Effective nonadditive pair potential for lock-and-key interacting particles: The role of the limited valence

Largo, J.; Tartaglia, P.; Sciortino, Francesco

doi:10.1103/physreve.76.011402

Cited by 22 publications

(42 citation statements)

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“…The effective potential between two ssDNA depends only on the intermolecular separation and their relative angular orientation. The parameters of the effective potential are obtained by a systematic coarsegraining of a more detailed model for the DNA interactions, and it has been verified that the coarse-grained model quantitatively reproduces the behavior of the more explicit model 34,35 . We study this model via Monte Carlo (MC) simulations in the canonical ensemble (fixed number of particles N, volume V , temperature T ).…”

Section: Modelingmentioning

confidence: 86%

Universal two-step crystallization of DNA-functionalized nanoparticles

2010

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We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by a highly-connected amorphous intermediate. For lower temperature quenches, the dynamics of unzipping strands in the amorphous state is sufficiently slow that crystallization is kinetically hindered. This accounts for the well-documented difficulty of forming crystals in these systems. The strong parallel to the crystallization behavior of proteins and colloids suggests that these disparate systems crystallize in an apparently universal manner.

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Section: Modelingmentioning

confidence: 86%

Universal two-step crystallization of DNA-functionalized nanoparticles

2010

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“…The ability of the effective potential to reproduce structural and thermodynamic properties of the explicit model has been verified in ref. 28 for the case L ϭ 8. We have confirmed that similar agreement in structural quantities is observed for the case L ϭ 4 and L ϭ 16, even in the region where multiple networks are observed.…”

Section: [1]mentioning

confidence: 99%

“…1 A and B. Here, we focus mainly on a simplified model (28) that is directly derived from the more complex model. We represent each dendrimer by a central core with rigid arms, representing the ssDNA, that point to the vertices of tetrahedron ( Fig.…”

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confidence: 99%

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Hierarchies of networked phases induced by multiple liquid–liquid critical points

Hsu

Largo

Sciortino

et al. 2008

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

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Nanoparticles and colloids functionalized by four single strands of DNA can be thought of as designed analogs to tetrahedral network-forming atoms and molecules, with a difference that the attached DNA strands allow for control of the length scale of bonding relative to the core size. We explore the behavior of an experimentally realized model for nanoparticles functionalized by four single strands of DNA (a tetramer), and show that this single-component model exhibits a rich phase diagram with at least three critical points and four thermodynamically distinct amorphous phases. We demonstrate that the additional critical points are part of the Ising universality class, like the ordinary liquid-gas critical point. The dense phases consist of a hierarchy of interpenetrating networks, reminiscent of a woven cloth. Thus, bonding specificity of DNA provides an effective route to generate new nano-networked materials with polyamorphic behavior. The concept of network interpenetration helps to explain the generation of multiple liquid phases in single-component systems, suggested to occur in some atomic and molecular network-forming fluids, including water and silica. DNA functionalization ͉ nanoparticles ͉ self-assembly ͉ polyamorphism ͉ nanotechnology T echnological developments are creating a wide variety of building blocks that play the role of ''functionalized atoms'' for designed materials (1, 2). Borrowing ideas from biological specificity (3-6), it is now possible to control bonding between engineered building blocks in a selective way, moving in the direction of an effective synthetic bottom-up strategy for selfassembly. The complementary binding of base pairs, combined with the ability to directly control the base sequence, makes DNA an ideal candidate for the development of network-based, nanostructured materials (5-8). A variety of experiments (7)(8)(9)(10)(11)(12)(13)(14)(15) have demonstrated the possibility to realize nanostructured, DNAbased materials, including ordered crystal structures (9, 10).By grafting short single strands of DNA to core particles, the core can act as a ''node'' of a complex network formed when single strands combine into dsDNA. Longer linking ''arms'' may be achieved by using a double-stranded spacer near the core nanoparticle (9, 10). With an intelligent choice of the core, it is possible to control the number of attached strands and thus the nearest-neighbor coordination of the functionalized nanoparticle, providing a direct route to study materials where the bonding coordination is much less than that of spherically symmetric molecules (16). In such limited coordination systems, the general features of network formation are expected to be observed.By functionalizing the central core with four DNA strands, we expect to generate an engineered analog of tetrahedral networkforming atoms or molecules, in which the bonding contribution to the interparticle interaction energy can be tuned by modulating the length L of the DNA strand, as well as the chemical properties of the solvent....

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“…Estimates of pairwise interactions between nanoparticles have been obtained by simulation with the help of CG DFP models (see section I) 56,57 . These previous studies consider pair interactions between DFPs for very low DNA grafting densities of 4 to 6 DNA molecules per particle.…”

Section: B Pair Interactions Between Dna-functionalized Particlesmentioning

confidence: 99%

Insights into DNA-mediated interparticle interactions from a coarse-grained model

Ding

Mittal

2014

The Journal of Chemical Physics

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DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNAfunctionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

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Effective nonadditive pair potential for lock-and-key interacting particles: The role of the limited valence

Cited by 22 publications

References 20 publications

Universal two-step crystallization of DNA-functionalized nanoparticles

Universal two-step crystallization of DNA-functionalized nanoparticles

Hierarchies of networked phases induced by multiple liquid–liquid critical points

Insights into DNA-mediated interparticle interactions from a coarse-grained model

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