arXiv subjects

Paul van der Schoot

Publications and source records attributed to Paul van der Schoot.

At least 19 recordsLinked to original sources

arXiv2026

Effects of Rim Fluctuations in Classical Nucleation Theory of Virus Capsids

Most spherical viruses exhibit icosahedral symmetry, yet the growth of viral shells remains poorly understood due to the short lifetimes and broad size distribution of assembly intermediates. Classical nucleation theory has been widely applied to describe this process, but it treats the boundary of a growing shell as rigid and structureless. Here, we extend classical nucleation theory by incorporating thermal fluctuations of the capsid rim using both discrete and continuum descriptions. Allowing the rim of a partially formed capsid to undergo small geometric undulations, we show that these fluctuations generate an entropic contribution that renormalizes the effective line tension. As a result, rim fluctuations can either promote or hinder capsid closure, depending on the subunit-subunit binding free energy, temperature, and fluctuation amplitude. We find that fluctuations generally lower the nucleation barrier when the binding free energy is below a threshold value, while for sufficiently strong binding, they can instead raise the barrier by stabilizing incomplete capsids through a finite-size entropy penalty associated with rim closure. By moving beyond the idealized capillarity approximation, our results provide a controlled extension of classical nucleation theory that clarifies how boundary fluctuations influence capsid nucleation and growth.

cond-mat.soft↗

arXiv2026

Thermodynamic stability and kinetic control of capsid morphologies in hepatitis B virus

Polymorphism has been observed in viral capsid assembly, demonstrating the ability of identical protein dimers to adopt multiple geometries under the same solution conditions. A well-studied example is the hepatitis B virus (HBV), which forms two stable capsid morphologies both in vivo and in vitro. These capsids differ in diameter, containing either 90 or 120 protein dimers. Experiments have shown that their relative prevalence depends on the ionic conditions of the solution during assembly. We developed a model that incorporates salt effects by altering the intermolecular binding free energy between capsid proteins, thereby shifting the relative thermodynamic stability of the two morphologies. This model reproduces experimental results on the prevalence ratios of the large and small HBV capsids. We also constructed a kinetic model that captures the time-dependent ratio of the two morphologies under subcritical capsid concentrations, consistent with experimental data.

physics.bio-ph↗

arXiv2026

Chirality Amplification and Chiral Segregation in Liquid Crystals

Liquid crystal mesophases of achiral molecules are normally achiral, yet in a few materials they spontaneously segregate and form right- and left-handed chiral domains. One mechanism that drives chiral segregation is molecular shape fluctuations between axial chiral conformations, where molecular interactions favor matching chirality and promote helical twist. Cooperative chiral ordering may also play a role in chirality amplification, as when a tiny fraction of chiral dopant drives a nematic phase to become cholesteric. We present a model of cooperative chiral ordering in liquid crystals using Maier-Saupe theory, and predict a phase diagram with a segregated cholesteric phase with alternating domains of left- and right-handed chiral twist, with opposite enantiomeric excess, in addition to racemic nematic and isotropic phases. Our model also demonstrates how chiral molecular fluctuations influence the helical twisting power of dopants in the nematic phase, which may be observed even in materials where the segregated cholesteric phase is preempted by a transition to another phase. We compare these results with Monte Carlo simulation studies of the switchable chiral Lebwohl-Lasher model, where each spin switches between right- and left-handed chiral states. Simulation results validate the predicted phase diagram, demonstrate chiral amplification in the racemic nematic phase, and reveal complex coarsening dynamics in the segregated cholesteric phase. These results suggest that molecular fluctuations between degenerate chiral configurations may be a common mechanism to produce cooperative chiral order in achiral liquid crystals.

cond-mat.soft↗

arXiv2025

An Assembly-Line Mechanism for In-Vitro Encapsulation of Fragmented Cargo in Virus-Like Particles

The ability of virus shells to encapsulate a wide range of functional cargoes, especially multiple cargoes - siRNAs, enzymes, and chromophores - has made them an essential tool in biotechnology for advancing drug delivery applications and developing innovative new materials. Here we present a mechanistic study of the processes and pathways that lead to multiple cargo encapsulation in the co-assembly of virus shell proteins with ligand-coated nanoparticles. Based on the structural identification of different intermediates, enabled by the contrast in electron microscopy provided by the metal nanoparticles that play the cargo role, we find that multiple cargo encapsulation occurs by self-assembly via a specific ``assembly line'' pathway that is different from previously described \emph{in vitro} assembly mechanisms of virus-like particles (VLP). The emerging model explains observations that are potentially important for delivery applications, for instance, the pronounced nanoparticle size selectivity.

cond-mat.soft↗

arXiv2025

Impact of the RNA Binding Domain Localization of the Protein Shell on Virus Particle Stability

The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat proteins and the negatively charged polyanions. Theoretically, this interaction is often modeled by coarse-graining the charge distribution of the binding domains, either by projecting the charges onto the inner surface of the protein shell or by spreading them across a region representing the capsid lumen where the binding domains are located. In practice, however, the positive charges are not uniformly distributed across the binding domains, which themselves are positioned at discrete, specific sites on the shell surface. Here, we use molecular dynamics simulations to investigate the impact of localized interactions on the most probable or optimal length of the encapsulated polymer, revealing that the specific location of charges along the binding domains plays a significant role, consistent with experimental observations. Comparing the simulations with predictions from a simple mean-field theory taken from the literature, we find that while the general trends are reasonably well captured, quantitative discrepancies arise between the two approaches.

physics.bio-ph↗

arXiv2024

Structuring in Thin Films during Meniscus-Guided Deposition

We study theoretically the evaporation-driven phase separation of a binary fluid mixture in a thin film deposited on a moving substrate, as occurs in meniscus-guided deposition for solution-processed materials. Our focus is on rapid substrate motion during, where phase separation takes place far removed from the coating device under conditions where the mixture is essentially stationary with respect to the substrate. We account for the hydrodynamic transport of the mixture within the lubrication approximation. In the early stages of demixing, diffusive and evaporative mass transport predominates, consistent with earlier studies on evaporation-driven spinodal decomposition. By contrast, in the late-stage coarsening of the demixing process, the interplay of solvent evaporation, diffusive, and hydrodynamic mass transport results in a number of distinct coarsening mechanisms. The effective coarsening rate is dictated by the (momentarily) dominant mass transport mechanism and therefore depends on the material properties, evaporation rate and time: slow solvent evaporation results in initially diffusive coarsening that for sufficiently strong hydrodynamic transport transitions to hydrodynamic coarsening, whereas rapid solvent evaporation can preempt and suppress either or both hydrodynamic and diffusive coarsening. We identify a novel hydrodynamic coarsening regime for off-critical mixtures, arising from the interaction of the interfaces between solute-rich and solute-poor regions in the film with the solution-gas interface. This interaction induces directional motion of solute-rich droplets along gradients in the film thickness, from regions where the film is relatively thick to where it is thinner. The solute-rich domains subsequently accumulate and coalesce in the thinner regions, enhancing domain growth.

cond-mat.soft↗

arXiv2024

Periodic phase-separation during meniscus-guided deposition

We numerically investigate the meniscus-guided coating of a binary fluid mixture containing a solute and a volatile solvent that phase separates via spinodal decomposition. Motivation is the evaporation-driven deposition of material during the fabrication of organic thin film electronics. We find a transition in the phase-separation morphology from an array of droplet-shaped domains deposited periodically parallel to the slot opening to isotropically dispersed solute-rich droplets with increasing coating velocity. This transition originates from the competition between the hydrodynamic injection of the solution into the film and diffusive transport that cannot keep up with replenishing the depletion of solute near the solute-rich domains. The critical velocity separating the two regimes and the characteristic length scale of the phase-separated morphologies are determined by the ratio of two emergent length scales: (i) the spinodal length, which implicitly depends on the evaporation rate and the properties of the solution, and (ii) a depletion length proportional to the ratio of the tracer diffusivity of the solute and the coating velocity. For coating below the critical velocity, an array of droplet-shaped domains is deposited periodically parallel to the slot opening, with the domain size and deposition wavelength proportional to a solute depletion length. As the competition in the mass transport is inherent in any kind of unidirectional deposition of demixing solutions, our findings should apply to a broad range of coating techniques and forced demixing processes.

cond-mat.soft↗

arXiv2024

Dynamics of elongation of nematic tactoids in an electric field

Nematic tactoids are spindle-shaped droplets of a nematic phase nucleated in the co-existing isotropic phase. According to equilibrium theory, their internal structure and shape are controlled by a balance between the elastic deformation of the director field, induced by the preferred anchoring of that director field to the interface, and the interfacial free energy. Recent experiments on tactoids of chitin nanocrystals dispersed in water show that electrical fields can very strongly elongate tactoids, at least if the tactoids are sufficiently large in volume. However, this observation contradicts the predictions of equilibrium theory as well as findings from Monte Carlo simulations that do not show this kind of extreme elongation to take place at all. To explain this, we put forward a relaxational model based on the Oseen-Frank free energy of elastic deformation of a director field coupled to an anisotropic surface free energy. In our model, we use two reaction coordinates to describe the director field and the extent of elongation of the droplets, and evaluate the evolution of both as a function of time following the switching on of an electric field. Depending on the relative magnitude of the fundamental relaxation rates associated with the two reaction coordinates, we find that the aspect ratio of the drops may develop a large and very long-lived overshoot before eventually relaxing to the much smaller equilibrium value. In that case, the response of the curvature of the director field lags behind, explaining the experimental observations. Our theory describes the experimental data reasonably well.

cond-mat.soft↗

arXiv2023

Electrostatic theory of the acidity of the solution in the lumina of viruses and virus-like particles

Recently, Maassen et al. measured an appreciable pH difference between the bulk solution and the solution in the lumen of virus-like particles, self-assembled in an aqueous buffer solution containing the coat proteins of a simple plant virus and polyanions. [Maassen, S. J.; et al. Small 2018, 14, 1802081] They attribute this to the Donnan effect, caused by an imbalance between the number of negative charges on the encapsulated polyelectrolyte molecules and the number of positive charges on the RNA binding domains of the coat proteins that make up the virus shell or capsid. By applying Poisson-Boltzmann theory, we confirm this conclusion and show that simple Donnan theory is accurate even for the smallest of viruses and virus-like particles. This, in part, is due to the additional screening caused by the presence of a large number of immobile charges in the cavity of the shell. The presence of a net charge on the outer surface of the capsid we find in practice to not have a large effect on the pH shift. Hence, Donnan theory can indeed be applied to connect the local pH and the amount of encapsulated material. The large shifts up to a full pH unit that we predict must have consequences for applications of virus capsids as nanocontainers in bionanotechnology and artificial cell organelles.

cond-mat.soft↗

arXiv2022

The dynamics of viruslike capsid assembly and disassembly

Cowpea chlorotic mottle virus (CCMV) is a widely used model for virus replication studies. A major challenge lies in distinguishing between the roles of the interaction between coat proteins and that between the coat proteins and the viral RNA in assembly and disassembly processes. Here, we report on the spontaneous and reversible size conversion of the empty capsids of a CCMV capsid protein functionalized with a hydrophobic elastin-like polypeptide which occurs following a pH jump. We monitor the concentration of T = 3 and T = 1 capsids as a function of time and show that the time evolution of the conversion from one T number to another is not symmetric: the conversion from T = 1 to T = 3 is a factor of 10 slower than that of T = 3 to T = 1. We explain our experimental findings using a simple model based on classical nucleation theory applied to virus capsids, in which we account for the change in the free protein concentration, as the different types of shells assemble and disassemble by shedding or absorbing single protein subunits. As far as we are aware, this is the first study confirming that both the assembly and disassembly of viruslike shells can be explained through classical nucleation theory, reproducing quantitatively results from time-resolved experiments.

physics.bio-ph↗

arXiv2022

Controlled gel expansion through colloid oscillation

We model the behaviour of a single colloid embedded in a cross-linked polymer gel, immersed in a viscous background fluid. External fields actuate the particle into a periodic motion, which deforms the embedding matrix and creates a local micro-cavity, containing the particle and any free volume created by its motion. This cavity exists only as long as the particle is actuated and, when present, reduces the local density of the material, leading to swelling. We show that the model exhibits rich resonance features, but is overall characterised by clear scaling laws at low and high driving frequencies, and a pronounced resonance at intermediate frequencies. Our model predictions suggest that both the magnitude and position of the resonance can be varied by varying the material's elastic modulus or cross-linking density, whereas the local viscosity primarily has a dampening effect. Our work implies appreciable free-volume generation is possible by dispersing a collection of colloids in the medium, even at the level of a simple superposition approximation.

cond-mat.soft↗

arXiv2022

Geometric percolation of colloids in shear flow

We combine a heuristic theory of geometric percolation and the Smoluchowski theory of colloid dynamics to predict the impact of shear flow on the percolation threshold of hard spherical colloidal particles, and verify our findings by means of molecular dynamics simulations. It appears that the impact of shear flow is subtle and highly non-trivial, even in the absence of hydrodynamic interactions between the particles. The presence of shear flow can both increase and decrease the percolation threshold, depending on the criterion used for determining whether or not two particles are connected and on the Péclet number. Our approach opens up a route to quantitatively predict the percolation threshold in nanocomposite materials that, as a rule, are produced under non-equilibrium conditions, making comparison with equilibrium percolation theory tenuous. Our theory can be adapted straightforwardly for application in other types of flow field, and particles of different shape or interacting via other than hard-core potentials.

cond-mat.soft↗

arXiv2022

Transient response and domain formation in electrically deforming liquid crystal networks

Recently, Van der Kooij and co-workers recognised three distinct, transient regimes in the dynamics of electrically-deforming liquid crystal networks [Van der Kooij et al., Nat. Commun. 10, 1 (2019)]. Based on a Landau-theoretical framework, which encompasses spatially resolved information, we interpret these regimes: initially, the response is dominated by thermal noise, then the top of the film expands, followed by a permeation of this response into the bulk. An important signature of this interpretation is a significant dependence of the regime time scales on film thickness, where we observe a clear thin-film-to-bulk transition. The point of transition coincides with the emergence of spatial inhomogeneities in the bulk, i.e., domain formation, and should be avoided due to the less predictable steady-state expansion it gives rise to. Finally, we show that this domain formation can be suppressed by decreasing the initial thickness of the film, and increasing the linear dimensions of the mesogens, or their orientational order when crosslinked into the network, though this comes at the cost of the deformation magnitude. Our results contribute to achieving finer control over how smart liquid crystal network coatings are activated.

cond-mat.soft↗

arXiv2021

Controlling permeation in electrically-deforming liquid crystal network films: a dynamical Landau theory

Liquid crystal networks exploit the coupling between the responsivity of liquid-crystalline mesogens, e.g., to electric fields, and the (visco)elastic properties of a polymer network. Because of this, these materials have been put forward for a wide array of applications, including responsive surfaces such as artificial skins and membranes. For such applications, the desired functional response must generally be realized under strict geometrical constraints, such as provided by supported thin films. To model such settings, we present a dynamical, spatially-heterogeneous Landau-type theory for electrically-actuated liquid crystal network films. We find that the response of the liquid crystal network permeates the film from top to bottom, and illustrate how this affects the time scale associated with macroscopic deformation. Finally, by linking our model parameters to experimental quantities, we suggest that the permeation rate can be controlled by varying the aspect ratio of the mesogens and their degree of orientational order when cross-linked into the polymer network, for which we predict a single optimum. Our results contribute specifically to the rational design of future applications involving transport or on-demand release of molecular cargo in liquid crystal network films.

cond-mat.soft↗

arXiv2021

Connectedness percolation of fractal liquids

We apply connectedness percolation theory to fractal liquids of hard particles, and make use of a Percus-Yevick liquid state theory combined with a geometric connectivity criterion. We find that in fractal dimensions the percolation threshold interpolates continuously between integer-dimensional values, and that it decreases monotonically with increasing (fractal) dimension. The influence of hard-core interactions is only significant for dimensions below three. Finally, our theory incorrectly suggests that a percolation threshold is absent below about two dimensions, which we attribute to the breakdown of the connectedness Percus-Yevick closure.

cond-mat.stat-mech↗

arXiv2021

Effect of Electric Fields on the Director Field and Shape of Nematic Tactoids

Tactoids are spindle shaped-droplets of a uniaxial nematic phase suspended in the co-existing isotropic phase. They are found in dispersions of a wide variety of elongated colloidal particles, including actin, fd virus, carbon nanotubes, vanadium peroxide and chitin nanocrystals. Recent experiments on tactoids of chitin nanocrystals in water show that electric fields can very strongly elongate tactoids even though the dielectric properties of the co-existing isotropic and nematic phases differ only subtly. We develop a model for partially bipolar tactoids, where the degree of bipolarness of the director field is free to adjust to optimize the sum of the elastic, surface and Coulomb energies of the system. By means of a combination of a scaling analysis and a numerical study, we investigate the elongation and director field's behavior of the tactoids as a function of their size, the strength of the electric field, the surface tension, anchoring strength, the elastic constants and the electric susceptibility anisotropy. We find that tactoids cannot elongate significantly due to an external electric field, unless the director field is bipolar or quasi bipolar and is somehow frozen in the field-free configuration. Presuming that this is the case, we find reasonable agreement with experimental data.

cond-mat.soft↗

arXiv2021

Nearest-neighbor connectedness theory: A general approach to continuum percolation

We introduce a method to estimate continuum percolation thresholds and illustrate its usefulness by investigating geometric percolation of non-interacting line segments and disks in two spatial dimensions. These examples serve as models for electrical percolation of elongated and flat nanofillers in thin film composites. While the standard contact volume argument and extensions thereof in connectedness percolation theory yield accurate predictions for slender nanofillers in three dimensions, they fail to do so in two dimensions, making our test a stringent one. In fact, neither a systematic order-by-order correction to the standard argument nor invoking the connectedness version of the Percus-Yevick approximation yield significant improvements for either type of particle. Making use of simple geometric considerations, our new method predicts a percolation threshold of $ρ_c l^2 \approx 5.83$ for segments of length $l$, which is close to the $ρ_c l^2 \approx 5.64$ found in Monte Carlo simulations. For disks of area $a$ we find $ρ_c a \approx 1.00$, close to the Monte Carlo result of $ρ_c a \approx 1.13$. We discuss the shortcomings of the conventional approaches and explain how usage of the nearest-neighbor distribution in our new method bypasses those complications.

cond-mat.stat-mech↗

arXiv2021

Enhanced ordering in length-polydisperse carbon nanotube solutions at high concentrations as revealed by small angle X-ray scattering

Carbon nanotubes (CNTs) are stiff, all-carbon macromolecules with diameters as small as one nanometer and few microns long. Solutions of CNTs in chlorosulfonic acid (CSA) follow the phase behavior of rigid rod polymers interacting via a repulsive potential and display a liquid crystalline phase at sufficiently high concentration. Here, we show that small-angle X-ray scattering and polarized light microscopy data can be combined to characterize quantitatively the morphology of liquid crystalline phases formed in CNT solutions at concentrations from 3 to 6.5 % by volume. We find that upon increasing their concentration, CNTs self-assemble into a liquid crystalline phase with a pleated texture and with a large inter-particle spacing that could be indicative of a transition to higher-order liquid crystalline phases. We explain how thermal undulations of CNTs can enhance their electrostatic repulsion and increase their effective diameter by an order of magnitude. By calculating the critical concentration, where the mean amplitude of undulation of an unconstrained rod becomes comparable to the rod spacing, we find that thermal undulations start to affect steric forces at concentrations as low as the isotropic cloud point in CNT solutions.

cond-mat.soft↗