A mean-field model of linker-mediated colloidal interactions

Design principles, growth laws, and competition of minimal autocatalysts

The difficulty of designing simple autocatalysts that grow exponentially in the absence of enzymes, external drives or ingenious internal mechanisms severely constrains scenarios for the emergence of evolution by natural selection in chemical and physical systems. Here, we systematically analyze these difficulties in the simplest and most generic autocatalyst: a dimeric molecule that duplicates by templated ligation. We show that despite its simplicity, such an autocatalyst can achieve exponential growth autonomously. We also show, however, that it is possible to design as simple sub-exponential autocatalysts that have an advantage over exponential autocatalysts when competing for a common resource. We reach these conclusions by developing a theoretical framework based on kinetic barrier diagrams. Besides challenging commonly accepted assumptions in the field of the origin of life, our results provide a blueprint for the experimental realization of elementary autocatalysts exhibiting a form of natural selection, whether on a molecular or colloidal scale.

Predicting the size and morphology of nanoparticle clusters driven by biomolecular recognition

Nanoparticle aggregation is a driving principle of innovative materials and biosensing methodologies, improving transduction capabilities displayed by optical, electrical or magnetic measurements. This aggregation can be driven by the biomolecular recognition between target biomolecules (analytes) and receptors bound onto nanoparticle surface. Despite theoretical advances on modelling the entropic interaction in similar systems, predictions of the fractal morphologies of the nanoclusters of bioconjugated nanoparticles are lacking. The morphology of resulting nanoclusters is sensitive to the location, size, flexibility, average number of receptors per particle f̄, and the analyte-particle concentration ratio. Here we considered bioconjugated iron oxide nanoparticles (IONPs) where bonds are mediated by a divalent protein that binds two receptors attached onto different IONPs. We developed a protocol combining analytical expressions for receptors and linker distributions, and Brownian dynamics simulations for bond formation, and validated it against experiments. As more bonds become available (e.g., by adding analytes), the aggregation deviates from the ideal Bethe's lattice scenario due to multivalence, loop formation, and steric hindrance. Generalizing Bethe's lattice theory with a (not-integer) effective functionality feff leads to analytical expressions for the cluster size distributions in excellent agreement with simulations. At high analyte concentration steric impediment imposes an accessible limit value facc to feff, which is bounded by facc < feff < f̄. A transition to gel phase, is correctly captured by the derived theory. Our findings offer new insights into quantifying analyte amounts by assessing nanocluster size, and predicting nanoassembly morphologies accurately is a first step towards understanding variations of physical properties in clusters formed after biomolecular recognition.

On Capacitance and Energy Storage of Supercapacitor with Dielectric Constant Discontinuity

The classical density functional theory (CDFT) is applied to investigate influences of electrode dielectric constant on specific differential capacitance Cd and specific energy storage E of a cylindrical electrode pore electrical double layer. Throughout all calculations the electrode dielectric constant varies from 5, corresponding to a dielectric electrode, to εwr= 10⁸ corresponding to a metal electrode. Main findings are summarized as below. (i): By using a far smaller value of the solution relative dielectric constant εr=10, which matches with the reality of extremely narrow tube, one discloses that a rather high saturation voltage is needed to attain the saturation energy storage in the ultra-small pore. (ii): Use of a realistic low εr=10 value brings two obvious effects. First, influence of bulk electrolyte concentration on the Cd is rather small except when the electrode potential is around the zero charge potential; influence on the E curve is almost unobservable. Second, there remain the Cd and E enhancing effects caused by counter-ion valency rise, but strength of the effects reduces greatly with dropping of the εr value; in contrast, the Cd and E reducing effects coming from the counter-ion size enhancing remain significant enough for the low εr value. (iii) A large value of electrode relative dielectric constant εrw always reduces both the capacitance and energy storage; moreover, the effect of the εrw value gets eventually unobservable for small enough pore when the εrw value is beyond the scope corresponding to dielectric electrode. It is analyzed that the above effects take their rise in the repulsion and attraction on the counter-ions and co-ions caused by the electrode bound charges and a strengthened inter-counter-ion electrostatic repulsion originated in the low εr value.

Self-Assembly of DNA-Grafted Colloids: A Review of Challenges

DNA-mediated self-assembly of colloids has emerged as a powerful tool to assemble the materials of prescribed structure and properties. The uniqueness of the approach lies in the sequence-specific, thermo-reversible hybridization of the DNA-strands based on Watson–Crick base pairing. Grafting particles with DNA strands, thus, results into building blocks that are fully programmable, and can, in principle, be assembled into any desired structure. There are, however, impediments that hinder the DNA-grafted particles from realizing their full potential, as building blocks, for programmable self-assembly. In this short review, we focus on these challenges and highlight the research around tackling these challenges.

Ligand Interactions and Nanoparticle Shapes Guide the Pathways toward Interfacial Self-Assembly

Non-equilibrium molecular dynamics simulations are used to probe the driving forces behind the formation of highly ordered, epitaxially connected superlattices of polyhedral-shaped nanoparticles (NPs) at fluid-fluid interfaces. By explicitly modeling coarse-grained ligands that cap the NP surface, it is shown that differences in NP shapes and time-dependent facet-specific ligand densities give rise to drastically different transformation mechanisms. Our results indicate that the extent of screening of the inter-particle interactions by the surrounding solvation environment has a significant impact on reversibility and ultimately the coherence of the final two-dimensional superlattice obtained. For the particle shapes examined, a hexagonal pre-assembly and a square superlattice final assembly (upon preferential ligand desorption from {100} facets) were prevalent; however, cuboctahedral NPs formed intermediate epitaxially bonded branched clusters, which eventually grew and rearranged into a square lattice; in contrast, truncated octahedral NPs exhibited an abrupt rhombic-to-square transition driven by the clustering of their numerous {111}-ligands that favored the stacking of linear NP rods. To track the incipient order in the system, we also outline a set of novel order parameters that measure the local orientation alignment between nearest-neighbor pairs. The simulation protocols advanced in this work could pave the way forward for exploration of the vast phase space associated with the interfacial self-assembly of NPs.

Multifarious colloidal structures: new insight into ternary and quadripartite ordered assemblies

DNA-mediated assembly of colloidal particles can be utilized to produce a variety of structures which may have desirable phononic, photonic, or electronic transport properties. Recent developments in linker-mediated assembly processes allow for interactions to be coordinated between many different types of colloidal particles more easily and with fewer unique sequences than direct hybridization. However, the dynamics of colloidal self-assembly becomes increasingly more complex when coordinating interactions between three or more distinct interacting elements. In such cases particle pairs with similar binding energies are allowed to interact unpredictably, and enthalpically degenerate binding sites will be noticeably more present while numerous secondary phases may also result from the self-assembly process. Therefore, it is necessary to develop procedures for predicting feasible superstructure geometries for these systems before they can be implemented in material design. Here we investigate the formation of multifarious ordered structures through self-assembly of multiple types of spherically symmetrical colloidal particles with a variety of interaction matrices. We utilize Molecular Dynamics (MD) simulations to study the growth behavior of systems with different types of interacting elements and different particle sizes, and also predict the formation and stability of the target structures. We also study the phononic spectra of various ternary structures in order to identify the influence of key structural parameters on phonon bandgap frequencies and ranges. Our results provide direct guidelines for designing ternary and quadripartite multifarious colloidal structures, and motivate new directions for future experimental work to target formation of multi-component colloidal superstructures beyond the well-established binary symmetries studied in the past.

Symmetry-derived structure directing agents for two-dimensional crystals of arbitrary colloids

We derive properties of self-assembling rings which can template the organization of an arbitrary colloid into any periodic symmetry in two Euclidean dimensions. By viewing this as a tiling problem, we illustrate how the shape and chemical patterning of these rings are derivable, and are explicitly reflected by the symmetry group's orbifold symbol. We performed molecular dynamics simulations to observe their self-assembly and found 5 different characteristics which could be easily rationalized on the basis of this symbol. These include systems which undergo chiral phase separation, are addressably complex, exhibit self-limiting growth into clusters, form ordered "rods" in only one-dimension akin to a smectic phase, and those from symmetry groups which are pluripotent and allow one to select rings which exhibit different behaviors. We discuss how the curvature of the ring's edges plays an integral role in achieving correct self-assembly, and illustrate how to obtain these shapes. This provides a method for patterning colloidal systems at interfaces without explicitly programming this information onto the colloid itself.