Diffusion, viscosity, and linear rheology of valence-limited disordered fluids.

We numerically investigate the dynamics and linear rheology of disordered systems made of patchy particles, focusing on the role of valence, temperature, and bonding mechanism. We demonstrate that the dynamics is enslaved to bonding, giving rise to an activated behavior at low temperatures. By independently computing the diffusion constant and the viscosity from the simulations, we also confirm the validity of the Stokes-Einstein relation in valence-limited systems, with two caveats: (i) the diffusion constant requires a finite-size correction, at least at the intermediate density we investigate, and (ii) there is the onset of a breakdown that appears at the lowest temperatures considered. Finally, our results show that the storage and loss moduli of mixtures of divalent and M-valent particles exhibit an apparent power-law dependence on frequency, hinting at the possibility of using the composition to finely tune the rheological response of these materials. Our results compare well with literature experimental data on valence-limited DNA nanostars. In addition, the wealth of data we present and analyze here will help develop and test theoretical frameworks aimed at describing the dynamics of flexible limited-valence particles that self-assemble into disordered networks.

Two-step deswelling in the Volume Phase Transition of thermoresponsive microgels.

Thermoresponsive microgels are one of the most investigated types of soft colloids, thanks to their ability to undergo a Volume Phase Transition (VPT) close to ambient temperature. However, this fundamental phenomenon still lacks a detailed microscopic understanding, particularly regarding the presence and the role of charges in the deswelling process. This is particularly important for the widely used poly(N-isopropylacrylamide)-based microgels, where the constituent monomers are neutral but charged groups arise due to the initiator molecules used in the synthesis. Here, we address this point combining experiments with state-of-the-art simulations to show that the microgel collapse does not happen in a homogeneous fashion, but through a two-step mechanism, entirely attributable to electrostatic effects. The signature of this phenomenon is the emergence of a minimum in the ratio between gyration and hydrodynamic radii at the VPT. Thanks to simulations of microgels with different cross-linker concentrations, charge contents, and charge distributions, we provide evidence that peripheral charges arising from the synthesis are responsible for this behavior and we further build a universal master curve able to predict the two-step deswelling. Our results have direct relevance on fundamental soft condensed matter science and on applications where microgels are involved, ranging from materials to biomedical technologies.

Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks.

The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.

OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures.

OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and analysis interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user's specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the technical aspects of molecular simulation. The webserver is freely available at oxdna.org.

Designing Enhanced Entropy Binding in Single-Chain Nanoparticles.

Single-chain nanoparticles (SCNPs) are a new class of bio- and soft-matter polymeric objects in which a fraction of the monomers are able to form equivalently intra- or interpolymer bonds. Here we numerically show that a fully entropic gas-liquid phase separation can take place in SCNP systems. Control over the discontinuous (first-order) change-from a phase of independent diluted (fully-bonded) polymers to a phase in which polymers entropically bind to each other to form a (fully-bonded) polymer network-can be achieved by a judicious design of the patterns of reactive monomers along the polymer chain. Such a sensitivity arises from a delicate balance between the distinct entropic contributions controlling the binding.

Designer protein assemblies with tunable phase diagrams in living cells.

Protein self-organization is a hallmark of biological systems. Although the physicochemical principles governing protein-protein interactions have long been known, the principles by which such nanoscale interactions generate diverse phenotypes of mesoscale assemblies, including phase-separated compartments, remain challenging to characterize. To illuminate such principles, we create a system of two proteins designed to interact and form mesh-like assemblies. We devise a new strategy to map high-resolution phase diagrams in living cells, which provide self-assembly signatures of this system. The structural modularity of the two protein components allows straightforward modification of their molecular properties, enabling us to characterize how interaction affinity impacts the phase diagram and material state of the assemblies in vivo. The phase diagrams and their dependence on interaction affinity were captured by theory and simulations, including out-of-equilibrium effects seen in growing cells. Finally, we find that cotranslational protein binding suffices to recruit a messenger RNA to the designed micron-scale structures.

Hydrodynamic instability and flow reduction in polymer brush coated channels.

A polymer brush is a passive medium. At equilibrium the knowledge of its chemical composition and thickness is enough for a full system characterization. However, when the brush is exposed to fluid flow it reveals a much more intriguing nature, in which filamentous protrusions and the way they interact among themselves and with the surrounding fluid are of outmost importance. Here we investigate such a rich behavior via numerical simulations. We focus on the brush hydrodynamic response at low Reynolds numbers, observing a significant fluid flow reduction inside a polymer-brush coated channel. We find that the reduction of the flow inside the channel is significantly larger than what would happen if the brush effect consisted only in reducing the effective channel width. This amplified reduction is understood as being due to the morphological instability of the brush-liquid interface which is shown to have an elastic origin: the mechanical stress acting on the brush due to the imposed flow is partially released by the interface modulation. In turn, this modulation dissipates more energy than a flat interface in the surrounding fluid, causing a reduction of flow velocity. Our results and interpretations provide an explanation for recent experimental measurements.

TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami.

Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc.

q-Independent Slow Dynamics in Atomic and Molecular Systems.

Investigating million-atom systems for very long simulation times, we demonstrate that the collective density-density correlation time (τ_{α}) in simulated supercooled water and silica becomes wave-vector independent (q^{0}) when the probing wavelength is several times larger than the interparticle distance. The q independence of the collective density-density correlation functions, a feature clearly observed in light-scattering studies of some soft-matter systems, is thus a genuine feature of many (but not all) slow-dynamics systems, either atomic, molecular, or colloidal. Indeed, we show that when the dynamics of the density fluctuations includes particle-type diffusion, as in the case of the Lennard-Jones binary-mixture model, the q^{0} regime does not set in and the relaxation time continues to scale as τ_{α}∼q^{-2} even at small q.

Numerical modelling of non-ionic microgels: an overview.

Microgels are complex macromolecules. These colloid-sized polymer networks possess internal degrees of freedom and, depending on the polymer(s) they are made of, can acquire a responsiveness to variations of the environment (temperature, pH, salt concentration, etc.). Besides being valuable for many practical applications, microgels are also extremely important to tackle fundamental physics problems. As a result, these last years have seen a rapid development of protocols for the synthesis of microgels, and more and more research has been devoted to the investigation of their bulk properties. However, from a numerical standpoint the picture is more fragmented, as the inherently multi-scale nature of microgels, whose bulk behaviour crucially depends on the microscopic details, cannot be handled at a single level of coarse-graining. Here we present an overview of the methods and models that have been proposed to describe non-ionic microgels at different length-scales, from the atomistic to the single-particle level. We especially focus on monomer-resolved models, as these have the right level of details to capture the most important properties of microgels, responsiveness and softness. We suggest that these microscopic descriptions, if realistic enough, can be employed as starting points to develop the more coarse-grained representations required to investigate the behaviour of bulk suspensions.

Numerical insights on ionic microgels: structure and swelling behaviour.

Recent progress has been made in the numerical modelling of neutral microgel particles with a realistic, disordered structure. In this work we extend this approach to the case of co-polymerised microgels where a thermoresponsive polymer is mixed with acidic groups. We compare the cases where counterions directly interact with microgel charges or are modelled implicitly through a Debye-Hückel description. We do so by performing extensive numerical simulations of single microgels across the volume phase transition (VPT) varying the temperature and the fraction of charged monomers. We find that the presence of charges considerably alters the microgel structure, quantified by the monomer density profiles and by the form factors of the microgels, particularly close to the VPT. We observe significant deviations between the implicit and explicit models, with the latter comparing more favourably to available experiments. In particular, we observe a shift of the VPT temperature to larger values as the amount of charged monomers increases. We also find that below the VPT the microgel-counterion complex is almost neutral, while it develops a net charge above the VPT. Interestingly, under these conditions the collapsed microgel still retains a large amount of counterions inside its structure. Since these interesting features cannot be captured by the implicit model, our results show that it is crucial to explicitly include the counterions in order to realistically model ionic thermoresponsive microgels.

On the effect of the thermostat in non-equilibrium molecular dynamics simulations.

The numerical investigation of the statics and dynamics of systems in non-equilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium systems can be successfully adapted to out-of-equilibrium cases. This is especially true for thermostats. Indeed, even though thermostats developed to work under equilibrium conditions sometimes display good agreement with rheology experiments, their performance rapidly degrades beyond weak dissipation and small shear rates. Here we focus on gauging the relative performances of three thermostats, Langevin, dissipative particle dynamics, and Bussi-Donadio-Parrinello under varying parameters and external conditions. We compare their effectiveness by looking at different observables and clearly demonstrate that choosing the right thermostat (and its parameters) requires a careful evaluation of, at least, temperature, density and velocity profiles. We also show that small modifications of the Langevin and DPD thermostats greatly enhance their performance in a wide range of parameters.

How to simulate patchy particles⋆.

Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed significantly to our understanding of the behaviour of patchy particles, but, although simple in principle, advanced simulation techniques are often required to sample the low temperatures and long time-scales associated with their self-assembly behaviour. In this work we review the most popular simulation techniques that have been used to study patchy particles, with a special focus on Monte Carlo methods. We cover many of the tools required to simulate patchy systems, from interaction potentials to biased moves, cluster moves, and free-energy methods. The review is complemented by an educationally oriented Monte Carlo computer code that implements all the techniques described in the text to simulate a well-known tetrahedral patchy particle model.

Connectivity, dynamics, and structure in a tetrahedral network liquid.

We report a detailed computational study by Brownian dynamics simulations of the structure and dynamics of a liquid of patchy particles which forms an amorphous tetrahedral network upon decreasing the temperature. The highly directional particle interactions allow us to investigate the system connectivity by discriminating the total set of particles into different populations according to a penta-modal distribution of bonds per particle. With this methodology we show how the particle bonding process is not randomly independent but it manifests clear bond correlations at low temperatures. We further explore the dynamics of the system in real space and establish a clear relation between particle mobility and particle connectivity. In particular, we provide evidence of anomalous diffusion at low temperatures and reveal how the dynamics is affected by the short-time hopping motion of the weakly bounded particles. Finally we widely investigate the dynamics and structure of the system in Fourier space and identify two quantitatively similar length scales, one dynamic and the other static, which increase upon cooling the system and reach distances of the order of few particle diameters. We summarize our findings in a qualitative picture where the low temperature regime of the viscoelastic liquid is understood in terms of an evolving network of long time metastable cooperative domains of particles.

Free energy calculations for rings and chains formed by dipolar hard spheres.

We employ a method based on Monte Carlo grand-canonical simulations to precisely calculate partition functions of non-interacting chains and rings formed by dipolar hard spheres (DHS) at low temperature. The extended low temperature region offered by such cluster calculations, compared to what had been previously achieved with standard simulations, opens up the possibility of exploring a part of the DHS phase diagram which was inaccessible before. The reported results offer the unique opportunity of verifying well-established theoretical models based on the ideal gas of cluster approximation in order to clarify their range of validity. They also provide the basis for future studies in which cluster-cluster interactions will be included.

Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules.

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 building blocks and in nature, where the isotropy of interactions is often a zero-th order description of the complicated reality. In this review, we span a vast range of systems characterized by limited bonding valence, from patchy colloids of new generation to polymer-based functionalized nanoparticles, DNA-based systems and proteins, and describe how the interaction patterns of the single building blocks can be designed to tailor the properties of the target final structures.

Communication: Re-entrant limits of stability of the liquid phase and the Speedy scenario in colloidal model systems.

A re-entrant gas-liquid spinodal was proposed as a possible explanation of the apparent divergence of the compressibility and specific heat off supercooling water. Such a counter-intuitive possibility, e.g., a liquid that becomes unstable to gas-like fluctuations on cooling at positive pressure, has never been observed, neither in real substances nor in off-lattice simulations. More recently, such a re-entrant scenario has been dismissed on the premise that the re-entrant spinodal would collide with the gas-liquid coexisting curve (binodal) in the pressure-temperature plane. Here we study, numerically and analytically, two previously introduced one-component patchy particle models that both show (i) a re-entrant limit of stability of the liquid phase and (ii) a re-entrant binodal, providing a neat in silico (and in charta) realization of such unconventional thermodynamic scenario.

A comparison between parallelization approaches in molecular dynamics simulations on GPUs.

We test the relative performances of two different approaches to the computation of forces for molecular dynamics simulations on graphics processing units. A "vertex-based" approach, where a computing thread is started per particle, is compared to an "edge-based" approach, where a thread is started per each potentially non-zero interaction. We find that the former is more efficient for systems with many simple interactions per particle while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent graphics processing unit technology, we predict that, if the current trend of increasing the number of processing cores--as opposed to their computing power--remains, the "edge-based" approach will gradually become the most efficient choice in an increasing number of cases.

How soft repulsion enhances the depletion mechanism.

We investigate binary mixtures of large colloids interacting through soft potentials with small, ideal depletants. We show that softness has a dramatic effect on the resulting colloid-colloid effective potential when the depletant-to-colloid size ratio q is small, with significant consequences on the colloidal phase behaviour. We provide an exact relationship that allows us to obtain the effective pair potential for any type of colloid-depletant interaction in the case of ideal depletants, without having to rely on complicated and expensive full-mixture simulations. We also show that soft repulsion among depletants further enhances the tendency of colloids to aggregate. Our theoretical and numerical results demonstrate that--in the limit of small q--soft mixtures cannot be mapped onto hard systems and hence soft depletion is not a mere extension of the widely used Asakura-Oosawa potential.

Temperature-induced structural transitions in self-assembling magnetic nanocolloids.

With the help of a unique combination of density functional theory and computer simulations, we discover two possible scenarios, depending on concentration, for the hierarchical self-assembly of magnetic nanoparticles on cooling. We show that typically considered low temperature clusters, i.e. defect-free chains and rings, merge into more complex branched structures through only three types of defects: four-way X junctions, three-way Y junctions and two-way Z junctions. Our accurate calculations reveal the predominance of weakly magnetically responsive rings cross-linked by X defects at the lowest temperatures. We thus provide a strategy to fine-tune magnetic and thermodynamic responses of magnetic nanocolloids to be used in medical and microfluidics applications.