A coarse-grained model for DNA-functionalized spherical colloids, revisited: Effective pair potential from parallel replica simulations

Theodorakis, Panagiotis E.; Dellago, Christoph; Kahl, Gerhard

doi:10.1063/1.4773920

Cited by 21 publications

(19 citation statements)

References 108 publications

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“…The use of DNA labeling to control binding specificity was originally pioneered for assembling nanoparticles (14)(15)(16)(17) into infinite crystals (18)(19)(20)(21)(22)(23)(24), where recently it was demonstrated that with two species with differing particle radii and DNA linker length a zoo of different crystal morphologies can be created (25). Work at the colloidal scale has begun to bear fruit (13,17,(26)(27)(28)(29)(30). However, the set of possible structures that could be coded is far more general, including structures of any shape and size, both rigid and flexible.…”

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confidence: 99%

Size limits of self-assembled colloidal structures made using specific interactions

Zeravcic

Manoharan

Brenner

2014

Proc. Natl. Acad. Sci. U.S.A.

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We establish size limitations for assembling structures of controlled size and shape out of colloidal particles with short-ranged interactions. Through simulations we show that structures with highly variable shapes made out of dozens of particles can form with high yield, as long as each particle in the structure binds only to the particles in their local environment. To understand this, we identify the excited states that compete with the ground-state structure and demonstrate that these excited states have a completely topological characterization, valid when the interparticle interactions are short-ranged. This allows complete enumeration of the energy landscape and gives bounds on how large a colloidal structure can assemble with high yield. For large structures the yield can be significant, even with hundreds of particles.assembly | DNA-coated particles | local minima | short-ranged interactions N ature uses hierarchical assembly of complicated building blocks to make highly functional structures such as biomolecules, virus shells, and microtubules without any external influence and with high fidelity. Mimicking this would not only give more insight into biological mechanisms but would also help realize the dream of "bottom-up" assembly that has been a central theme of nanotechnology for many decades (1).As in biology, the information needed for assembling arbitrary macroscopic structures can be stored in the building blocks through the design of their interactions and interaction rules. Over the years great advances have been made by synthesizing new building blocks differing in geometry, composition, and interactions (2-10), allowing for study of more complex objects. However, basic rules necessary for robust and efficient assembly of a desired structure in a scalable fashion and reasonable time scales are still not understood. A number of schemes for approaching this "inverse" statistical mechanics problem have been proposed (11-13), but a general framework and systematic studies are still missing. One of the essential underlying questions, having both practical and conceptual impact, is whether any desired macroscopic structure can be assembled with a high yield, out of a given set of building blocks. Or are there fundamental constraints limiting the structures that can be effectively built?In this paper we address these general questions using the model system of DNA-coated particles, itself of considerable recent interest. We consider an isolated system of N spherical colloidal particles, each of which is isotropically coated with DNA strands to control interparticle interactions. At the colloidal scale, such interactions have a range that is much shorter than the size of the particles. The use of DNA labeling to control binding specificity was originally pioneered for assembling nanoparticles (14-17) into infinite crystals (18-24), where recently it was demonstrated that with two species with differing particle radii and DNA linker length a zoo of different crystal morphologies can be created (25). ...

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confidence: 99%

Size limits of self-assembled colloidal structures made using specific interactions

Zeravcic

Manoharan

Brenner

2014

Proc. Natl. Acad. Sci. U.S.A.

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“…Classical experiments showed that DNA-based specific interactions allow assembly of crystals of nanoparticles (9)(10)(11)(12). More recently, efforts for self-assembly at the colloidal scale have begun to bear fruit (12)(13)(14)(15)(16)(17)(18). To achieve the exponentially growing catalytic cycles of the current study, we find that it is necessary to use time-dependent interactions between the particles, whose strength can be modulated over a programmable timescale.…”

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confidence: 85%

Spontaneous emergence of catalytic cycles with colloidal spheres

Zeravcic

Brenner

2017

Proc. Natl. Acad. Sci. U.S.A.

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Colloidal particles endowed with specific time-dependent interactions are a promising route for realizing artificial materials that have the properties of living ones. Previous work has demonstrated how this system can give rise to self-replication. Here, we introduce the process of colloidal catalysis, in which clusters of particles catalyze the creation of other clusters through templating reactions. Surprisingly, we find that simple templating rules generically lead to the production of huge numbers of clusters. The templating reactions among this sea of clusters give rise to an exponentially growing catalytic cycle, a specific realization of Dyson's notion of an exponentially growing metabolism. We demonstrate this behavior with a fixed set of interactions between particles chosen to allow a catalysis of a specific sixparticle cluster from a specific seven-particle cluster, yet giving rise to the catalytic production of a sea of clusters of sizes between 2 and 11 particles. The fact that an exponentially growing cycle emerges naturally from such a simple scheme demonstrates that the emergence of exponentially growing metabolisms could be simpler than previously imagined.catalytic cycles | DNA-coated colloids | metabolism | templating T he origin of life is usually associated with self-replication, the ability of an entity to create copies of itself (1). Thus inspired, there have been many efforts in recent years aimed at creating artificial systems with self-replicative capacity. These are typically inspired by the linear chain mechanism of DNA. However, living systems are more than individual entities that can replicate themselves. Dyson (2) and Oparin (3) argued that a more critical aspect of living systems is the creation of a metabolism, a complex cascade of chemical reactions that together are able to accomplish more than any single chemical reaction can do on its own. Using a simple mathematical model, the so-called "garbage bag model," Dyson presented a scenario through which such a complex metabolism could arise spontaneously. His idea is that a random set of catalysts will catalyze arbitrary chemical reactions in a nonsynergistic fashion. However, if each catalyst is more likely to function when there are others that are synergistic with it, then there is a critical amount of cooperativity above which metabolic cycles spontaneously emerge. This idea has been explored through abstract simulations (4). In a similar spirit, Kauffman and coworkers have shown that if the probability of one species catalyzing the formation of another is above a threshold, then catalytic cycles naturally emerge (5-7).Whether this scenario can naturally occur in practice remains obscure. The fundamental question is to determine how likely it is for a soup of interacting catalysts to self-organize into an exponentially growing catalytic cycle. How special do the interactions between the different components need to be for spontaneous exponentially growing catalytic cycles to emerge? In this work, we present an explicit demon...

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“…Various simulation models for DNA chains have been contrived over the last years [132][133][134][135][136][137][138][139][140][141][142][143]. As it usually happens with these models, they aim at reproducing only the properties of interest of the system.…”

Section: Computer Simulationsmentioning

confidence: 99%

“…It has been found for this model that relaxing the condition of kinetically immobile strands on the surface of the particles, a slight increase or decrease in the melting temperature occurs. Larger changes to the melting temperature result from increasing the number of strands, which increases the melting temperature, or by increasing the core NP diameter, which decreases the melting temperature [143]. A quantitative description of the melting temperature has been provided by the model of Starr and Sciortino [142][143][144].…”

Section: Coarse-grained Modelsmentioning

confidence: 99%

Self-assembly of DNA-functionalized colloids

Theodorakis¹,

Fytas²,

Kahl³

et al. 2015

Condens. Matter Phys.

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Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure. Depending on the geometry and the size of the particles, the grafting density of the ssDNA chains, and the length and choice of DNA sequences, a number of different crystalline structures can be fabricated. However, understanding how these factors contribute synergistically to the self-assembly process of DNA-functionalized nano-or micro-sized particles remains an intensive field of research. Moreover, the fabrication of long-range structures due to kinetic bottlenecks in the self-assembly are additional challenges. Here, we discuss the most recent advances from theory and experiment with particular focus put on recent simulation studies.

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A coarse-grained model for DNA-functionalized spherical colloids, revisited: Effective pair potential from parallel replica simulations

Cited by 21 publications

References 108 publications

Size limits of self-assembled colloidal structures made using specific interactions

Size limits of self-assembled colloidal structures made using specific interactions

Spontaneous emergence of catalytic cycles with colloidal spheres

Self-assembly of DNA-functionalized colloids

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