Polymer Thermophoresis by Mesoscale Simulations.

We employ mesoscopic simulations to study the thermophoretic motion of polymers in a solvent via multiparticle collision dynamics (MPCD). As the usual solvent-monomer collision rules employed in MPCD involving polymers fail to cause thermophoresis, we extend the technique by introducing explicit solvent-monomer interactions, while the solvent molecules remain ideal with respect to one another. We find that with purely repulsive polymer-solvent interaction, the polymer exhibits thermophilic behavior, whereas to display thermophobic behavior, the polymer-solvent potential requires the presence of attractions between solvent particles and monomers, in accordance with previous experimental findings.

Influence of the rigidity of the backbone and arms on the dynamical and conformational properties of the comb polymer in shear flow.

The dynamical and conformational properties of the comb polymer with various rigidities of the backbone and arms in steady shear flow are studied by using a hybrid mesoscale simulation approach that combines multiparticle collision dynamics with standard molecular dynamics. First, during the process of the comb polymer undergoing periodic tumbling motion, we find that the rigidity of the arms always promotes the tumbling motion of the comb polymer, but the rigidity of the backbone shifts from hindering to promoting it with increasing the rigidity of the arms. In addition, the comb polymer transitions from vorticity tumbling to gradient tumbling with the increase in shear rate.

Core-shell nanogels: the effects of morphology, electro- and magnetostatic interactions.

We study the influence of core-shell morphology on the structural characteristics of nanogels. Using computer simulations, we examine three different types of systems, distinguished by their intermonomer interactions: those with excluded volume only; those with charged monomers and excluded volume; and those with excluded volume combined with a certain number of magnetised nanoparticles incorporated within the nanogel. We observe that if the polymers in the shell are short and dense, they tend to penetrate the core.

Interpenetrated and Bridged Nanocylinders from Self-Assembled Star Block Copolymers.

The design of functional polymeric materials with tunable response requires a synergetic use of macromolecular architecture and interactions. Here, we combine experiments with computer simulations to demonstrate how physical properties of gels can be tailored at the molecular level, using star block copolymers with alternating block sequences as a paradigm. Telechelic star polymers containing attractive outer blocks self-assemble into soft patchy nanoparticles, whereas their mirror-image inverted architecture with inner attractive blocks yields micelles.

Adsorption characteristics of Janus tadpole polymers.

The shape of Janus particles is directly connected to their adsorption behavior. Janus tadpole polymers offer a unique topological architecture that includes competition between entropic, enthalpic, and topological terms in the adsorption free energy; accordingly, non-trivial adsorption behavior patterns are expected. We study the surface adsorption of Janus tadpole polymers by means of Monte Carlo simulations, finding that, depending on which part of the tadpole polymers is preferentially adsorbing on the surface, very different types of behavior for both the adsorbed polymeric phase and of the brush arise.

Reply to the 'Comment on "Effects of topological constraints on linked ring polymers in solvents of varying quality"' by M. Tsige and H. Guo, , 2024, , DOI: 10.1039/D3SM01614E.

In the preceding Comment, Drs Tsige and Guo compare their findings about the -temperatures of linear chains, ring polymers and poly[]catenanes with those of previous work by us [Z. A. Dehaghani, I.

Supercoiled ring polymers under shear flow.

We apply monomer-resolved computer simulations of supercoiled ring polymers under shear, taking full account of the hydrodynamic interactions, accompanied, in parallel, by simulations in which these are switched off. The combination of bending and torsional rigidities inherent in these polymers, in conjunction with hydrodynamics, has a profound impact on their flow properties. In contrast to their flexible counterparts, which dramatically deform and inflate under shear [Liebetreu , 2020, , 4], supercoiled rings undergo only weak changes in their overall shape and they display both a reduced propensity to tumbling (at fixed Weissenberg number) and a much stronger orientational resistance with respect to their flexible counterparts.

Engineering Ultrasoft Interactions in Stiff All-DNA Dendrimers by Site-Specific Control of Scaffold Flexibility.

A combined experimental and theoretical study of the structural correlations in moderately concentrated suspensions of all-DNA dendrimers of the second generation (G2) with controlled scaffold rigidity is reported here. Small-angle X-ray scattering experiments in concentrated aqueous saline solutions of stiff all-DNA G2 dendritic constructs reveal a novel anomalous liquid-like phase behavior which is reflected in the calculated structure factors as a two-step increase at low scattering wave vectors. By developing a new design strategy for adjusting the particle's internal flexibility based on site-selective incorporation of single-stranded DNA linkers into the dendritic scaffold, it is shown that this unconventional type of self-organization is strongly contingent on the dendrimer's stiffness.

Glassy phases of the Gaussian core model.

We present results from molecular dynamics simulations exploring the supercooled dynamics of the Gaussian Core Model in the low- and intermediate-density regimes. In particular, we analyse the transition from the low-density hard-sphere-like glassy dynamics to the high-density one. The dynamics at low densities is well described by the caging mechanism, giving rise to intermittent dynamics.

Mixing Linear Polymers with Rings and Catenanes: Bulk and Interfacial Behavior.

We derive and parameterize effective interaction potentials between a multitude of different types of ring polymers and linear chains, varying the bending rigidity and solvent quality for the former species. We further develop and apply a density functional treatment for mixtures of both disconnected (chain-ring) and connected (chain-polycatenane) mixtures of the same, drawing coexistence binodals and exploring the ensuing response functions as well as the interface and wetting behavior of the mixtures. We show that worsening of the solvent quality for the rings brings about a stronger propensity for macroscopic phase separation in the linear-polycatenane mixtures, which is predominantly of the demixing type between phases of similar overall particle density.

Cluster Formation in Solutions of Polyelectrolyte Rings.

We use molecular dynamics simulations to explore concentrated solutions of semiflexible polyelectrolyte ring polymers, akin to the DNA mini-circles, with counterions of different valences. We find that the assembly of rings into nanoscopic cylindrical stacks is a generic feature of the systems, but the morphology and dynamics of such a cluster can be steered by the counterion conditions. In general, a small addition of trivalent ions can stabilize the emergence of clusters due to the counterion condensation, which mitigates the repulsion between the like-charged rings.

Multi-particle collision dynamics for a coarse-grained model of soft colloids applied to ring polymers.

The simulation of polymer solutions often requires the development of methods that accurately include hydrodynamic interactions. Resolution on the atomistic scale is too computationally expensive to cover mesoscopic time and length scales on which the interesting polymer phenomena are observed. Therefore, coarse-graining methods have to be applied.

Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency.

A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles.

To thread or not to thread? Effective potentials and threading interactions between asymmetric ring polymers.

We use computer simulations to study a system of two unlinked ring polymers, whose length and bending stiffness are systematically varied. We derive the effective potentials between the rings, calculate the areas of minimal surfaces of the same, and characterize the threading between them. When the two rings are of the same kind, threading of a one ring through the surface of the other is immanent for small ring-ring separations.

Electroosmotic Flow Induced Lift Forces on Polymer Chains in Nanochannels.

A major objective of research in nanofluidics is to achieve better selectivity in manipulating the fluxes of nano-objects and in particular of biopolymers. Numerical simulations allow one to better understand the physical mechanisms at play in such situations. We performed hybrid mesoscale simulations to investigate the properties of polymers under flows in slit pores at the nanoscale.

Validity of Effective Potentials in Crowded Solutions of Linear and Ring Polymers with Reversible Bonds.

We perform simulations to compute the effective potential between the centers-of-mass of two polymers with reversible bonds. We investigate the influence of the topology on the potential by employing linear and ring backbones for the precursor (unbonded) polymer, finding that it leads to qualitatively different effective potentials. In the linear and ring cases the potentials can be described by Gaussians and generalized exponentials, respectively.

Glass quantization of the Gaussian core model.

We use the replica method to study the dynamical glass transition of the Gaussian core model, a system of ultrasoft repulsive spheres interacting via a Gaussian potential, focusing on low temperatures and low-to-moderate densities. At constant temperature, an amorphous glassy state is entered upon a first compression but this glass melts as the density is further increased. In addition to this reentrant transition, a second, smooth transition is discovered between a continuous and a discretized glass.

Active Topological Glass Confined within a Spherical Cavity.

We study active topological glass under spherical confinement, allowing us to exceed the chain lengths simulated previously and determine the critical exponents of the arrested conformations. We find a previously unresolved "tank-treading" dynamic mode of active segments along the ring contour. This mode can enhance active-passive phase separation in the state of active topological glass when both diffusional and conformational relaxation of the rings are significantly suppressed.

Blunt-End Driven Re-entrant Ordering in Quasi Two-Dimensional Dispersions of Spherical DNA Brushes.

We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids coated with ultralong double-stranded DNA (dsDNA) fragments reveal nonmonotonic particle shrinking, aggregation, and re-entrant ordering. Theory and simulations show that aggregation and re-entrant ordering arise from the combined effect of shrinking, which is induced by the osmotic pressure exerted by the counterions absorbed in neighbor brushes and of a short-range attractive interaction competing with electrostatic repulsion.

Self assembling cluster crystals from DNA based dendritic nanostructures.

Cluster crystals are periodic structures with lattice sites occupied by several, overlapping building blocks, featuring fluctuating site occupancy, whose expectation value depends on thermodynamic conditions. Their assembly from atomic or mesoscopic units is long-sought-after, but its experimental realization still remains elusive. Here, we show the existence of well-controlled soft matter cluster crystals.

Effect of softness on glass melting and re-entrant solidification in mixtures of soft and hard colloids.

We present a systematic investigation of the structure and dynamic properties of model soft-hard colloidal mixtures. Results of a coarse-grained theoretical model are contrasted with rheological data, where the soft and hard colloids are mimicked by large star polymers with high functionality as the soft component and smaller stars with ultrahigh functionality as the hard one. Previous work by us revealed the recovery of the ergodicity of glassy soft star solutions and subsequent arrested phase separation and re-entrant solid transition upon progressive addition of small hard depletants.

Multiscale Approaches for Confined Ring Polymer Solutions.

We apply a hierarchy of multiscale modeling approaches to investigate the structure of ring polymer solutions under planar confinement. In particular, we employ both monomer-resolved (MR-DFT) and a coarse-grained (CG-DFT) density functional theories for fully flexible ring polymers, with the former based on a flexible tangent hard-sphere model and the latter based on an effective soft-colloid representation, to elucidate the ring polymer organization within slits of variable width in different concentration regimes. The predicted monomer and polymer center-of-mass densities in confinement, as well as the surface tension at the solution-wall interface, are compared to explicit molecular dynamics (MD) simulations.

Grafting density induced reentrant disorder-order-disorder transition in planar di-block copolymer brushes.

By means of multiscale molecular simulation, we show that solvophilic-solvophobic AB diblock copolymer brushes in the semi-dilute regime present a re-entrant disorder/order/disorder transition. The latter is fully controllable through two parameters: the grafting density and the solvophobic to solvophilic ratio of the tethered macromolecules. Upon increasing density, chains first aggregate into patches, then further order into a crystalline phase and finally melt into a disordered phase.