David A. Head

Ecological approaches to oral biofilms: control without killing.

Humans have co-evolved with micro-organisms and have a symbiotic or mutualistic relationship with their resident microbiome. As at other body surfaces, the mouth has a diverse microbiota that grows on oral surfaces as structurally and functionally organised biofilms. The oral microbiota is natural and provides important benefits to the host, including immunological priming, down-regulation of excessive pro-inflammatory responses, regulation of gastrointestinal and cardiovascular systems, and colonisation by exogenous microbes. On occasions, this symbiotic relationship breaks down, and previously minor components of the microbiota outcompete beneficial bacteria, thereby increasing the risk of disease. Antimicrobial agents have been formulated into many oral care products to augment mechanical plaque control. A delicate balance is needed, however, to control the oral microbiota at levels compatible with health, without killing beneficial bacteria and losing the key benefits delivered by these resident microbes. These antimicrobial agents may achieve this by virtue of their recommended twice daily topical use, which results in pharmacokinetic profiles indicating that they are retained in the mouth for relatively long periods at sublethal levels. At these concentrations they are still able to inhibit bacterial traits implicated in disease (e.g. sugar transport/acid production; protease activity) and retard growth without eliminating beneficial species. In silico modelling studies have been performed which support the concept that either reducing the frequency of acid challenge and/or the terminal pH, or by merely slowing bacterial growth, results in maintaining a community of beneficial bacteria under conditions that might otherwise lead to disease (control without killing).

Non-Gaussian athermal fluctuations in active gels

Dynamic networks designed to model the cell cytoskeleton can be reconstituted from filamentous actin, the motor protein myosin and a permanent cross-linker. They are driven out of equilibrium when the molecular motors are active. This gives rise to athermal fluctuations that can be recorded by tracking probe particles that are dispersed in the network. We have here probed athermal fluctuations in such “active gels” using video microrheology. We have measured the full distribution of probe displacements, also known as the van Hove correlation function. The dominant influence of thermal or athermal fluctuations can be detected by varying the lag time over which the displacements are measured. We argue that the exponential tails of the distribution derive from single motors close to the probes, and we extract an estimate of the velocity of motor heads along the actin filaments. The distribution exhibits a central Gaussian region which we assume derives from the action of many independent motor proteins far from the probe particles when athermal fluctuations dominate. Recording the whole distribution rather than just the typically measured second moment of probe fluctuations (mean-squared displacement) thus allowed us to differentiate between the effect of individual motors and the collective action of many motors.

Mechanical response of semiflexible networks to localized perturbations.

Previous research on semiflexible polymers including cytoskeletal networks in cells has suggested the existence of distinct regimes of elastic response, in which the strain field is either uniform (affine) or nonuniform (nonaffine) under external stress. Associated with these regimes, it has been further suggested that a mesoscopic length scale emerges, which characterizes the scale for the crossover from nonaffine to affine deformations. Here, we extend these studies by probing the response to localized forces and force dipoles. We show that the previously identified nonaffinity length [D. A. Head, Phys. Rev. E 68, 061907 (2003)] controls the mesoscopic response to point forces and the crossover to continuum elastic behavior at large distances.

Nonlocal fluctuation correlations in active gels

Many active materials and biological systems are driven far from equilibrium by embedded agents that spontaneously generate forces and distort the surrounding material. Probing and characterizing these athermal fluctuations are essential to understand the properties and behaviors of such systems. Here we present a mathematical procedure to estimate the local action of force-generating agents from the observed fluctuating displacement fields. The active agents are modeled as oriented force dipoles or isotropic compression foci, and the matrix on which they act is assumed to be either a compressible elastic continuum or a coupled network-solvent system. Correlations at a single point and between points separated by an arbitrary distance are obtained, giving a total of three independent fluctuation modes that can be tested with microrheology experiments. Since oriented dipoles and isotropic compression foci give different contributions to these fluctuation modes, ratiometric analysis allows us characterize the force generators. We also predict and experimentally find a high-frequency ballistic regime, arising from individual force-generating events in the form of the slow buildup of stress followed by rapid but finite decay. Finally, we provide a quantitative statistical model to estimate the mean filament tension from these athermal fluctuations, which leads to stiffening of active networks.

Critical Scaling and Aging in Cooling Systems Near the Jamming Transition

We conduct athermal simulations of freely cooling, viscous soft spheres around the jamming transition density varphi(J) and find evidence for a growing length xi(t) that governs relaxation to mechanical equilibrium. xi(t) is manifest in both the velocity correlation function and the spatial correlations in a scalar measure of local force balance which we define. Data for different densities varphi can be collapsed onto two master curves by scaling xi(t) and t by powers of |varphi-varphi(J)|, indicative of critical scaling. Furthermore, particle transport for varphi>varphi(J) exhibits aging and superdiffusion similar to a range of soft matter experiments, suggesting a common origin. Finally, we explain how xi(t) at late times maps onto known behavior away from varphi(J).

Prospects of oral disease control in the future - an opinion.

The mouth supports a diverse microbiota which provides major benefits to the host. On occasions, this symbiotic relationship breaks down (dysbiosis), and disease can be a consequence. We argue that progress in the control of oral diseases will depend on a paradigm shift away from approaches that have proved successful in medicine for many diseases with a specific microbial aetiology. Factors that drive dysbiosis in the mouth should be identified and, where possible, negated, reduced or removed, while antimicrobial agents delivered by oral care products may function effectively, even at sub-lethal concentrations, by modulating the activity and growth of potentially pathogenic bacteria. In this way, the beneficial activities of the resident oral microbiota will be retained and the risk of dysbiosis occurring will be reduced.

Modeling the elastic deformation of polymer crusts formed by sessile droplet evaporation.

Evaporating droplets of polymer or colloid solution may produce a glassy crust at the liquid-vapor interface, which subsequently deforms as an elastic shell. For sessile droplets, the known radial outward flow of solvent is expected to generate crusts that are thicker near the pinned contact line than the apex. Here we investigate, by nonlinear quasistatic simulation and scaling analysis, the deformation mode and stability properties of elastic caps with a nonuniform thickness profile. By suitably scaling the mean thickness and the contact angle between crust and substrate, we find that data collapse onto a master curve for both buckling pressure and deformation mode, thus allowing us to predict when the deformed shape is a dimple, Mexican hat, and so on. This master curve is parameterized by a dimensionless measure of the nonuniformity of the shell. We also speculate on how overlapping time scales for gelation and deformation may alter our findings.

Non-lethal control of the cariogenic potential of an agent-based model for dental plaque.

Dental caries or tooth decay is a prevalent global disease whose causative agent is the oral biofilm known as plaque. According to the ecological plaque hypothesis, this biofilm becomes pathogenic when external challenges drive it towards a state with a high proportion of acid-producing bacteria. Determining which factors control biofilm composition is therefore desirable when developing novel clinical treatments to combat caries, but is also challenging due to the system complexity and the existence of multiple bacterial species performing similar functions. Here we employ agent-based mathematical modelling to simulate a biofilm consisting of two competing, distinct types of bacterial populations, each parameterised by their nutrient uptake and aciduricity, periodically subjected to an acid challenge resulting from the metabolism of dietary carbohydrates. It was found that one population was progressively eliminated from the system to give either a benign or a pathogenic biofilm, with a tipping point between these two fates depending on a multiplicity of factors relating to microbial physiology and biofilm geometry. Parameter sensitivity was quantified by individually varying the model parameters against putative experimental measures, suggesting non-lethal interventions that can favourably modulate biofilm composition. We discuss how the same parameter sensitivity data can be used to guide the design of validation experiments, and argue for the benefits of in silico modelling in providing an additional predictive capability upstream from in vitro experiments.

Linear surface roughness growth and flow smoothening in a three-dimensional biofilm model.

The sessile microbial communities known as biofilms exhibit varying architectures as environmental factors are varied, which for immersed biofilms includes the shear rate of the surrounding flow. Here we modify an established agent-based biofilm model to include affine flow and employ it to analyze the growth of surface roughness of single-species, three-dimensional biofilms. We find linear growth laws for surface geometry in both horizontal and vertical directions and measure the thickness of the active surface layer, which is shown to anticorrelate with roughness. Flow is shown to monotonically reduce surface roughness without affecting the thickness of the active layer. We argue that the rapid roughening is due to nonlocal surface interactions mediated by the nutrient field, which are curtailed when advection competes with diffusion. We further argue the need for simplified models to elucidate the underlying mechanisms coupling flow to growth.

Spindles and active vortices in a model of confined filament-motor mixtures

BackgroundRobust self-organization of subcellular structures is a key principle governing the dynamics and evolution of cellular life. In fission yeast cells undergoing division, the mitotic spindle spontaneously emerges from the interaction of microtubules, motor proteins and the confining cell walls, and asters and vortices have been observed to self-assemble in quasi-two dimensional microtubule-kinesin assays. There is no clear microscopic picture of the role of the active motors driving this pattern formation, and the relevance of continuum modeling to filament-scale structures remains uncertain.ResultsHere we present results of numerical simulations of a discrete filament-motor protein model confined to a pressurised cylindrical box. Stable spindles, nematic configurations, asters and high-density semi-asters spontaneously emerge, the latter pair having also been observed in cytosol confined within emulsion droplets. State diagrams are presented delineating each stationary state as the pressure, motor speed and motor density are varied. We further highlight a parameter regime where vortices form exhibiting collective rotation of all filaments, but have a finite life-time before contracting to a semi-aster. Quantifying the distribution of life-times suggests this contraction is a Poisson process. Equivalent systems with fixed volume exhibit persistent vortices with stochastic switching in the direction of rotation, with switching times obeying similar statistics to contraction times in pressurised systems. Furthermore, we show that increasing the detachment rate of motors from filament plus-ends can both destroy vortices and turn some asters into vortices.ConclusionsWe have shown that discrete filament-motor protein models provide new insights into the stationary and dynamical behavior of active gels and subcellular structures, because many phenomena occur on the length-scale of single filaments. Based on our findings, we argue the need for a deeper understanding of the microscopic activities underpinning macroscopic self-organization in active gels and urge further experiments to help bridge these lengths.