Folded protein hydrogels are emerging as promising new materials for medicine and healthcare applications. Folded globular proteins can be modelled as colloids which exhibit site specific cross-linking for controlled network formation. However, folded proteins have inherent mechanical stability and unfolded in response to an applied force. It is not yet understood how colloidal network theory maps onto folded protein hydrogels and whether it models the impact of protein unfolding on network properties. To address this, we study a hybrid system which contains folded proteins (patchy colloids) and unfolded proteins (biopolymers). We use a model protein, bovine serum albumin (BSA), to explore network architecture and mechanics in folded protein hydrogels. We alter both the photo-chemical cross-linking reaction rate and the mechanical properties of the protein building block, via illumination intensity and redox removal of robust intra-protein covalent bonds, respectively. This dual approach, in conjunction with rheological and structural techniques, allows us to show that while reaction rate can 'fine-tune' the mechanical and structural properties of protein hydrogels, it is the force-lability of the protein which has the greatest impact on network architecture and rigidity. To understand these results, we consider a colloidal model which successfully describes the behaviour of the folded protein hydrogels but cannot account for the behaviour observed in force-labile hydrogels containing unfolded protein. Alternative models are needed which combine the properties of colloids (folded proteins) and biopolymers (unfolded proteins) in cross-linked networks. This work provides important insights into the accessible design space of folded protein hydrogels without the need for complex and costly protein engineering, aiding the development of protein-based biomaterials.

The structural evolution of hierarchical structures of nanoscale biomolecules is crucial for the construction of functional networks in vivo and in vitro. Despite the ubiquity of these networks, the physical mechanisms behind their formation and self-assembly remains poorly understood. Here, this study uses photochemically cross-linked folded protein hydrogels as a model biopolymer network system, with a combined time-resolved rheology and small-angle x-ray scattering (SAXS) approach to probe both the load-bearing structures and network architectures respectively thereby providing a cross-length scale understanding of the network formation. Combining SAXS, rheology, and kinetic modeling, a dual formation mechanism consisting of a primary formation phase is proposed, where monomeric folded proteins create the preliminary protein network scaffold; and a subsequent secondary formation phase, where both additional intra-network cross-links form and larger oligomers diffuse to join the preliminary network, leading to a denser more mechanically robust structure. Identifying this as the origin of the structural and mechanical properties of protein networks creates future opportunities to understand hierarchical biomechanics in vivo and develop functional, designed-for-purpose, biomaterials.

Fibrous networks constructed from high aspect ratio protein building blocks are ubiquitous in nature. Despite this ubiquity, the functional advantage of such building blocks over globular proteins is not understood. To answer this question, we engineered hydrogel network building blocks with varying numbers of protein L domains to control the aspect ratio. The mechanical and structural properties of photochemically crosslinked protein L networks were then characterised using shear rheology and small angle neutron scattering. We show that aspect ratio is a crucial property that defines network architecture and mechanics, by shifting the formation from translationally diffusion dominated to rotationally diffusion dominated. Additionally, we demonstrate that a similar transition is observed in the model living system: fibrin blood clot networks. The functional advantages of this transition are increased mechanical strength and the rapid assembly of homogenous networks above a critical protein concentration, crucial for in vivo biological processes such as blood clotting. In addition, manipulating aspect ratio also provides a parameter in the design of future bio-mimetic and bio-inspired materials.

Background: Dental caries develops under actively sugar-fermenting dental biofilms, but the most successful control methods available only target mineral loss. Reduced salivary flow rates (hyposalivation) significantly exacerbate caries progression by lessening sugar and acid clearance near tooth surfaces. Maintaining dental biofilm symbiosis (health) under hyposalivation requires knowledge of the impact of acid inhibition under given dietary regimens. Methods: An individual-based mathematical model was used to predict biofilm dysbiosis under normal or hyposalivatory conditions by regulating the frequency of sugar intake and inhibiting microbial glycolysis, reducing the acid challenge to the tooth mineral. The impact of pH-dependent (stronger inhibition at lower pH [eg, fluoride]) and pH-independent (general percentage reduction in acid production) strategies on pH near the tooth surface during sugar intake, and the corresponding compositional changes in the biofilm, were quantified. Results: Under normal saliva flow, reducing the frequency of sugar intake and increasing the inhibition of acid production by pH-dependent or pH-independent strategies could prevent bacterial dysbiosis and prevent the biofilm from having a caries-associated (dysbiotic) to a health-associated (symbiotic) composition. However, under hyposalivatory conditions, dysbiosis occurred beyond 2 sugar intakes per day, and the degree of inhibition of glycolysis required to prevent dysbiosis was not feasible with available therapeutics. Conclusions: Model data predict that to counteract the drastic effect of hyposalivation on biofilm dysbiosis, it will be essential to significantly reduce the frequency of fermentable sugar intake and any direct inhibition of bacterial metabolism.

Globular folded protein-based hydrogels are becoming increasingly attractive due to their specific biological functionality, as well as their responsiveness to stimuli. By modelling folded proteins as colloids, there are rich opportunities to explore network formation mechanisms in protein hydrogels that negate the need for computationally expensive simulations which capture the full complexity of proteins. Here we present a kinetic lattice-based model which simulates the formation of irreversibly chemically crosslinked, folded protein-based hydrogels. We identify the critical point of gel percolation, explore the range of network regimes covering diffusion-limited to reaction-limited cluster aggregation (DLCA and RLCA, respectively) network formation mechanisms and predict the final network structure, fractal dimensions and final gel porosity. We reveal a crossover between DLCA and RLCA mechanisms as a function of protein volume fraction and show how the final network structure is governed by the structure at the percolation point, regardless of the broad variation of non-percolating cluster masses observed across all systems. An analysis of the pore size distribution in the final network structures reveals that, approaching RLCA, gels have larger maximal pores than the DLCA counterparts for both volume fractions studied. This general kinetic model and the analysis tools generate predictions of network structure and concurrent porosity over a broad range of experimentally controllable parameters that are consistent with current expectations and understanding of experimental results.

A family of marginally rigid (isostatic) spring networks with fractal structure up to a controllable length was devised, and the viscoelastic spectra G^{*}(ω) calculated. Two nontrivial scaling regimes were observed, (i) G^{'}≈G^{''}∝ω^{Δ} at low frequencies, consistent with Δ=1/2, and (ii) G^{'}∝G^{''}∝ω^{Δ^{'}} for intermediate frequencies corresponding to fractal structure, consistent with a theoretical prediction Δ^{'}=(ln3-ln2)/(ln3+ln2). The crossover between these two regimes occurred at lower frequencies for larger fractals in a manner suggesting diffusivelike dispersion. Solid gels generated by introducing internal stresses exhibited similar behavior above a low-frequency cutoff, indicating the relevance of these findings to real-world applications.

Fractal structure emerges spontaneously from the chemical cross­linking of monomers into hydrogels, and has been directly linked to power law visco­elasticity at the gel transition, as recently demonstrated for isostatic (marginally–rigid) spring networks based on the Sierpinski triangle. Here we generalize the Sierpinski triangle generation rules to produce 4 fractals, all with the same dimension d_ f=log 3/log 2, with the Sierpinski triangle being one case. We show that spring networks derived from these fractals are all isostatic, but exhibit one of two distinct exponents for their power–law viscoelasticity. We conclude that, even for networks with fixed connectivity, power–law viscoelasticity cannot generally be a function of the fractal dimension alone.

Root caries progression is aggravated by hyposalivation, which can accelerate the conversion of a dental biofilm from having a symbiotic microbial relationship with the host (predominance of nonaciduric species) to a dysbiotic one (dominated by aciduric species). Using a mathematical model previously employed to investigate factors associated with biofilm dysbiosis, we systematically explored the deleterious effect of hyposalivation on the composition of the biofilm and the risk of root dentin demineralization. By varying the clearance half-times of sugar (i.e., readily fermented dietary carbohydrates), we simulated hyposalivation and investigated its effect on 1) the time that the biofilm pH spends below the minimum for dentin or enamel demineralization and 2) the conversion of the biofilm from a symbiotic to dysbiotic composition. The effect of increasing sugar clearance half-times on the time that the biofilm pH is below the threshold for demineralization was more pronounced for dentin than for enamel (e.g., increasing the clearance half-time from 2 to 6 min doubled the time that the biofilm pH was below the threshold for dentin demineralization). The effect on biofilm composition assessed at 50 d showed that the conversion from a symbiotic to a dysbiotic biofilm happened around a frequency of 6 sugar intakes per day when the clearance half-time was 2 min but only 3 sugar intakes per day when the clearance half-time was 6 min. Taken together, the results confirm the profound effect that prolonged sugar clearance has on the dynamics of dental biofilm composition and the subsequent risk of root caries. This in silico model should be applied to study how interventions that alter salivary clearance rates or modify biofilm pH can affect clinical conditions such as root caries.

Hydrogels constructed from folded protein domains are of increasing interest as resilient and responsive biomaterials, but their optimization for applications requires time-consuming and costly molecular design. Here, we explore a complementary approach to control their properties by examining the influence of crosslinking rate on the structure and viscoelastic response of a model hydrogel constructed from photochemically crosslinked bovine serum albumin (BSA). Gelation is observed to follow a heterogeneous nucleation pathway in which BSA monomers crosslink into compact nuclei that grow into fractal percolated networks. Both the viscoelastic response probed by shear rheology and the nanostructure probed by small-angle X-ray scattering (SAXS) are shown to depend on the photochemical crosslinking reaction rate, with increased reaction rates corresponding to higher viscoelastic moduli, lower fractal dimension, and higher fractal cluster size. Reaction rate-dependent changes are shown to be consistent with a transition between diffusion- and rate-limited assembly, and the corresponding changes to viscoelastic response are proposed to arise from the presence of nonfractal depletion regions, as confirmed by SAXS. This controllable nanostructure and viscoelasticity constitute a potential route for the precise control of hydrogel properties, without the need for molecular modification.

Mechanically bonded fabrics account for a significant portion of nonwoven products, and serve many niche areas of nonwoven manufacturing. Such fabrics are characterized by layers of disordered fibrous webs, but we lack an understanding of how such microstructures determine bulk material response. Here we numerically determine the linear shear response of needle-punched fabrics modeled as cross-linked sheets of two-dimensional (2D) Mikado networks. We systematically vary the intra-sheet fiber density, inter-sheet separation distance, and direction of shear, and quantify the macroscopic shear modulus alongside the degree of affinity and energy partition. For shear parallel to the sheets, the response is dominated by intrasheet fibers and follows known trends for 2D Mikado networks. By contrast, shears perpendicular to the sheets induce a softer response dominated by either intrasheet or intersheet fibers depending on a quadratic relation between sheet separation and fiber density. These basic trends are reproduced and elucidated by a simple scaling argument that we provide. We discuss the implications of our findings in the context of real nonwoven fabrics.

We employ a matrix-based solver for the linear rheology of fluid-immersed disordered spring networks to reveal four distinct dynamic response regimes. One regime-completely absent in the known vacuum response-exhibits coupled fluid flow and network deformation, with both components responding nonaffinely. This regime contains an additional plateau (peak) in the frequency-dependent storage (loss) modulus-features that vanish without full hydrodynamic interactions. The mechanical response of immersed networks such as biopolymers and hydrogels is thus richer than previously established and offers additional modalities for design and control through fluid interactions.

Modelling a random fibre network representative of a real world material leads to a large sparse linear matrix system with a high condition number. Current off-lattice networks are not a realistic model for the mechanical properties of the large volume of random fibres seen in actual materials. In this paper, we present the numerical methods employed within our two-dimensional and three-dimensional models that improve the computational time limitations seen in existing off-lattice models. Specifically, we give a performance comparison of two-dimensional random fibre networks solved iteratively with different choices of preconditioner, followed by some initial results of our three-dimensional model.

Biological organisms make use of hierarchically organised structures to modulate mechanical behaviour across multiple lengthscales, allowing microscopic objects to generate macroscopic effects. Within these structural hierarchies, the resultant physical behaviour of the entire system is determined not only by the intrinsic mechanical properties of constituent subunits, but also by their organisation in three-dimensional space. When these subunits are polyproteins, colloidal chains or other globular domain polymers, the Kratky-Porod model is often assumed for the individual subunits. Hence, it is implicitly asserted that the polymeric object has an intrinsic parameter, the persistence length, that defines its flexibility. However, the persistence lengths extracted from experiment vary, and are often relatively small. Through a series of simulations on polymer chains formed of globular subunits, we show that the persistence length itself is a hierarchical structural property, related not only to the intrinsic mechanical properties of the underlying monomeric subunits, but emerging due to the organisation of inhomogenous geometry along the polymer contour.

Dental caries is the most prevalent infection globally and a substantial economic burden in developed countries. Dietary sugars are the main risk factor, and drive increased proportions of acid-producing and acid-tolerating (aciduric) bacterial species within dental biofilms. Recent longitudinal studies have suggested that caries is most strongly correlated with total sugar intake, contrasting with the prevailing view that intake frequency is the primary determinant. To explore this possibility, we employed a computational model for supragingival plaque to systematically sample combinations of sugar frequency and total amount, allowing their independent contributions on the ratio of aciduric (i.e. cariogenic) to non-aciduric bacteria to be unambiguously determined. Sugar frequency was found to be irrelevant for either very high or very low daily total amounts as the simulated biofilm was predicted to be always or never cariogenic, respectively. Frequency was a determining factor for intermediate total amounts of sugar, including the estimated average human consumption. An increased risk of caries (i.e. high prevalence of aciduric/non-aciduric species) was predicted for high intake frequencies. Thus, both total amount and frequency of sugar intake may combine to influence plaque cariogenicity. These findings could be employed to support public guidance for dietary change, leading to improved oral healthcare.

Measurement of a tissue-specific electrical resistance may offer a discriminatory metric for evaluation of tissue health during cancer surgery. With a move toward minimally-invasive procedures, applicable contact sensing modalities must be scalable, fast and robust. A passive resistance characterisation method utilising a biogalvanic cell as an intrinsic power source has been proposed as a potentially suitable solution. Previous work has evaluated this system with results showing effective discrimination of tissue type and damage (through electroporation). However, aspects of the biogalvanic cell have been found to influence the characterisation performance, and are not currently accounted for within the system model. In particular, the electrode and salt-bridge resistance are not independently determined, leading to over-predictions of tissue resistivity. This paper describes a more comprehensive model and characterisation scheme, with electrode parameters and salt-bridge resistivity being evaluated independently. In a generalised form, the presented model illustrates how the relative resistive contributions from the electrodes and medium relate to the existing characterisation method efficacy. We also describe experiments with physiologically relevant salt solutions (1.71, 17.1, 154 mM), used for validation and comparison. The presented model shows improved performance over the current biogalvanic measurement technique at the median conductivity. Both the proposed and extant system models become unable to predict conductivity accurately at high conductivity due to the dominance of the electrodes. The characterisation techniques have also been applied to data collected on freshly excised human colon tissue (healthy and cancerous). The findings suggest that the resistance of the cell under the test conditions is electrode dominated, leading to erroneous tissue resistance determination. Measurement optimisation strategies and the surgical applicability of the biogalvanic technique are discussed in light of these findings.

Biomimetic hydrogels based on natural polymers are a promising class of biomaterial, mimicking the natural extra-cellular matrix of biological tissues and providing cues for cell attachment, proliferation, and differentiation. With a view to providing an upstream method to guide subsequent experimental design, the aim of this study was to introduce a mathematical model that described the rheological properties of a hydrogel system based on covalently cross-linked collagen triple helices. In light of their organization, such gels exhibit limited collagen bundling that cannot be described by existing fibril network models. The model presented here treats collagen triple helices as discrete semiflexible polymers, permits full access to metrics for network microstructure, and should provide a comprehensive understanding of the parameter space associated with the development of such multifunctional materials. Triple helical hydrogel networks were experimentally obtained via the reaction of type I collagen with both aromatic and aliphatic diacids. The complex modulus G* was found from rheological testing in linear shear and quantitatively compared to model predictions. In silico data from the computational model successfully described the experimental trends in hydrogel storage modulus with either (i) the concentration of collagen triple helices during the cross-linking reaction or (ii) the type of cross-linking segment introduced in resulting hydrogel networks. This approach may pave the way to a step change in the rational design of biomimetic triple helical collagen systems with controlled multifunctionality.

Disordered fibre networks are ubiquitous in nature and have a wide range of industrial applications as novel biomaterials. Predicting their viscoelastic response is straightforward for affine deformations that are uniform over all length scales, but when affinity fails, as has been observed experimentally, modelling becomes challenging. Here we present a numerical methodology, related to an existing framework for amorphous packings, to predict the steady-state viscoelastic spectra and degree of affinity for disordered fibre networks driven at arbitrary frequencies. Applying this method to a peptide gel model reveals a monotonic increase of the shear modulus as the soft, non-affine normal modes are successively suppressed as the driving frequency increases. In addition to being dominated by fibril bending, these low frequency network modes are also shown to be delocalised. The presented methodology provides insights into the importance of non-affinity in the viscoelastic response of peptide gels, and is easily extendible to all types of fibre networks.

The removal of infectious biofilms from tissues or implanted devices and their transmission through fluid transport systems depends in part of the mechanical properties of their polymeric matrix. Linking the various physical and chemical microscopic interactions to macroscopic deformation and failure modes promises to unveil design principles for novel therapeutic strategies targeting biofilm eradication, and provide a predictive capability to accelerate the development of devices, water lines, etc, that minimise microbial dispersal. Here, our current understanding of biofilm mechanics is appraised from the perspective of biophysics , with an emphasis on constitutive modelling that has been highly successful in soft matter. Fitting rheometric data to viscoelastic models has quantified linear and nonlinear stress relaxation mechanisms, how they vary between species and environments, and how candidate chemical treatments alter the mechanical response. The rich interplay between growth, mechanics and hydrodynamics is just becoming amenable to computational modelling and promises to provide unprecedented characterisation of infectious biofilms in their native state.

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).

Background: The mouth supports a diverse microbiota which exists as structurally-organised biofilms on mucosal and dental surfaces. The oral microbiota provides major benefits to the host including: (a) colonisation resistance, (b) down-regulation of potentially damaging host inflammatory responses, and (c) active contributions to the normal development of the physiology of the mouth and the host defences.Highlight: Generally, these communities live in harmony (symbiosis) with the host but, on occasions, this symbiotic relationship breaks down and disease occurs (dysbiosis). Disease is associated with shifts in the balance of the oral microbiota driven by changes in the local environment. These changes include more regular conditions of low pH in the biofilm, as a result of an altered diet or reduced saliva flow, thereby favouring the growth and metabolism of acidogenic and acid-tolerating bacteria, at the expense of beneficial oral micro-organisms, and increasing the risk of dental caries. The host mounts an inflammatory response if biofilm accumulates around the gingivae beyond levels compatible with health. If this fails to reduce the biomass, the altered environment selects for increased proportions of obligately anaerobic and proteolytic species that can subvert the host response leading, ultimately, to pocket formation and loss of attachment.Conclusion: An appreciation of ecological principles can lead to new strategies for treatment by identifying and removing the factors that drive dysbiosis, while actively supporting the growth of the natural oral microbiota. Also, the beneficial activities of the resident oral microbiota are retained and the risk of dysbiosis is reduced. (C) 2015 Japanese Association for Oral Biology. Published by Elsevier B.V. All rights reserved.