A general theory of DNA-mediated and other valence-limited colloidal interactions

Varilly, Patrick; Angioletti‐Uberti, Stefano; Mognetti, Bortolo Matteo; Frenkel, Daan

doi:10.1063/1.4748100

Cited by 106 publications

(259 citation statements)

References 45 publications

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“…The structure with the highest predicted percent of DNA duplexes is considered to be the stable structure realized from the building blocks (for further details, see Materials and Methods). It must be stressed here that this model ignores important entropic contributions to the hybridization process as noted by both Frenkel and coworkers and Dreyfus and coworkers (13,(17)(18)(19). With this caveat we use this contact model, along with the genetic algorithm (GA) approach, to design the building blocks that will assemble into desired crystal structures selected from the Inorganic Crystal Structure Database.…”

Section: Significancementioning

confidence: 99%

“…Crocker and coworker developed a quantitative model based on experimental studies to predict ssDNA-induced particle interactions, the driving force for self-assembly (16). Similarly, Frenkel and coworkers has also defined a general accurate theory of valence-limited colloidal interactions (17). In a similar vein, Mirkin and coworkers proposed a rule-based complementary contact model (CCM) to predict the formation of crystal structures by ssDNA-grafted colloids (7).…”

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confidence: 99%

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Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

Srinivasan

Zhang

et al. 2013

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

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In conventional research, colloidal particles grafted with singlestranded DNA are allowed to self-assemble, and then the resulting crystal structures are determined. Although this Edisonian approach is useful for a posteriori understanding of the factors governing assembly, it does not allow one to a priori design ssDNA-grafted colloids that will assemble into desired structures. Here we address precisely this design issue, and present an experimentally validated evolutionary optimization methodology that is not only able to reproduce the original phase diagram detailing regions of known crystals, but is also able to elucidate several previously unobserved structures. Although experimental validation of these structures requires further work, our early success encourages us to propose that this genetic algorithm-based methodology is a promising and rational materials-design paradigm with broad potential applications.DNA-grafted colloids | inverse design | nanostructures | crystal lattice predictions | evolutionary algorithm A topic of much interest in the current literature is the selfassembly of colloid particles multiply grafted with ssDNA molecules (1-10). The typical experimental system consists of two types of colloids grafted with complementary ssDNA sequences. Upon cooling, hybridization of the DNA occurs, crosslinking the colloids. Under the right conditions this cross-linking can facilitate the ordering of the colloids into crystal structures. The typical dimensions of colloids result in periodicities comparable to the wavelength of visible length, which have made them attractive for various emergent technologies, e.g., photonic bandgap materials. Classes of plasmonic, light-emitting, and catalytic metamaterials can be realized via the self-assembly of ssDNAgrafted colloids into specified 3D arrays.Although much work has examined the effects of temperature, DNA length, linker DNA groups, size of colloids, etc., on structure formation, it has been largely empirically driven. However, there has been some progress in theory and simulation on understanding this assembly process (5, 6, 11-13). The recent work of Starr and coworkers, for example, has emphasized the complicated phase and assembly behavior of these materials (11,12,14). Travesset and coworkers (5) and Olvera de la Cruz and coworkers (15) have used large-scale molecular dynamics simulations to study equilibrium aspects and the kinetics of self-assembly, including kinetic traps like gel formation. Crocker and coworker developed a quantitative model based on experimental studies to predict ssDNA-induced particle interactions, the driving force for self-assembly (16). Similarly, Frenkel and coworkers has also defined a general accurate theory of valence-limited colloidal interactions (17). In a similar vein, Mirkin and coworkers proposed a rule-based complementary contact model (CCM) to predict the formation of crystal structures by ssDNA-grafted colloids (7). This model was used to explain the four crystal structures experimentally observed.Althou...

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Section: Significancementioning

confidence: 99%

mentioning

confidence: 99%

Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

Srinivasan

Zhang

et al. 2013

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

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“…Despite the success of these theories in providing insights into the ground-state free energy, they are generally limited to enumerating interactions at the twoparticle level. They also ignore any entropic effects relevant to this self-assembly process (9)(10)(11)(12)(17)(18)(19)(20)(21). Molecular dynamics simulations avoid these difficulties and extend this analysis to superlattice self-assembly so as to provide a detailed understanding of the effects of kinetics (13), DNA sequence (14), and electrostatics (15,16,22) on lattice stability.…”

mentioning

confidence: 99%

“…A large number of theories and simulations have been developed to delineate the hybridization interactions between two interacting DNA-NPs (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). Despite the success of these theories in providing insights into the ground-state free energy, they are generally limited to enumerating interactions at the twoparticle level.…”

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confidence: 99%

Stoichiometric control of DNA-grafted colloid self-assembly

Venkatasubramanian

Kumar

et al. 2015

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

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There has been considerable interest in understanding the selfassembly of DNA-grafted nanoparticles into different crystal structures, e.g., CsCl, AlB 2 , and Cr 3 Si. Although there are important exceptions, a generally accepted view is that the right stoichiometry of the two building block colloids needs to be mixed to form the desired crystal structure. To incisively probe this issue, we combine experiments and theory on a series of DNA-grafted nanoparticles at varying stoichiometries, including noninteger values. We show that stoichiometry can couple with the geometries of the building blocks to tune the resulting equilibrium crystal morphology. As a concrete example, a stoichiometric ratio of 3:1 typically results in the Cr 3 Si structure. However, AlB 2 can form when appropriate building blocks are used so that the AlB 2 standard-state free energy is low enough to overcome the entropic preference for Cr 3 Si. These situations can also lead to an undesirable phase coexistence between crystal polymorphs. Thus, whereas stoichiometry can be a powerful handle for direct control of lattice formation, care must be taken in its design and selection to avoid polymorph coexistence. colloidal interactions | functional particle | superlattice engineering | molecular design | modeling O ver the past several decades, there has been increasing interest in programmable self-assembly for materials fabrication. Rather than using traditional methods of shaping bulk materials, the emerging concept is to focus on the design of nanoscale building blocks that self-organize into desired structures. This "design" philosophy has led to the development of novel techniques such as DNA origami, where specific interactions are used to direct the folding of oligonucleotides into a variety of assemblies (1-6). Another vein of research is to focus on the directed assembly of DNA-grafted nanoparticles (DNA-NPs) into superlattices with well-defined crystal morphologies. These systems have unusual photonic and plasmonic properties with applications in spectroscopy, surface imaging, and optical sensors (7,8).A large number of theories and simulations have been developed to delineate the hybridization interactions between two interacting DNA-NPs (9-20). Despite the success of these theories in providing insights into the ground-state free energy, they are generally limited to enumerating interactions at the twoparticle level. They also ignore any entropic effects relevant to this self-assembly process (9-12, 17-21). Molecular dynamics simulations avoid these difficulties and extend this analysis to superlattice self-assembly so as to provide a detailed understanding of the effects of kinetics (13), DNA sequence (14), and electrostatics (15, 16, 22) on lattice stability. We particularly highlight the work of Li et al. (16), who explicitly considered the role of stoichiometry on the crystal morphology formed. They selected several stoichiometries, i.e., 1:1, 2:1, and 3:1. We focus here on one specific case, 2:1. As the size and linker ratios of ...

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“…An extension to immobile linkers can be derived following Ref. 20. Bonds can either involve linkers tethered to the same particle or to different particles.…”

Section: Introductionmentioning

confidence: 99%

Communication: Free energy of ligand-receptor systems forming multimeric complexes

Michele

Bachmann

Parolini

et al. 2016

The Journal of Chemical Physics

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Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although complex functionalities often emerge from the simultaneous interaction of more than just two linker molecules, state of the art theoretical frameworks enable the calculation of the free energy only in systems featuring one-to-one ligand/receptor binding. In this Communication, we derive a general formula to calculate the free energy of systems featuring simultaneous direct interaction between an arbitrary number of linkers. To exemplify the potential and generality of our approach, we apply it to the systems recently introduced by Parolini et al. [ACS Nano 10, 2392

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A general theory of DNA-mediated and other valence-limited colloidal interactions

Cited by 106 publications

References 45 publications

Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

Stoichiometric control of DNA-grafted colloid self-assembly

Communication: Free energy of ligand-receptor systems forming multimeric complexes

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