arXiv subjects

Tine Curk

Publications and source records attributed to Tine Curk.

At least 19 recordsLinked to original sources

arXiv2026

Mechanistic Framework for Multicomponent Nanoparticle Assembly: Predicting RNA-lipid and PEI-DNA nanoparticle assembly

The assembly of multicomponent nanoparticles is often kinetically controlled and exhibits strong pathway dependence. Transport, solvent exchange, nucleation/growth, and collision-driven coalescence together determine not only ensemble-averaged properties but also particle-to-particle compositional heterogeneity. Here, we present a computational modeling framework for predicting nanoparticle property distributions by coupling processing conditions, early-stage self-assembly physics, and molecular chemical details with kinetic Monte Carlo (kMC) simulations. The framework combines (i) mixing conditions with solvent-exchange-mediated particle initialization and growth, and (ii) kMC simulations that resolve stochastic collision histories, electrostatics-controlled coalescence, and composition at the level of individual particles. Applied to mRNA lipid nanoparticles, the model predicts size-loading correlations and provides insight into how processing-dependent assembly pathways lead to heterogeneous payload distributions. The kMC simulations further provide merging lineage histories, which explain the emergence of log-normal volume and payload distributions through multiplicative particle-growth pathways. The same framework is also applied to PEI-DNA polyelectrolytic complexation, yielding single-particle-resolved DNA-PEI stoichiometry distributions. The framework and its open-source implementation, FormLNP, provide a process-aware route to predicting and controlling single-particle property distributions across a broad range of multicomponent nanoparticle systems.

cond-mat.soft↗

arXiv2026

Kinetic Superselectivity in Multivalent Binding

Multivalent binding employs multiple simultaneous supramolecular interactions, increasing avidity and selectivity compared with monovalent binding. While equilibrium aspects of multivalency are well characterized, non-equilibrium behavior remains poorly understood. By combining experiments on hyaluronic acid polymers with kinetic modeling based on stochastic chemical kinetics and molecular dynamics simulations, we systematically investigate the kinetics of multivalent binding. Notably, we find that both association and dissociation kinetics can be more selective than equilibrium binding. We explain this behavior using a two-step binding model featuring a combination of fast, weak and slow, strong interactions. These findings demonstrate a new approach: superselective targeting based on the association rate instead of the equilibrium state. The kinetic theory and experiments presented here provide a fundamental understanding of multivalent kinetics and establish design rules for superselective targeting in out-of-equilibrium systems.

cond-mat.soft↗

arXiv2026

Designing Multivalent Copolymers for Selective Targeting of Multicomponent Surfaces

Selective targeting of membranes with a specific receptor profile is an ongoing challenge in targeted drug delivery. We investigate the adsorption of copolymers on a multicomponent receptor-covered surface using grand-canonical Monte Carlo simulations and demonstrate that polymers can be designed to target a particular receptor density profile. To achieve this, the ligand profile on the polymers should match the targeted receptor profile, and the ligand--receptor affinity should be inversely proportional to the ligand profile. While the same can be obtained using multivalent nanoparticles, the entropic effects due to polymer conformations significantly enhance the binding selectivity of multivalent polymers compared to nanoparticles. Surprisingly, the ligand distribution on the polymer plays a crucial role, whereas the persistence length does not. The optimal selectivity to the overall receptor concentration is obtained by the Poisson distribution of ligands (random copolymer), whereas the maximal selectivity to a specific receptor profile is obtained by a defined sequence of grouped alternating ligands (regular copolymer). Interestingly, the regular copolymer can become anti-selective when ligands of the same type are in homogenous blocks, showing that specific ligand distribution qualitatively affects the targeting ability. These findings suggest that sequence control is necessary to selectively target a specific density profile of membrane receptors using linear copolymers.

cond-mat.soft↗

arXiv2026

Multiscale Analysis of Plasma-Modified Silk Fibroin and Chitosan Films

Biological interactions with material surfaces span a wide range of length scales, yet conventional surface measurements often fail to account for scale, limiting the insights they provide for surface engineering. Here, we investigate how multiscale surface descriptors of plasma-modified silk fibroin and chitosan surfaces modify bacterial and immune cell response. Surface chemistry and topography were characterized using X-ray Photoelectron Spectroscopy (XPS) and Atomic Force Microscopy (AFM), followed by sliding bandpass filtration and multiscale curvature tensor-based methods to measure scale-dependent topographic features. Macrophage response and biofilm growth were assessed by fluorescence microscopy. Correlation strength showed scale-dependence with respect to surface features and biological structure: individual bacteria and small colonies correlated more strongly with fine-scale topographic features, whereas macrophage morphology correlated more strongly with larger-scale surface features. Notably, measured surface chemical descriptors generally did not correlate strongly with biofilm formation; nonetheless, chitosan and silk fibroin showed distinct trends in bacterial support, suggesting that material identity was not captured by the measured surface properties and that prevention of biofilms likely benefits from combinatorial approaches as opposed to physical surface modification alone. These results show that different biological structures interact with material surfaces at distinct length scales, as well as demonstrate the utility of multiscale analysis in identifying scales of interest in biological interactions with surfaces. Moreover, the data suggests that tailoring topographic feature size to the characteristic scale of the targeted biological entity is a potential strategy for antibacterial wound-healing materials without incurring cytotoxicity.

cond-mat.mtrl-sci↗

arXiv2024

Collapse/expansion dynamics and actuation of pH-responsive nanogels

Polyelectrolyte (PE) hydrogels can dynamically respond to external stimuli, such as changes in pH and temperature, which benefits their use for smart materials and nanodevices with tunable properties. We investigate equilibrium conformations and phase transition dynamics of pH-responsive nanogels using hybrid molecular dynamics/Monte Carlo simulations with full consideration of electrostatic and hydrodynamic interactions. We demonstrate that PE nanogels exhibit a closed-loop phase behavior with a discontinuous swelling--collapse transition that occurs only at intermediate pH values. A 50~nm nanogel particle close to a critical point functions as a pH-driven actuator with a microsecond conformational response and work density $\approx 10^5~\mathrm{J/m}^3$, an order of magnitude larger than skeletal muscles. The collapse/expansion time scales as $L^{2}$ and the power density scales as $L^{-2}$ where $L$ is the linear size of the gel. Our work provides fundamental insight into phase behavior and non-equilibrium dynamics of the swelling--collapse transition, and our method enables the investigation of charge--structure--hydrodynamic coupling in soft materials.

cond-mat.soft↗

arXiv2024

Collapse and expansion kinetics of a single polyelectrolyte chain with hydrodynamic interactions

We investigate the collapse and expansion dynamics of a linear polyelectrolyte (PE) with hydrodynamic interactions. Using dissipative particle dynamics with a bead-spring PE model, long-range electrostatics and explicit ions we examine how the timescales of collapse $t_\text{col}$ and expansion $t_\text{exp}$ depend on the chain length $N$, and obtain scaling relationships $t_\text{col}\sim N^\alpha$ and $t_\text{exp}\sim N^\beta$. For neutral polymers, we derive values of $\alpha=0.94\pm0.01$ and $\beta=1.97\pm0.10$. Interestingly, the introduction of electrostatic interaction markedly shifts $\alpha$ to $\alpha\approx1.4\pm0.1$ for salt concentrations within $c=10^{-4}$ M to $10^{-2}$ M. A reduction in ion-to-monomer size ratio noticeably reduces $\alpha$. On the other hand, the expansion scaling remains approximately constant, $\beta \approx 2$, regardless of salt concentration or ion size considered. We find $\beta > \alpha$ for all conditions considered, implying that expansion is always slower than collapse in the limit of long polymers. This asymmetry is explained by distinct kinetic pathways of collapse and expansion processes.

cond-mat.soft↗

arXiv2024

Dissipative particle dynamics for coarse-grained models

We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully off-lattice method that allows straightforward incorporation of hydrodynamics at desired solvent viscosity, compressibility and solute diffusivity with any particle-based solute model. Solutes interact with the solvent only through the DPD thermostat, which ensures that the equilibrium properties of the solute system are not affected by the introduction of the DPD solvent. Thus, DPDS can be used as a replacement for traditional molecular dynamics thermostats such as Nos\'e-Hoover and Langevin. We demonstrate the applicability of DPDS on the case of polymer dynamics and electroosmotic flow through a nanopore. The method should be broadly useful as means to introduce hydrodynamics to existing coarse-grained models of molecules and soft materials.

cond-mat.soft↗

arXiv2024

Discontinuous transition in electrolyte flow through charge-patterned nanochannels

We investigate the flow of an electrolyte through a rigid nanochannel decorated with a surface charge pattern. Employing lattice Boltzmann and dissipative particle dynamics methods, as well as analytical theory, we show that the electro-hydrodynamic coupling leads to two distinct flow regimes. The accompanying discontinuous transition between slow, ionic, and fast, Poiseuille flows is observed at intermediate ion concentrations, channel widths, and electrostatic coupling strengths. These findings indicate routes to design nanochannels containing a typical aqueous electrolyte that exhibit a digital on/off flux response, which could be useful for nanofluidics and ionotronic applications.

cond-mat.soft↗

arXiv2023

Spool-nematic ordering of dsDNA and dsRNA under confinement

The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong non-linear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that kink formation entails a mixed spool-nematic ordering of double-stranded DNA or RNA in spherical capsids, consisting of an outer spool domain and an inner, twisted nematic domain. These findings explain the experimentally observed nematic domains in viral capsids and imply that non-linear elasticity must be considered to predict the configurations and dynamics of double-stranded genomes in viruses, bacterial nucleoids or gene-delivery vehicles. The non-linear elastic theory suggests that spool-nematic ordering is a general feature of strongly confined kinkable polymers.

cond-mat.soft↗

arXiv2022

Accelerated simulation method for charge regulation effects

The net charge of solvated entities, ranging from polyelectrolytes and biomolecules to charged nanoparticles and membranes, depends on the local dissociation equilibrium of individual ionizable groups. Incorporation of this phenomenon, \emph{charge regulation}, in theoretical and computational models requires dynamic, configuration-dependent recalculation of surface charges and is therefore typically approximated by assuming constant net charge on particles. Various computational methods exist that address this. We present an alternative, particularly efficient charge regulation Monte Carlo method (CR-MC), which explicitly models the redistribution of individual charges and accurately samples the correct grand-canonical charge distribution. In addition, we provide an open-source implementation in the LAMMPS molecular dynamics (MD) simulation package, resulting in a hybrid MD/CR-MC simulation method. This implementation is designed to handle a wide range of implicit-solvent systems that model discreet ionizable groups or surface sites. The computational cost of the method scales linearly with the number of ionizable groups, thereby allowing accurate simulations of systems containing thousands of individual ionizable sites. By matter of illustration, we use the CR-MC method to quantify the effects of charge regulation on the nature of the polyelectrolyte coil--globule transition and on the effective interaction between oppositely charged nanoparticles.

cond-mat.soft↗

arXiv2022

Phase Separation and Ripening in a Viscoelastic Gel

The process of phase separation in elastic solids and viscous fluids is of fundamental importance to the stability and function of soft materials. We explore the dynamics of phase separation and domain growth in a viscoelastic material such as a polymer gel. Using analytical theory and Monte Carlo simulations we report a new domain growth regime, in which the domain size increases algebraically with a ripening exponent $\alpha$ that depends on the viscoelastic properties of the material. For a prototypical Maxwell material, we obtain $\alpha=1$, which is markedly different from the well-known Ostwald ripening process with $\alpha=1/3$. We generalize our theory to systems with arbitrary power-law relaxation behavior and discuss our findings in the context of the long-term stability of materials as well as recent experimental results on phase separation in cross-linked networks and cytoskeleton.

cond-mat.soft↗

arXiv2021

Charge-regulation effects in nanoparticle self-assembly

Nanoparticles in solution acquire charge through dissociation or association of surface groups. Thus, a proper description of their electrostatic interactions requires the use of charge-regulating boundary conditions rather than the commonly employed constant-charge approximation. We implement a hybrid Monte Carlo/Molecular Dynamics scheme that dynamically adjusts the charges of individual surface groups of objects while evolving their trajectories. Charge-regulation effects are shown to qualitatively change self-assembled structures due to global charge redistribution, stabilizing asymmetric constructs. We delineate under which conditions the conventional constant-charge approximation may be employed and clarify the interplay between charge regulation and dielectric polarization.

cond-mat.soft↗

arXiv2019

First-Order "Hyper-selective" Binding Transition of Multivalent Particles Under Force

Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells, virus binding, synthetic ligand-coated micrometer-scale vesicles or smaller nano-particles, functionalised polymers, and toxins. Equilibrium multivalent binding is a continuous yet super-selective transition with respect to the number of ligands and receptors involved in the interaction. Increasing the ligand or receptor density on the two particles leads to sharp growth in the number of bound particles at equilibrium. Here we present a theory and Monte Carlo simulations to show that applying mechanical force to multivalent particles causes their adsorption/desorption isotherm on a surface to become sharper and more selective, with respect to variation in the number of ligands and receptors on the two objects. When the force is only applied to particles bound to the surface by one or more ligands, then the transition can become infinitely sharp and first-order---a new binding regime which we term "hyper-selective". Force may be imposed by, e.g. flow of solvent around the particles, a magnetic field, chemical gradients, or triggered uncoiling of inert oligomers/polymers tethered to the particles to provide a steric repulsion to the surface. This physical principle is a step towards "all or nothing" binding selectivity in the design of multivalent constructs.

cond-mat.soft↗

arXiv2019

Spontaneous Domain Formation in Spherically-Confined Elastic Filaments

Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity-driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calculations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously-ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links. We discuss our results in the context of metallic wires, viral DNA, and flexible polymers.

cond-mat.soft↗

arXiv2018

Coarse-Grained Simulation of DNA using LAMMPS

During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.

cond-mat.soft↗

arXiv2018

Controlling cargo trafficking in multicomponent membranes

Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such `inert' components can be crucial for precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can hence all be actively participating in controlling membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity towards the cargo size, and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general way to control cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors nor the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets.

cond-mat.soft↗

arXiv2017

Design principles for super selectivity using multivalent interactions

Multivalent particles have the ability to form multiple bonds to a substrate. Hence, a multivalent interaction can be strong, even if the individual bonds are weak. However, much more interestingly, multivalency greatly increases the sensitivity of the particle-substrate interaction to external conditions, resulting in an ultra-sensitive and highly non-linear dependence of the binding strength on parameters such as temperature, pH or receptor concentration. In this chapter we focus on super-selectivity: the high sensitivity of the strength of multivalent binding to the number of accessible binding sites on the target surface. For example, the docking of a multivalent particle on a cell-surface can be very sensitive (super-selective) to the concentration of the receptors to which the multiple ligands can bind. We present a theoretical analysis of systems of multivalent particles and describe the mechanism by which multivalency leads to super-selectivity. We introduce a simple analytical model that allows us to predict the overall strength of interactions based on physiochemical characteristics of multivalent binders. Finally, we formulate a set of simple design rules for multivalent interactions that yield optimal selectivity.

cond-mat.soft↗

arXiv2016

Nanoparticle ordering in sandwiched polymer brushes

The organization of nano-particles inside grafted polymer layers is governed by the interplay of polymer-induced entropic interactions and the action of externally applied fields. Earlier work had shown that strong external forces can drive the formation of colloidal structures in polymer brushes. Here we show that external fields are not essential to obtain such colloidal patterns: we report Monte Carlo and Molecular dynamics simulations that demonstrate that ordered structures can be achieved by compressing a `sandwich' of two grafted polymer layers, or by squeezing a coated nanotube, with nano-particles in between. We show that the pattern formation can be efficiently controlled by the applied pressure, while the characteristic length--scale, i.e. the typical width of the patterns, is sensitive to the length of the polymers. Based on the results of the simulations, we derive an approximate equation of state for nano-sandwiches.

cond-mat.soft↗