We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered crystalline assemblies, and instead, disordered structures start to form when the chain length exceeds a certain threshold, which is consistent with the previous experiments. Further analysis of the simulation data suggests weakening interparticle interactions with increasing chain length, thereby shifting the suitable assembly conditions to lower temperatures at which assembly dynamics are unfavorable. This highlights a complex interplay between thermodynamics and dynamics, which we suggest can be modulated by changing the system parameters such as DNA grafting density, resulting in successful crystallization of particles with longer DNA chain lengths. Our results highlight the power of computational modeling in elucidating the fundamental design principles and guiding the assembly of nanoparticles to form complex nanostructures.
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 part…
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 remain…
To prevent the flocculation and phase separation of nanoparticles in solution, nanoparticles are often functionalized with short chain surfactants. Here we present fully-atomistic molecular dynamics simulations which characterize how these functional coatings affect the interactions between nanoparticles and with the surrounding solvent. For 5 nm diameter silica nanoparticles coated with poly(ethylene oxide) (PEO) oligomers in water, we determined the hydrodynamic drag on two approaching nanoparticles moving through solvent and on a single nanoparticle as it approaches a planar surface. In mos…
Solvation of gold nanoparticles passivated with end group functionalized alkylthiols, namely CH$_3$, NH$_2$ or COOH is studied in solvents of varying degrees of repulsion-dispersion and electrostatic interactions ranging from strongly polar SPC/E water to modified hybrid water models, where the Lennard-Jones contribution to the potential energy is enhanced relative to SPC/E to completely non-polar, decane. The effects due to solvent reorganization around the nanoparticle as a function of the ligand and solvent chemistry are monitored using the nanoparticle-solvent pair correlation functions an…
We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies (R. Jin et al., JACS 125, 1643 (2003); T. A. Taton et al., Science 289, 1757 (2000)). The binding of DNA-coated nano-particles by dissolved DNA linker can be described by exploiting an analogy with quantum particles obeying fractional statistics. In accordance with experimental findings, we predict that the phase-separation temperature of the nano-colloids increases with the DNA coverage of the colloidal surface. Upon the addition of salt, the demixing temperature increases logarit…
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 collo…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase behavior of DNA-functionalized nano-colloids without assuming pairwise additivity of the inter-colloidal interactions. Our simulations show that for nano-colloids, the assumption of pairwise additivity leads to substantial errors in the estimate of the free energy of the crystal phase. We compare our results with available experimental data and find that the simul…
Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate [-S (CH2)6-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers observed to undergo a rapid conformational change during the 25 ns long simulation period. From the RMSD values of ssDNAs, we find relative stability in the case of purine rich s…
Limited bonding valence, usually accompanied by well-defined directional interactions and selective bonding mechanisms, is nowadays considered among the key ingredients to create complex structures with tailored properties: even though isotropically interacting units already guarantee access to a vast range of functional materials, anisotropic interactions can provide extra instructions to steer the assembly of specific architectures. The anisotropy of effective interactions gives rise to a wealth of self-assembled structures both in the realm of suitably synthesized nano- and micro-sized buil…
Multifunctional mesoporous silica nanoparticles (MSN) have attracted substantial attention with regard to their high potential for targeted drug delivery. For future clinical applications it is crucial to address safety concerns and understand the potential immunotoxicity of these nanoparticles. In this study, we assess the biocompatibility and functionality of multifunctional MSN in freshly isolated, primary murine immune cells. We show that the functionalized silica nanoparticles are rapidly and efficiently taken up into the endosomal compartment by specialized antigen-presenting cells such …
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA tethered nanoparticles.
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form …
Nanoparticles functionalized with multiple ligands can be programmed to bind biological targets depending on the receptors they express, providing a general mechanism exploited in various technologies, from selective drug-delivery to biosensing. For binding to be highly selective, ligands should exclusively interact with specific targeted receptors, because formation of bonds with other, untargeted ones would lead to non-specific binding and potentially harmful behaviour. This poses a particular problem for multivalent nanoparticles, because even very weak bonds can collectively lead to strong…
Nanoparticles with multiple ligands have been proposed for use in nanomedicine. The multiple targeting ligands on each nanoparticle can bind to several locations on a cell surface facilitating both drug targeting and uptake. Experiments show that the distribution of conjugated ligands is unexpectedly broad, and the desorption rate appears to depends exponentially upon the mean number of attached ligands. These two findings are explained with a model in which ligands conjugate to the nanoparticle with a positive cooperativity of $\approx 4kT$, and that nanoparticles bound to a surface by multip…
In a recent publication, we have highlighted the potential of phosphonic acid terminated PEG oligomers to functionalize strong UV absorption cerium oxide nanoparticles[1], which yield suspensions that are stable in aqueous or organic solvents and are redispersible in different solvent after freeze-drying. In the present work, we highlight the interfacial activity of the functional ceria nanoparticles and their potential to modify hydrophobic surfaces. We first investigated Phosphonated-PEG amphiphilic oligomers behavior as strong surface active species forming irreversibly adsorbed layers. We …
Many industrial soft materials often include oil-in-water (O/W) emulsions at the core of their formulations. By using tuneable interface stabilizing agents, such emulsions can self-assemble into complex structures. DNA has been used for decades as a thermoresponsive highly specific binding agent between hard and, recently, soft colloids. Up until now, emulsion droplets functionalized with DNA had relatively low coating densities and were expensive to scale up. Here a general O/W DNA-coating method using functional non-ionic amphiphilic block copolymers, both diblock and triblock, is presented.…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interac…
The response in capacitance to low external magnetic fields (up to 0.1 T) of suspensions of spherical magnetic nanoparticles, single-wall carbon nanotubes (SWCNT), SWCNT functionalized with carboxyl group (SWCNT-COOH) and SWCNT functionalized with Fe$_3$O$_4$ nanoparticles in a nematic liquid crystal has been studied experimentally. The volume concentration of nanoparticles was $ϕ_1$ = 10$^{-4}$ and $ϕ_2$ = 10$^{-3}$. Independent of the type and the volume concentration of the nanoparticles, a linear response to low magnetic fields (far below the magnetic Fréederiksz transition threshold) has …
We report in detail our experiments on the conduction of $λ$ DNA molecules over a wide range of temperature deposited across slits in a few nanometers thick platinum film. These insulating slits were fabricated using focused ion beam etching and characterized extensively using near field and electron microscopy. This characterization revealed the presence of metallic Ga nanoparticles inside the slits, as a result of the ion etching. After deposition of $λ$ DNA molecules, using a protocol that we describe in detail, some of the slits became conducting and exhibited superconducting fluctuations …
We study theoretically a new generic scheme of programmable self-assembly of nanoparticles into clusters of desired geometry. The problem is motivated by the feasibility of highly selective DNA-mediated interactions between colloidal particles. By analyzing both a simple generic model and a more realistic description of a DNA-colloidal system, we demonstrate that it is possible to suppress the glassy behavior of the system, and to make the self-assembly nearly error-proof. This regime requires a combination of stretchable interparticle linkers (e.g. sufficiently long DNA), and a soft repulsive…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by systems lacking selective interactions. The scales at which the functional properties of these materials emerge are difficult to model, especially in the reversible regime where such properties result from many binding/unbinding events. This difficulty is related to large entropic barriers associated with the formation of intra-molecular loops. In this work …
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built from a single type of vertex. Here we use analytic theory and equilibrium and dynamic simulation to show that a model particle, whose rotational properties lie between those those of the vertices of the 6.6.6 and 4.8.8 networks, can self-assemble into a network built from three types of vertex. Important in forming this network is the ability of the particle t…
DNA origami is a novel self-assembly technique allowing one to form various 2D shapes and position matter with nanometer accuracy. It has been used to coordinate placement of nanoscale objects, both organic and inorganic; to make molecular motors and walkers; and to create optically active nanostructures. Here we use DNA origami templates to engineer Surfaced Enhanced Raman Scattering (SERS) substrates. Specifically, gold nanoparticles were selectively attached to the corners of rectangular origami and subsequently enlarged via solution-based metal deposition. The resulting assemblies were des…
Functionalizing colloids with reactive DNA linkers is a versatile way of programming self-assembly. DNA selectivity provides direct control over colloid-colloid interactions allowing the engineering of structures such as complex crystals or gels. However, self-assembly of localized and finite structures remains an open problem with many potential applications. In this work, we present a system in which functionalized surfaces initiate a cascade reaction between linkers leading to self-assembly of crystals with a controllable number of layers. Specifically, we consider colloidal particles funct…
Functionalization of photocatalytic metal oxide nanoparticles of TiO2, ZnO, WO3 and CuO with amine-terminated (oleylamine) and thiol-terminated (1-dodecanethiol) alkyl chained ligands was studied under ambient conditions. A high selectivity was observed in the binding specificity of a ligand towards nanoparticles of these different oxides. It was observed that oleylamine binds stably to only TiO2 and WO3, while 1-dodecanethiol binds stably only to ZnO and CuO. Similarly, polar to non-polar solvent phase transfer of TiO2 and WO3 nanoparticles could be achieved by using oleylamine, but not by 1-…
DNA-driven self-assembly enables precise positioning of the colloidal nanoparticles owing to specific Watson-Crick interactions. Another important feature of this self-assembly method is its reversibility by controlling the temperature of the medium. In this work, we study the potential of another mechanism to control binding/unbinding process of the DNA-functionalized gold nanoparticles. We employ the laser radiation that can be absorbed by the gold nanoparticles to heat their network and disassociate it. Here, we show that we can actively control the optical properties of the nanoparticle ne…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since hybridization of double strands will only occur if the base sequences of single strands are complementary. 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 rela…
During the past years we have investigated the complexation between nanocolloids and oppositely charged polymers. The nanocolloids examined were ionic surfactant micelles and inorganic oxide nanoparticles. For the polymers, we used homopolyelectrolytes and block copolymers with linear and comb architectures. In general, the attractive interactions between oppositely charged species are strong and as such, the simple mixing of solutions containing dispersed constituents yield to a precipitation, or to a phase separation. We have developed means to control the electrostatically-driven attraction…
We present a theoretical discussion of a self-assembly scheme which makes it possible to use DNA to uniquely encode the composition and structure of micro- and nanoparticle clusters. These anisotropic DNA-decorated clusters can be further used as building blocks for hierarchical self-assembly of larger structures. We address several important aspects of possible experimental implementation of the proposed scheme: the competition between different types of clusters in a solution, possible jamming in an unwanted configuration, and the degeneracy due to symmetry with respect to particle permutati…
We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs directionally-functionalized with DNA. The combination of directionality and selectivity of interactions allows one to avoid unwanted metastable configurations which have been shown to lead to slow self-assembly kinetics even in much simpler systems. With numerical simulations, we show that a variety of target mesoscopic objects can be designed and self-assembled in near perfect yield. They include …
An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge, mainly due to unspec…
We have functionalized the sides of fd bacteriophage virions with oligonucleotides to induce DNA hybridization driven self-assembly of high aspect ratio filamentous particles. Potential impacts of this new structure range from an entirely new building block in DNA origami structures, inclusion of virions in DNA nanostructures and nanomachines, to a new means of adding thermotropic control to lyotropic liquid crystal systems. A protocol for producing the virions in bulk is reviewed. Thiolated oligonucleotides are attached to the viral capsid using a heterobifunctional chemical linker. A commonl…
We report a study of reversible adsorption of DNA-coated colloids on complementary functionalized oil droplets. We show that it is possible to control the surface coverage of oil droplets by colloidal particles, by exploiting the fact that during slow adsorption, compositional arrest takes place well before structural arrest occurs. As a consequence, we can prepare colloid-coated oil droplets with a `frozen' degree of loading, but with fully ergodic colloidal dynamics on the droplets. We illustrate the equilibrium nature of the adsorbed colloidal phase by exploring the quasi two-dimensional (2…
In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using DNA scaffolds. In this letter we consider a DNA scaffold method to self-assemble clusters of "colored" particles. Stable clusters of microspheres have recently been produced by an entirely different method. Our DNA based approach self-assembles clusters with additional degrees of freedom associated with particle permutation. We demonstrate that in the non-equ…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby restricting their use as model systems. We overcome this limitation by assembling reconfigurable colloidal molecules from silica particles functionalized with mobile DNA linkers in high yields. We achieve this by steering the self-assembly pathway towards the formation of finite-sized clusters by employing high number ratios of particles functionalized with comple…
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of complex architectures. The assembly can be directed via solid `patchy' particles with prescribed geometries to make, for example, a colloidal diamond. We demonstrate here that the nanoscale ordering of individual molecular linkers can combine to program the structure of microscopic assemblies. Specifically, we experimentally show that covering initially isotrop…
Recent years have seen a surge of interest in nanopores because such structures show a strong potential for characterizing nanoparticles, proteins, DNA, and even single molecules. These systems have been extensively studied in experiment as well as by all-atom and coarse-grained simulations, with a strong focus on DNA translocation. However, the equally interesting problem of particle characterization using nanopores has received far less attention. Here, we theoretically investigate the translocation of a nanoparticle through a conical nanocapillary. We use a model based on numerically solvin…
Recent surveys have shown that the number of nanoparticle-based formulations actually used at the clinical level is significantly lower than expected a decade ago. One reason for this is that the nanoparticle physicochemical properties fall short for handling the complexity of biological environments and for preventing nonspecific protein adsorption. In this study, we address the issue of the interactions of plasma proteins with polymer coated surfaces. To this aim, we use a non-covalent grafting-to method to functionalize iron oxide sub-10 nm nanoparticles and iron oxide flat substrates, and …
Star polymers with magnetically functionalized end groups are presented as a novel polymeric system whose morphology, self-aggregation, and orientation can easily be tuned by exposing these macromolecules simultaneously to an external magnetic field and to shear forces. Our investigations are based on a specialized simulation technique which faithfully takes into account the hydrodynamic interactions of the surrounding, Newtonian solvent. We find that the combination of magnetic field (including both strength and direction) and shear rate controls the mean number of magnetic clusters, which in…
Most binary superlattices created using DNA functionalization or other approaches rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized micron-sized particles (DFPs), and employ a strategy that leverages the tunable disparity in interparticle interactions, and thus enthalpic driving forces, to open new avenues for design of binary superlattices that do not rely on the ability to tune particle size (i.e., entropic driving forces). Our strategy employs tailored blends of complementary strands o…
Downsizing microswimmers to the nanoscale, and using light as an externally controlled fuel, are two important goals within the field of active matter. Here we demonstrate using all-atom molecular dynamics simulations that solvation relaxation, the solvent dynamics induced after visible light electronic excitation of a fluorophore, can be used to propel nanoparticles immersed in polar solvents. We show that fullerenes functionalized with fluorophore molecules in liquid water exhibit substantial enhanced mobility under external excitation, with a propulsion speed proportional to the power dissi…
The specificity and thermal reversibility of DNA interactions have enabled the self-assembly of crystal structures, self-replicating materials and colloidal molecules. Grafting DNA onto liquid interfaces of emulsions leads to exciting new architectural possibilities due to the mobility of the DNA ligands and the patches they form between bound droplets. Here we show that the size and number of these adhesion patches (valency) can be controlled. Valence 2 leads to flexible polymers of emulsion droplets, while valence above 4 leads to rigid droplet networks. A simple thermodynamic model quantita…
Engineering shape and interactions of nanoscopic building blocks allows for the assembly of rationally designed macroscopic three-dimensional (3D) materials with spatial accuracy inaccessible to top-down fabrication methods. Owing to its sequence-specific interaction, DNA is often used as selective binder to connect metallic nanoparticles into highly ordered lattices. Moreover, 3D crystals assembled entirely from DNA have been proposed and implemented with the declared goal to arrange guest molecules in predefined lattices. This requires design schemes that provide high rigidity and sufficient…
Surface plasmon resonances generated in metallic nanostructures can be utilized to tailor electromagnetic fields. The precise spatial arrangement of such structures can result in surprising optical properties that are not found in any naturally occurring material. Here, the designed activity emerges from collective effects of singular components equipped with limited individual functionality. Top-down fabrication of plasmonic materials with a predesigned optical response in the visible range by conventional lithographic methods has remained challenging due to their limited resolution, the comp…
