arXiv subjects

Paul van der Schoot

Publications and source records attributed to Paul van der Schoot.

At least 37 records · Page 2Linked to original sources

arXiv2020

Dynamical Landau-de Gennes Theory for Electrically-Responsive Liquid Crystal Networks

Liquid crystal networks combine the orientational order of liquid crystals with the elastic properties of polymer networks, leading to a vast application potential in the field of responsive coatings, e.g., for haptic feedback, self-cleaning surfaces and static and dynamic pattern formation. Recent experimental work has further paved the way toward such applications by realizing the fast and reversible surface modulation of a liquid crystal network coating upon in-plane actuation with an AC electric field. Here, we construct a Landau-type theory for electrically-responsive liquid crystal networks and perform Molecular Dynamics simulations to explain the findings of these experiments and inform on rational design strategies. Qualitatively, the theory agrees with our simulations and reproduces the salient experimental features. We also provide a set of testable predictions: the aspect ratio of the nematogens, their initial orientational order when cross-linked into the polymer network and the cross-linking fraction of the network all increase the plasticization time required for the film to macroscopically deform. We demonstrate that the dynamic response to oscillating electric fields is characterized by two resonances, which can likewise be influenced by varying these parameters, providing an experimental handle to fine-tune device design.

cond-mat.soft↗

arXiv2019

Combined force-torque spectroscopy of proteins by means of multiscale molecular simulation

Assessing the structural properties of large proteins is important to gain an understanding of their function in, e.g., biological systems or biomedical applications. We propose a method to examine the mechanical properties of proteins subject to applied forces by means of multiscale simulation. We consider both stretching and torsional forces, which can be applied independently of each other. We apply torsional forces to a coarse-grained continuum model of the antibody protein immunoglobulin G (IgG) using Fluctuating Finite Element Analysis and identify the area of strongest deformation. This region is essential to the torsional properties of the molecule as a whole, as it represents the softest, most deformable domain. We subject this part of the molecule to torques and stretching forces on an atomistic level, using molecular dynamics simulations, in order to investigate its torsional properties. We calculate the torsional resistance as a function of the rotation of the domain, while subjecting it to various stretching forces. We learn how these obtained torsion profiles evolve with increasing stretching force and show that they exhibit torsion stiffening, which is in qualitative agreement with experimental findings. We argue that combining the torsion profiles for various stretching forces effectively results in a combined force-torque spectroscopy analysis, which may serve as a mechanical signature for the examined molecule.

physics.bio-ph↗

arXiv2019

Geometric percolation of hard nanorods: the interplay of spontaneous and externally induced uniaxial particle alignment

We present a numerical study on geometric percolation in liquid dispersions of hard slender colloidal particles subjected to an external orienting field. In the formulation and liquid-state processing of nanocomposite materials, the alignment of particles by external fields such as electric, magnetic or flow fields is practically inevitable, and often works against the emergence of large nanoparticle networks. Using continuum percolation theory in conjunction with Onsager theory, we investigate how the interplay between externally induced alignment and the spontaneous symmetry breaking of the uniaxial nematic phase affects cluster formation within nanoparticle dispersions. It is known that the enhancement of particle alignment by means of a density increase or an external field may result in the breakdown of an already percolating network. As a result, percolation can be limited to a small region of the phase diagram only. Here, we demonstrate that the existence and shape of such a "percolation island" in the phase diagram crucially depends on the connectivity length -- a critical distance defining direct connections between neighbouring particles. Deformations of this percolation island can lead to peculiar re-entrance effects, in which a system-spanning network forms and breaks down multiple times with increasing particle density.

cond-mat.soft↗

arXiv2019

Unusual geometric percolation of hard nanorods in the uniaxial nematic liquid crystalline phase

We investigate by means of continuum percolation theory and Monte Carlo simulations how spontaneous uniaxial symmetry breaking affects geometric percolation in dispersions of hard rod-like particles. If the particle aspect ratio exceeds about twenty, percolation in the nematic phase can be lost upon adding particles to the dispersion. This contrasts with percolation in the isotropic phase, where a minimum particle loading is always required to obtain system-spanning clusters. For sufficiently short rods, percolation in the uniaxial nematic mimics that of the isotropic phase, where the addition of particles always aids percolation. For aspect ratios between twenty and infinity, but not including infinity, we find re-entrance behavior: percolation in the low-density nematic may be lost upon increasing the amount of nanofillers but can be re-gained by the addition of even more particles to the suspension. Our simulation results for aspect ratios of 5, 10, 20, 50 and 100 strongly support our theoretical predictions, with almost quantitative agreement. We show that a new closure of the connectedness Ornstein-Zernike equation, inspired by Scaled Particle Theory, is more accurate than the Lee-Parsons closure that effectively describes the impact of many-body direct contacts.

cond-mat.soft↗

arXiv2019

Self-organisation of tip functionalised elongated colloidal particles

Weakly attractive interactions between the tips of rod-like colloidal particles affect their liquid-crystal phase behaviour due to a subtle interplay between enthalpy and entropy. Here, we employ molecular dynamics simulations on semi-flexible, repulsive bead-spring chains of which one of the two end beads attract each other. We calculate the phase diagram as a function of both the volume fraction of the chains and the strength of the attractive potential. We identify a large number of phases that include isotropic, nematic, smectic A, smectic B and crystalline states. For tip attraction energies lower than the thermal energy, our results are qualitatively consistent with experimental findings: we find that an increase of the attraction strength shifts the nematic to smectic A phase transition to lower volume fractions, with only minor effect on the stability of the other phases. For sufficiently strong tip attraction, the nematic phase disappears completely, in addition leading to the destabilisation of the isotropic phase. In order to better understand the underlying physics of these phenomena, we also investigate the clustering of the particles at their attractive tips and the effective molecular field experienced by the particles in the smectic A phase. Based on these results, we argue that the clustering of the tips only affects the phase stability if lamellar structures (``micelles'') are formed. We find that an increase of the attraction strength increases the degree of order in the layered phases.Interestingly, we also find evidence for the existence of an anti-ferroelectric smectic A phase transition induced by the interaction between the tips. A simple Maier-Saupe-McMillan model confirms our findings.

cond-mat.soft↗

arXiv2019

Compound redistribution due to droplet evaporation on a thin polymeric film: theory

A thin polymeric film in contact with a fluid body may leach low-molecular-weight compounds into the fluid. If this fluid is a small droplet, the compound concentration within the liquid increases due to ongoing leaching in combination with the evaporation of the droplet. This may eventually lead to an inversion of the transport process and a redistribution of the compounds within the thin film. In order to gain an understanding of the compound redistribution, we apply a macroscopic model for the evaporation of a droplet and combine that with a diffusion model for the compound transport. In the model, material deposition and the resulting contact line pinning are associated with the precipitation of a fraction of the dissolved material. We find three power law regimes for the size of the deposit area as a function of the initial droplet size, dictated by the competition between evaporation, diffusion and the initial compound concentrations in the droplet and the thin film. The strength of the contact line pinning determines the deposition profile of the precipitate, characterised by a pronounced edge and a linearly decaying profile towards the centre of the stain. Our predictions for the concentration profile within the solid substrate resemble patterns found experimentally.

cond-mat.soft↗

arXiv2019

Directing liquid crystalline self-organization of rod-like particles through tunable attractive single tips

Dispersions of rodlike colloidal particles exhibit a plethora of liquid crystalline states, including nematic, smectic A, smectic B, and columnar phases. This phase behavior can be explained by presuming the predominance of hard-core volume exclusion between the particles. We show here how the self-organization of rodlike colloids can be controlled by introducing a weak and highly localized directional attractive interaction between one of the ends of the particles. This has been performed by functionalizing the tips of filamentous viruses by means of regioselectively grafting fluorescent dyes onto them, resulting in a hydrophobic patch whose attraction can be tuned by varying the number of bound dye molecules. We show, in agreement with our computer simulations, that increasing the single tip attraction stabilizes the smectic phase at the expense of the nematic phase, leaving all other liquid crystalline phases invariant. For a sufficiently strong tip attraction, the nematic state may be suppressed completely to get a direct isotropic liquid-to-smectic phase transition. Our findings provide insights into the rational design of building blocks for functional structures formed at low densities.

cond-mat.soft↗

arXiv2019

Connectivity, Not Density, Dictates Percolation in Nematic Liquid Crystals of Slender Nanoparticles

We show by means of continuum theory and simulations that geometric percolation in uniaxial nematics of hard slender particles is fundamentally different from that in isotropic dispersions. In the nematic, percolation depends only very weakly on the density and is, in essence, determined by a distance criterion that defines connectivity. This unexpected finding has its roots in the non-trivial coupling between the density and the degree of orientational order that dictate the mean number of particle contacts. Clusters in the nematic are much longer than wide, suggesting the use of nematics for nanocomposites with strongly anisotropic transport properties.

cond-mat.soft↗

arXiv2018

Supramolecular copolymers predominated by alternating order: theory and application

We investigate the copolymerization behavior of a two-component system into quasi-linear self-assemblies under conditions that interspecies binding is favored over identical species binding. The theoretical framework is based on a coarse-grained self-assembled Ising model with nearest neighbor interactions. In Ising language, such conditions correspond to the anti-ferromagnetic case giving rise to copolymers with predominantly alternating configurations. In the strong coupling limit, we show that the maximum fraction of polymerized material and the average length of strictly alternating copolymers depend on the stoichiometric ratio and the activation free energy of the more abundant species. They are substantially reduced when the stoichiometric ratio noticeably differs from unity. Moreover, for stoichiometric ratios close to unity, the copolymerization critical concentration is remarkably lower than the homopolymerization critical concentration of either species. We further analyze the polymerization behavior for a finite and negative coupling constant and characterize the composition of supramolecular copolymers. Our theoretical insights rationalize experimental results of supramolecular polymerization of oppositely charged monomeric species in aqueous solutions.

cond-mat.soft↗

arXiv2018

A macroscopic model for sessile droplet evaporation on a flat surface

The evaporation of sessile droplets on a flat surface involves a complex interplay between phase change, diffusion, advection and surface forces. In an attempt to significantly reduce the complexity of the problem and to make it manageable, we propose a simple model hinged on a surface free energy-based relaxation dynamics of the droplet shape, a diffusive evaporation model and a contact line pinning mechanism governed by a yield stress. Our model reproduces the known dynamics of droplet shape relaxation and of droplet evaporation, both in the absence and in the presence of contact line pinning. We show that shape relaxation during evaporation significantly affects the lifetime of a drop. We find that the dependence of the evaporation time on the initial contact angle is a function of the competition between the shape relaxation and evaporation, and is strongly affected by any contact line pinning.

cond-mat.soft↗

arXiv2018

Connectedness percolation of hard convex polygonal rods and platelets

The properties of polymer composites with nanofiller particles change drastically above a critical filler density known as the percolation threshold. Real nanofillers, such as graphene flakes and cellulose nanocrystals, are not idealized disks and rods but are often modeled as such. Here we investigate the effect of the shape of the particle cross section on the geometric percolation threshold. Using connectedness percolation theory and the second-virial approximation, we analytically calculate the percolation threshold of hard convex particles in terms of three single-particle measures. We apply this method to polygonal rods and platelets and find that the universal scaling of the percolation threshold is lowered by decreasing the number of sides of the particle cross section. This is caused by the increase of the surface area to volume ratio with decreasing number of sides.

cond-mat.soft↗

arXiv2018

The effect of RNA stiffness on the self-assembly of virus particles

Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between a ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.

physics.bio-ph↗

arXiv2018

Continuum Percolation of Polydisperse Rods in Quadrupole Fields: Theory and Simulations

We investigate percolation in mixtures of nanorods in the presence of external fields that align or disalign the particles with the field axis. Such conditions are found in the formulation and processing of nanocomposites, where the field may be electric, magnetic, or due to elongational flow. Our focus is on the effect of length polydispersity, which -- in the absence of a field -- is known to produce a percolation threshold that scales with the inverse weight average of the particle length. Using a model of non-interacting spherocylinders in conjunction with connectedness percolation theory, we show that a quadrupolar field always increases the percolation threshold and that the universal scaling with the inverse weight average no longer holds if the field couples to the particle length. Instead, the percolation threshold becomes a function of higher moments of the length distribution, where the order of the relevant moments crucially depends on the strength and type of field applied. The theoretical predictions compare well with the results of our Monte Carlo simulations, which eliminate finite size effects by exploiting the fact that the universal scaling of the wrapping probability function holds even in anisotropic systems. Theory and simulation demonstrate that the percolation threshold of a polydisperse mixture can be lower than that of the individual components, confirming recent work based on a mapping onto a Bethe lattice as well as earlier computer simulations involving dipole fields. Our work shows how the formulation of nanocomposites may be used to compensate for the adverse effects of aligning fields that are inevitable under practical manufacturing conditions.

cond-mat.soft↗

arXiv2017

Entropy of water and the temperature-induced stiffening of amyloid networks

In water, networks of semi-flexible fibrils of the protein $α$-synuclein stiffen significantly with increasing temperature. We make plausible that this reversible stiffening is a result of hydrophobic contacts between the fibrils that become more prominent with increasing temperature. The good agreement of our experimentally observed temperature dependence of the storage modulus of the network with a scaling theory linking network elasticity with reversible crosslinking enables us to quantify the endothermic binding enthalpy and an estimate the effective size of hydrophobic patches on the fibril surface.

cond-mat.soft↗

arXiv2017

Connectedness percolation of hard deformed rods

Nanofiller particles, such as carbon nanotubes or metal wires, are used in functional polymer composites to make them conduct electricity. They are often not perfectly straight cylinders, but may be tortuous or exhibit kinks. Therefore we investigate the effect of shape deformations of the rodlike nanofillers on the geometric percolation threshold of the dispersion. We do this by using connectedness percolation theory within a Parsons-Lee type of approximation, in combination with Monte Carlo integration for the average overlap volume in the isotropic fluid phase. We find that a deviation from a perfect rodlike shape has very little effect on the percolation threshold, unless the particles are strongly deformed. This demonstrates that idealized rod models are useful even for nanofillers that superficially seem imperfect. In addition, we show that for small or moderate rod deformations, the universal scaling of the percolation threshold is only weakly affected by the precise particle shape.

cond-mat.soft↗

arXiv2017

Self-organisation of semi-flexible rod-like particles

We report on a comprehensive computer simulation study of the liquid-crystal phase behaviour of purely repulsive, semi-flexible rod-like particles. For the four aspect ratios we consider, the particles form five distinct phases depending on their packing fraction and bending flexibility: the isotropic, nematic, smectic A, smectic B and crystal phase. Upon increasing the particle bending flexibility, the various phase transitions shift to larger packing fractions. Increasing the aspect ratio achieves the opposite effect. We find two different ways how the layer spacing of the particles in the smectic A phase may respond to an increase in concentration. The layer spacing may either decrease or increase depending on the aspect ratio and flexibility. For the smectic B and the crystalline phases, increasing the concentration always decreases the layer spacing. We find that the layer spacing jumps to a larger value on transitioning from the smectic A to the smectic B phase.

cond-mat.soft↗

arXiv2017

On the Kinetics of Body versus End Evaporation and Addition of Supramolecular Polymers

Although pathway-specific kinetic theories are fundamentally important to describe and understand reversible polymerisation kinetics, they come in principle at a cost of having a large number of system-specific parameters. Here, we construct a dynamical Landau theory to describe the kinetics of activated linear supramolecular self-assembly, which drastically reduces the number of parameters and still describes most of the interesting and generic behavior of the system in hand. This phenomenological approach hinges on the fact that if nucleated, the polymerisation transition resembles a phase transition. We are able to describe hysteresis, overshooting, undershooting and the existence of a lag time before polymerisation takes off, and pinpoint the conditions required for observing these types of phenomenon in the assembly and disassembly kinetics. We argue that the phenomenological kinetic parameter in our theory is a pathway controller, i.e., it controls the relative weights of the molecular pathways through which self-assembly takes place.

cond-mat.soft↗

arXiv2017

Impact of a non-uniform charge distribution on virus assembly

Many spherical viruses encapsulate their genome in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genome. We model the effect of the icosahedral charge distribution from the protein shell instead of uniform using a mean-field theory. We find that the non-uniform charge distribution strongly affects the optimal genome length, and that it can explain the experimentally observed phenomenon of overcharging of virus and virus-like particles.

physics.bio-ph↗