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We study the melting behavior of charged colloidal crystals, using a simulation technique that combines a continuous mean-field Poisson–Boltzmann description for the microscopic electrolyte ions with a Brownian-dynamics simulation for the mesoscopic colloids. This technique ensures that many-body interactions among the colloids are fully taken into account, and thus allows us to investigate how many-body interactions affect the solid–liquid phase behavior of charged colloids. Using the Lindemann criterion, we determine the melting line in a phase-diagram spanned by the colloidal charge and the salt concentration. We compare our results to predictions based on the established description of colloidal suspensions in terms of pairwise additive Yukawa potentials, and find good agreement at high-salt, but not at low-salt concentration. Analyzing the effective pair-interaction between two colloids in a crystalline environment, we demonstrate that the difference in the melting behavior observed at low salt is due to many-body interactions. If the salt concentration is high, we find configuration-independent pair forces of perfect Yukawa form with effective charges and screening constants that are in good agreement with well-established theories. At low added salt, however, the pair forces are Yukawa-type only at short distances with effective parameters that depend on the analyzed colloidal configuration. At larger distances, the pair-forces decay to zero much faster than they would following a Yukawa force law. Based on these findings, we suggest a simple model potential for colloids in suspension which has the form of a Yukawa potential, truncated after the first coordination shell of a colloid in a crystal. Using this potential in a one-component simulation, we find a melting line that shows good agreement with the one derived from the full Poisson–Boltzmann–Brownian-dynamics simulation. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present molecular dynamics simulations to study the thermodynamics of nanobubbles trapped at the mouth of narrow slit pores. Except when the slit dimensions are comparable to typical molecular sizes, the predictions of macroscopic thermodynamic theory are recovered by our simulations. Our simulations confirm that in this case, the internal pressure of stable nanobubbles is independent of the bubble radius and the surface tension and only depends on the bulk properties of the solute-containing solution, i.e., the chemical potential balance. However, in the case of extreme confinement, the pressure is not a suitable quantity to describe the thermodynamics of the bubbles, while the balance of the chemical potentials is., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong nonlinear 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 nonlinear elasticity must be considered to predict the configurations and dynamics of double-stranded genomes in viruses, bacterial nucleoids or gene-delivery vehicles. The nonlinear elastic theory suggests that spool-nematic ordering is a general feature of strongly confined kinkable polymers.

The introduction of neutrally wetting colloidal particles into coarsening binary fluids is known to arrest the dynamics of the phase separation, as the colloids tend to be captured by the growing interfaces to reduce the free energy of the system. This phenomenon has often been studied in systems with symmetric fluid viscosities. In this study, we investigate the behavior of colloidal particles introduced into asymmetric binary fluids with a viscosity contrast. Our results show that due to the broken symmetry the colloidal particles more easily escape from the interface towards the more viscous fluid, which reduces the lifetime of the jammed phase. Moreover, the presence of colloidal particles near the interfaces promotes the formation of micro-droplets with typical sizes comparable to the colloids.

In this work, we quantitatively compare computer simulations and existing cell tracking data of P. aeruginosa surface motility in order to analyse the underlying motility mechanism. We present a three dimensional twitching motility model, that simulates the extension, retraction and surface association of individual Type IV Pili (TFP), and is informed by recent experimental observations of TFP. Sensitivity analysis is implemented to minimise the number of model parameters, and quantitative estimates for the remaining parameters are inferred from tracking data by approximate Bayesian computation. We argue that the motility mechanism is highly sensitive to experimental conditions. We predict a TFP retraction speed for the tracking data we study that is in a good agreement with experimental results obtained under very similar conditions. Furthermore, we examine whether estimates for biologically important parameters, whose direct experimental determination is challenging, can be inferred directly from tracking data. One example is the width of the distribution of TFP on the bacteria body. We predict that the TFP are broadly distributed over the bacteria pole in both walking and crawling motility types. Moreover, we identified specific configurations of TFP that lead to transitions between walking and crawling states., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Barton et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

We present a technique for measuring the interactions between pairs of colloidal particles in two optical traps. This method is particularly suitable for measuring strongly attractive potentials, an otherwise challenging task. The interaction energy is calculated from the distribution of inter-particle separations by accounting for the contribution from the optical traps with arbitrary trap profiles. The method is simple to implement and applicable to different types of pair potentials and optical trapping geometries. We apply the method to measure dipolar pair interactions in experiments with paramagnetic colloids in external magnetic fields. We obtain consistent and accurate results in all regimes, from strongly attractive to repulsive potentials. By means of computer simulations, we demonstrate that the proposed method can be successfully applied to systems with complex pair interactions characterized by multiple attractive and repulsive regimes, which are ubiquitous in soft and biological matter., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

We study the interaction between two charge regulating spherical macroions with dielectric interior and dissociable surface groups immersed in a monovalent electrolyte solution. The charge dissociation is modelled via the Frumkin-Fowler-Guggenheim isotherm, which allows for multiple adsorption equilibrium states. The interactions are derived from the solutions of the mean-field Poisson-Boltzmann type theory with charge regulation boundary conditions. For a range of conditions we find symmetry breaking transitions from symmetric to asymmetric charge distribution exhibiting annealed charge patchiness, which results in like-charge attraction even in a univalent electrolyte-thus fundamentally modifying the nature of electrostatic interactions in charge-stabilized colloidal suspensions., (© 2023. The Author(s), under exclusive licence to EDP Sciences, SIF and Springer-Verlag GmbH Germany, part of Springer Nature.)

We propose a classical density functional theory model to study the self-assembly of polymeric surfactants on curved surfaces. We use this model to investigate the thermodynamics of phase separation of a binary mixture of size asymmetric miscible surfactants on cylindrical and spherical surfaces, and observe that phase separation driven by size alone is thermodynamically unfavorable on both cylindrical and spherical surfaces. We use the theory, supplemented by dissipative particle dynamics (DPD) simulations, to predict pattern formation on a non-uniform surface with regions of positive and negative curvature. Our results suggest potential ways to couple surface topography and polymeric surfactants to design surfaces coated with non-uniform patterns.

The Onsager reciprocity relations were formulated in the context of irreversible thermodynamics, but they are based on assumptions that have a wider applicability. Here, we present simulations testing the Onsager relations between surface-coupled diffusive and bulk fluxes in a system prepared in a nonequilibrium steady state. The system consists of a mixture of two identical species maintained at different temperatures inside a channel. In order to tune the friction of the two species with the walls independently, while keeping the particle-wall interaction potentials the same, we allow the kinematics of particle-wall collisions to be different: "bounce-back" (B) or "specular" (S). In the BB case, diffusio-capillary transport can only take place if the two species have different temperatures. We find that the Onsager reciprocity relations are obeyed in the linear regime, even in the BB case where all fluxes are the result of perturbing the system from a nonequilibrium steady state in a way that does not satisfy time-reversal symmetry. Our Letter provides a direct, numerical illustration of the validity of the Onsager relations outside their original range of application, and suggests their relevance for transport in driven or active systems.

We show that arbitrarily large polar flocks are susceptible to the presence of a single small obstacle. In a wide region of parameter space, the obstacle triggers counterpropagating dense bands leading to reversals of the flow. In very large systems, these bands interact, yielding a never-ending chaotic dynamics that constitutes a new disordered phase of the system. While most of these results were obtained using simulations of aligning self-propelled particles, we find similar phenomena at the continuous level, not when considering the basic Toner-Tu hydrodynamic theory, but in simulations of truncations of the relevant Boltzmann equation.

The Lennard-Jones 12-6 potential (LJ) is arguably the most widely used pair potential in molecular simulations. In fact, it is so popular that the question is rarely asked whether it is fit for purpose. In this paper, we argue that, whilst the LJ potential was designed for noble gases such as argon, it is often used for systems where it is not expected to be particularly realistic. Under those circumstances, the disadvantages of the LJ potential become relevant: most important among these is that in simulations the LJ potential is always modified such that it has a finite range. More seriously, there is by now a whole family of different potentials that are all called Lennard-Jones 12-6, and that are all different - and that may have very different macroscopic properties. In this paper, we consider alternatives to the LJ 12-6 potential that could be employed under conditions where the LJ potential is only used as a typical short-ranged potential with attraction. We construct a class of potentials that are, in many respects LJ-like but that are by construction finite ranged, vanishing quadratically at the cut-off distance, and that are designed to be computationally cheap. Below, we present this potential and report numerical data for its thermodynamic and transport properties, for the most important cases (cut-off distance r c = 2σ ("LJ-like") and r c = 1.2σ (a typical "colloidal" potential)).

Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target-probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

Gradients in temperature, concentration or electrostatic potential cannot exert forces on a bulk fluid; they can, however, exert forces on a fluid in a microscopic boundary layer surrounding a (nano)colloidal solute, resulting in so-called phoretic flow. Here we present a simulation study of phoretic flow around a spherical colloid held fixed in a concentration gradient. We show that the resulting flow velocity depends non-monotonically on the strength of the colloid-fluid interaction. The reason for this non-monotonic dependence is that solute particles are effectively trapped in a shell around the colloid and cannot contribute to diffusio-phoresis. We also observe that the flow depends sensitively on the anisotropy of solute-colloid interaction.

Bacteria traverse surfaces as part of colonizing solids, and it is of interest to hinder this motion to potentially thwart infections in humans. Here, we demonstrate that topographical steps hinder the ability of Pseudomonas aeruginosa PAO1 ( P. aeruginosa ) to traverse a solid-liquid interface. Using time-lapse fluorescence microscopy and image analysis, we analyzed the motion of P. aeruginosa that were challenged with steps ranging in height from 0.4 to 9.0 μm. Bacterial trajectories are sensitive to the height of the step, the curvature of the step face, and the direction of their motion relative to gravity. When the step height is ≥0.9 μm, which is similar to the cell diameter, there is a reduced probability of the cell crossing the step. For those bacteria that do cross a step, there is a time penalty for crossing steps of height 2-3 μm; this height is similar to the length of the bacterium. For higher steps, the bacteria reorient their cell body while traversing the step riser. Our findings elucidate how topography influences the motion of bacteria and informs strategies for hindering bacterial motion at surfaces.