arXiv subjects

Ran Ni

Publications and source records attributed to Ran Ni.

51 records · Page 3Linked to original sources

arXiv2018

Entropy stabilizes floppy crystals of mobile DNA-coated colloids

Grafting linkers with open ends of complementary single-stranded DNA makes a flexible tool to tune interactions between colloids,which facilitates the design of complex self-assembly structures. Recently, it has been proposed to coat colloids with mobile DNA linkers, which alleviates kinetic barriers without high-density grafting, and also allows the design of valency without patches.However, the self-assembly mechanism of this novel system is poorly understood.Using a combination of theory and simulation, we obtain phase diagrams forthe system in both two and three dimensional spaces, and find stable floppy squareand CsCl crystals when the binding strength is strong, even in the infinite bindingstrength limit. We demonstrate that these floppy phases are stabilized by vibrational entropy, and "floppy" modes play an important role in stabilizing the floppy phases for the infinite binding strength limit. This special entropic effect in the self-assembly of mobile DNA-coated colloids is very different from conventional molecular self-assembly, and it offers new axis to help design novel functional materials using mobile DNA-coated colloids.

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arXiv2017

Driving dynamic colloidal assembly using eccentric self-propelled colloids

Designing protocols to dynamically direct the self-assembly of colloidal particles has become an important direction in soft matter physics because of the promising applications in fabrication of dynamic responsive functional materials. Here using computer simulations, we found that in the mixture of passive colloids and eccentric self-propelled active particles, when the eccentricity and self-propulsion of active particles are high enough, the eccentric active particles can push passive colloids to form a large dense dynamic cluster, and the system undergoes a novel dynamic demixing transition. Our simulations show that the dynamic demixing occurs when the eccentric active particles move much faster than the passive particles such that the dynamic trajectories of different active particles can overlap with each other while passive particles are depleted from the dynamic trajectories of active particles. Our results suggest that this is in analogy to the entropy driven demixing in colloid-polymer mixtures, in which polymer random coils can overlap with each other while deplete the colloids. More interestingly, we find that by fixing the passive colloid composition at certain value, with increasing the density, the system undergoes an intriguing re-entrant mixing, and the demixing only occurs within certain intermediate density range. This suggests a new way of designing active matter to drive the self-assembly of passive colloids and fabricate dynamic responsive materials.

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arXiv2017

Role of local assembly in the hierarchical crystallization of associating colloidal hard hemispheres

Hierarchical self-assembly consisting of local associations of simple building-blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using computer simulations, we study a simple model system consisting of associating colloidal hemispheres crystallizing into face-centered-cubic crystals comprised of spherical dimers of hemispheres, focusing on the effect of dimer formation on the hierarchical crystallization. We found that besides assisting the crystal nucleation because of increasing the symmetry of building-blocks, the association between hemispheres can also induce both re-entrant melting and re-entrant crystallization depending on the range of interaction. Especially when the interaction is highly sticky, we observe a novel re-entrant crystallization of identical crystals, which melt only in certain temperature range. This offers a new axis in fabricating responsive crystalline materials by tuning the fluctuation of local association.

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arXiv2017

Reply to "Failure to replicate long-range tunable attractions in colloidal system"

An arxiv paper, ref. [1] by Cao et al., claimed that the tunable attraction reported in our ref. [2] could not be detected. Ref. [1] was submitted to Nature in Apr. 2016 as a Comment on our ref. [2]. Our reply in May 2016 responded to ref. [1] and was reviewed by the editor of Nature and an external referee. Ref. [1] was rejected by Nature in Aug. 2016. We provide our reply, which answers all of the criticisms in ref. [1], in Appendix I. The main text contains a brief reply to the main criticisms.

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arXiv2015

The competition between surface adsorption and folding of fibril-forming polypeptides

Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse grained model, we systematically studied the folding and adsorption behavior of a $β$-roll forming polypeptide. We find that there are two different folding pathways depending on the temperature: (i) at low temperature, the polypeptide folds in solution into a $β$-roll before adsorbing onto the attractive surface, (ii) at higher temperature, the polypeptide first adsorbs in a disordered state, and folds while on the surface. The folding temperature increases with increasing attraction, as the folded $β$-roll is stabilized by the surface. Surprisingly, further increasing the attraction lowers the folding temperature again, as strong attraction also stabilizes the adsorbed disordered state, which competes with folding of the polypeptide. Our results suggest that to enhance the folding, one should use a weakly attractive surface. They also explain the recent experimental observation of the non-monotonic effect of charge on the fibril formation on an oppositely charged surface [C. Charbonneau, et al., ACS Nano, 8, 2328 (2014)].

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arXiv2014

Tunable long range forces mediated by self-propelled colloidal hard spheres

Using Brownian dynamics simulations, we systematically study the effective interaction between two parallel hard walls in a 2D suspension of self-propelled (active) colloidal hard spheres, and we find that the effective force between two hard walls can be tuned from a long range repulsion into a long range attraction by changing the density of active particles. At relatively high densities, the active hard spheres can form a dynamic crystalline bridge, which induces a strong oscillating long range dynamic wetting repulsion between the walls. With decreasing density, the dynamic bridge gradually breaks, and an intriguing long range dynamic depletion attraction arises. A similar effect occurs in a quasi-2D suspension of self-propelled colloidal hard spheres by changing the height of the confinement. Our results open up new possibilities to manipulate the motion and assembly of microscopic objects by using active matter.

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arXiv2014

Crystallizing hard-sphere glasses by doping with active particles

Crystallization and vitrification are two different routes to form a solid. Normally these two processes suppress each other, with the glass transition preventing crystallization at high density (or low temperature). This is even true for systems of colloidal hard spheres, which are commonly used as building blocks for novel functional materials with potential applications, e.g. photonic crystals. By performing Brownian dynamics simulations of glassy systems consisting of mixtures of active and passive hard spheres, we show that the crystallization of such hard-sphere glasses can be dramatically promoted by doping the system with small amounts of active particles. Surprisingly, even hard-sphere glasses of packing fraction up to $ϕ= 0.635$ crystallize, which is around $0.5\%$ below the random close packing at $ϕ\simeq 0.64$. Our results suggest a novel way of fabricating crystalline materials from (colloidal) glasses. This is particularly important for materials that get easily kinetically trapped in glassy states, and crystal nucleation hardly occurs.

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arXiv2013

Pushing the glass transition towards random close packing using self-propelled hard spheres

Although the concept of random close packing with an almost universal packing fraction of ~ 0.64 for hard spheres was introduced more than half a century ago, there are still ongoing debates. The main difficulty in searching the densest packing is that states with packing fractions beyond the glass transition at ~ 0.58 are inherently non-equilibrium systems, where the dynamics slows down with a structural relaxation time diverging with density; hence, the random close packing is inaccessible. Here we perform simulations of self-propelled hard spheres, and we find that with increasing activity the relaxation dynamics can be sped up by orders of magnitude. The glass transition shifts to higher packing fractions upon increasing the activity, allowing the study of sphere packings with fluid-like dynamics at packing fractions close to random close packing. Our study opens new possibilities of investigating dense packings and the glass transition in systems of hard particles.

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arXiv2013

Interplay between folding and assembly of fibril-forming polypeptides

Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this self-assembly as a function of temperature and hydrophobicity of the residues on the outside of the building block. We find the self-assembly can occur via two different pathways - a random aggregation-folding route, and a templated-folding process - thus indicating a strong coupling between folding and assembly. The simulation results can explain experimental evidence that assembly through stacking of folded building blocks is rarely observed, at the experimental concentrations. The model thus provides a generic picture of hierarchical fibril formation.

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arXiv2012

Entropy-Driven Phase Transitions in Colloidal Systems

This thesis can be divided into two independent parts. In the first part of this thesis, we focus on studying the kinetic pathways of nucleation in colloidal systems. In Chapter 2, we briefly introduce the relevant theory of nucleation, i.e., classic nucleation theory. Then in Chapter 3, we investigate the crystal nucleation in the "simplest" model system for colloids, i.e., the monodisperse hard-sphere system, by using three different simulation methods, i.e., molecular dynamics, forward flux sampling and umbrella sampling simulations. Subsequently, we apply our simulation methods to a more realistic system of colloidal hard spheres in Chapter 4. Furthermore, we study the nucleation in a variety of systems consisting of hard particles, i.e., hard dumbbells (Chapter 5), hard rods (Chapter 6), hard colloidal polymers (Chapter 7) and binary hard-sphere mixtures (Chapter 8). In the second part of this thesis, we study the phase behavior of several colloidal systems. In Chapter 9, we study the equilibrium phase diagram of colloidal hard superballs whose shape interpolates from cubes to octahedra via spheres. We investigate the micellization of asymmetric patchy dumbbells induced by the depletion attraction in Chapter 10.

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arXiv2012

Effect of bond length fluctuations on crystal nucleation of hard bead chains

We study the spontaneous nucleation and crystallization of linear and cyclic chains of flexibly connected hard spheres using extensive molecular dynamics simulations. To this end, we present a novel event-driven molecular dynamics simulation method, which is easy to implement and very efficient. We find that the nucleation rates are predominately determined by the number of bonds per sphere in the system, rather than the precise details of the chain topology, chain length, and polymer composition. O ur results thus show that the crystal nucleation rate of bead chains can be enhanced by adding monomers to the system. In addition, we find that the resulting crystal n uclei contain significantly more face-centered-cubic than hexagonal-close-packed ordered particles. More surprisingly, the resulting crystal nuclei possess a range of crystal morphologies including structures with a five-fold symmetry.

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arXiv2012

Phase diagram of colloidal hard superballs: from cubes via spheres to octahedra

The phase diagram of colloidal hard superballs, of which the shape interpolates between cubes and octahedra via spheres, is determined by free-energy calculations in Monte Carlo simulations. We discover not only a stable face-centered cubic (fcc) plastic crystal phase for near-spherical particles, but also a stable body-centered cubic (bcc) plastic crystal close to the octahedron shape, and in fact even coexistence of these two plastic crystals with a substantial density gap. The plastic fcc and bcc crystals are, however, unstable in the cube and octahedron limit, suggesting that the rounded corners of superballs play an important role in stablizing the rotator phases. In addition, we observe a two-step melting phenomenon for hard octahedra, in which the Minkowski crystal melts into a metastable bcc plastic crystal before melting into the fluid phase.

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arXiv2010

Crystal nucleation of colloidal hard dumbbells

Using computer simulations we investigate the homogeneous crystal nucleation in suspensions of colloidal hard dumbbells. The free energy barriers are determined by Monte Carlo simulations using the umbrella sampling technique. We calculate the nucleation rates for the plastic crystal and the aperiodic crystal phase using the kinetic prefactor as determined from event driven molecular dynamics simulations. We find good agreement with the nucleation rates determined from spontaneous nucleation events observed in event driven molecular dynamics simulations within error bars of one order of magnitude. We study the effect of aspect ratio of the dumbbells on the nucleation of plastic and aperiodic crystal phases and we also determine the structure of the critical nuclei. Moreover, we find that the nucleation of the aligned CP1 crystal phase is strongly suppressed by a high free energy barrier at low supersaturations and slow dynamics at high supersaturations.

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arXiv2010

Glassy dynamics, spinodal fluctuations, and the kinetic limit of hard-rod nucleation

Using simulations we identify three dynamic regimes in supersaturated isotropic fluid states of short hard rods: (i) for moderate supersaturations we observe nucleation of multi-layered crystalline clusters; (ii) at higher supersaturation, we find nucleation of small crystallites which arrange into long-lived locally favored structures that get kinetically arrested, while (iii) at even higher supersaturation the dynamic arrest is due to the conventional cage-trapping glass transition. For longer rods we find that the formation of the (stable) smectic phase out of a supersaturated isotropic state is strongly suppressed by an isotropic-nematic spinodal instability that causes huge spinodal-like orientation fluctuations with nematic clusters diverging in size. Our results show that glassy dynamics and spinodal instabilities set kinetic limits to nucleation in a highly supersaturated hard-rod fluids.

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arXiv2010

Crystal nucleation of hard spheres using molecular dynamics, umbrella sampling and forward flux sampling: A comparison of simulation techniques

Over the last number of years several simulation methods have been introduced to study rare events such as nucleation. In this paper we examine the crystal nucleation rate of hard spheres using three such numerical techniques: molecular dynamics, forward flux sampling and a Bennett-Chandler type theory where the nucleation barrier is determined using umbrella sampling simulations. The resulting nucleation rates are compared with the experimental rates of Harland and Van Megen [J. L. Harland and W. van Megen, Phys. Rev. E 55, 3054 (1997)], Sinn et al. [C. Sinn et al., Prog. Colloid Polym. Sci. 118, 266 (2001)] and Schatzel and Ackerson [K. Schatzel and B.J. Ackerson, Phys. Rev. E, 48, 3766 (1993)] and the predicted rates for monodisperse and 5% polydisperse hard spheres of Auer and Frenkel [S. Auer and D. Frenkel, Nature 409, 1020 (2001)]. When the rates are examined in long-time diffusion units, we find agreement between all the theoretically predicted nucleation rates, however, the experimental results display a markedly different behaviour for low supersaturation. Additionally, we examined the pre-critical nuclei arising in the molecular dynamics, forward flux sampling, and umbrella sampling simulations. The structure of the nuclei appear independent of the simulation method, and in all cases, the nuclei contain on average significantly more face-centered-cubic ordered particles than hexagonal-close-packed ordered particles.

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