-based SMHs have thus far not realized the potential of the optical properties of SWCNTs to enable reversible response to near-infrared irradiation. Here, we present a novel SMH architecture comprised solely of DNA and SWCNTs, wherein noncovalent interactions provide structural integrity without compromising the intrinsic properties of SWCNTs. The mechanical properties of these SMHs are readily tuned by varying the relative concentrations of DNA and SWCNTs, which varies the cross-linking density as shown by molecular dynamics simulations. Moreover, the SMH gelation transition is fully reversible and can be triggered by a change in temperature or near-infrared irradiation. This work explores a new regime for SMHs with potential utility for a range of applications including sensors, actuators, responsive substrates, and 3D printing.

Linking synchronization to self-assembly using magnetic Janus colloids.

Synchronization occurs widely in the natural and technological worlds, from the rhythm of applause and neuron firing to the quantum mechanics of coupled Josephson junctions, but has not been used to produce new spatial structures. Our understanding of self-assembly has evolved independently in the fields of chemistry and materials, and with a few notable exceptions has focused on equilibrium rather than dynamical systems. Here we combine these two phenomena to create synchronization-selected microtubes of Janus colloids, micron-sized spherical particles with different surface chemistry on their opposing hemispheres, which we study using imaging and computer simulation. A thin nickel film coats one hemisphere of each silica particle to generate a discoid magnetic symmetry, such that in a precessing magnetic field its dynamics retain crucial phase freedom. Synchronizing their motion, these Janus spheres self-organize into micrometre-scale tubes in which the constituent particles rotate and oscillate continuously. In addition, the microtube must be tidally locked to the particles, that is, the particles must maintain their orientation within the rotating microtube. This requirement leads to a synchronization-induced structural transition that offers various applications based on the potential to form, disintegrate and fine-tune self-assembled in-motion structures in situ. Furthermore, it offers a generalizable method of controlling structure using dynamic synchronization criteria rather than static energy minimization, and of designing new field-driven microscale devices in which components do not slavishly follow the external field.

Accurate and efficient numerical simulation of dielectrically anisotropic particles.

A variety of electrostatic phenomena, including the structure of electric double layers and the aggregation of charged colloids and proteins, are affected by nonuniform electric permittivity. These effects are frequently ignored in analytical and computational studies and particularly difficult to handle in situations where multiple dielectric contrasts are present, such as in colloids that are heterogeneous in permittivity. We present an extension to the Iterative Dielectric Solver developed by Barros and Luijten [Phys. Rev. Lett. 113, 017801 (2014)] that makes it possible to accurately compute the polarization of anisotropic particles with multiple dielectric contrasts. This efficient boundary-element-method-based approach is applicable to geometries that are not amenable to other solvers, opening the possibility of studying collective phenomena of dielectrically anisotropic particles. We provide insight into the underlying physical reasons for this efficiency.