Cooperative mechanosensitivity and allostery of focal adhesion clusters.

We analyse the role of cooperative interaction between neighbouring adhesion-mechanosensor complexes by constructing an Ising-like Hamiltonian describing the free energy of cell adhesion on a substrate as a lattice of 3-state mechanosensing sites involving focal adhesion kinase (FAK). We use a Monte Carlo stochastic algorithm to find equilibrium configurations of these mechanosensors in two representative geometries: on a 1D ring representing the rim of a cell on a flat surface, and a 2D bounded surface representing the whole area of cell contact with a flat surface. The level of FAK activation depends on the pulling force applied to the individual FAK-integrin via actin-myosin contractile networks, and the details of the coupling between individual sensors in a cluster. Strong coupling is shown to make the FAK sensors experience a sharp on-off behaviour in their activation, while at low coupling the activation/autoinhibition transition occurs over a broad range of pulling force. We find that the activation/autoinhibition transition of FAK in the 2D system with strong coupling occurs with a hysteresis, the width of which depends on the rate of change of force. The effect of introducing a regulating protein (such as Src) in a limited quantity to control FAK activation is explored, and visualizations of clustering in both topologies are presented. In particular the results on the bounded 2D surface indicate that clustering of active FAK occurs preferentially at the boundary, in agreement with experimental observations of focal adhesions in cells.

Kinetics of fragmentation and dissociation of two-strand protein filaments: Coarse-grained simulations and experiments.

While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation. We quantify the orders of magnitude by which the depolymerization rate from the filament ends koff is larger than fragmentation rate k- and establish the law koff/k- = exp[(ε‖ - ε⊥)/kBT] = exp[0.5ε/kBT], which accounts for the topology and energy of bonds holding the filament together. This mechanism and the order-of-magnitude predictions are well supported by direct experimental measurements of depolymerization of insulin amyloid filaments.

Fragmentation and depolymerization of non-covalently bonded filaments.

Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly rate, at which inter-protein bonds break due to the thermal motion. Existing models often assume that the thermal dissociation of subunits occurs uniformly along the filament, or even preferentially in the middle, while the well-known propensity of F-actin to depolymerize from one end is mediated by biochemical factors. Here, we show for a very general (and generic) model, using Brownian dynamics simulations and theory, that the breakup location along the filament is strongly controlled by the asymmetry of the binding force about the minimum, as well as by the bending stiffness of the filament. We provide the basic connection between the features of the interaction potential between subunits and the breakup topology. With central-force (that is, fully flexible) bonds, the breakup rate is always maximum in the middle of the chain, whereas for semiflexible or stiff filaments this rate is either a minimum in the middle or flat. The emerging framework provides a unifying understanding of biopolymer fragmentation and depolymerization and recovers earlier results in its different limits.

Spatial propagation of protein polymerization.

We consider the spatial dependence of filamentous protein self-assembly. Through studying the cases where the spreading of aggregated material is dominated either by diffusion or by growth, we derive analytical results for the spatial evolution of filamentous protein aggregation, which we validate against Monte Carlo simulations. Moreover, we compare the predictions of our theory with experimental measurements of two systems for which we identify the propagation as either growth or diffusion controlled. Our results connect the macroscopic observables that characterize the spatial propagation of protein self-assembly with the underlying microscopic processes and provide physical limits on spatial propagation and prionlike behavior associated with protein aggregation.

Role of the potential landscape on the single-file diffusion through channels.

Transport of colloid particles through narrow channels is ubiquitous in cell biology as well as becoming increasingly important for microfluidic applications or targeted drug delivery. Membrane channels in cells are useful models for artificial designs because of their high efficiency, selectivity, and robustness to external fluctuations. Here, we model the passive channels that let cargo simply diffuse through them, affected by a potential profile along the way. Passive transporters achieve high levels of efficiency and specificity from binding interactions with the cargo inside the channel. This however leads to a paradox: why should channels which are so narrow that they are blocked by their cargo evolve to have binding regions for their cargo if that will effectively block them? Using Brownian dynamics simulations, we show that different potentials, notably symmetric, increase the flux through narrow passive channels - and investigate how shape and depth of potentials influence the flux. We find that there exist optimal depths for certain potential shapes and that it is most efficient to apply a small force over an extended region of the channel. On the other hand, having several spatially discrete binding pockets will not alter the flux significantly. We also explore the role of many-particle effects arising from pairwise particle interactions with their neighbours and demonstrate that the relative changes in flux can be accounted for by the kinetics of the absorption reaction at the end of the channel.

Theory of thermally activated ionization and dissociation of bound states.

Calculating the microscopic dissociation rate of a bound state, such as a classical diatomic molecule, has been difficult so far. The problem was that standard theories require an energy barrier over which the bound particle (or state) escapes into the preferred low-energy state. This is not the case when the long-range repulsion responsible for the barrier is either absent or screened (as in Cooper pairs, plasmas, or biomolecular complexes). We solve this classical problem by accounting for entropic driving forces at the microscopic level. The theory predicts dissociation rates for arbitrary potentials and is successfully tested on the example of plasma, where it yields an estimate of ionization in the core of the Sun in excellent agreement with experiments. In biology, the new theory accounts for crowding in receptor-ligand kinetics and protein aggregation.

Fabrication and electromechanical characterization of near-field electrospun composite fibers.

We report the use of near-field electrospinning (NFES) as a route to fabricate composite electrodes. Electrodes made of composite fibers of multi-walled carbon nanotubes in polyethylene oxide (PEO) are formed via liquid deposition, with precise control over their configuration. The electromechanical properties of free-standing fibers and fibers deposited on elastic substrates are studied in detail. In particular, we examine the elastic deformation limit of the resulting free-standing fibers and find, similarly to bulk PEO composites, that the plastic deformation onset is below 2% of tensile strain. In comparison, the apparent deformation limit is much improved when the fibers are integrated onto a stretchable, elastic substrate. It is hoped that the NFES fabrication protocol presented here can provide a platform to direct-write polymeric electrodes, and to integrate both stiff and soft electrodes onto a variety of polymeric substrates.

Thermodynamically stable blue phases.

We show theoretically that flexoelectricity stabilizes blue phases in chiral liquid crystals. Induced internal polarization reduces the elastic energy cost of splay and bend deformations surrounding singular lines in the director field. The energy of regions of double twist is unchanged. This in turn reduces the free energy of the blue phase with respect to that of the chiral nematic phase, leading to stability over a wider temperature range. The theory explains the discovery of large temperature range blue phases in highly flexoelectric "bimesogenic" and "bent-core" materials, and predicts how this range may be increased further.

Micro-Raman spectroscopy of algae: composition analysis and fluorescence background behavior.

Preliminary feasibility studies were performed using Stokes Raman scattering for compositional analysis of algae. Two algal species, Chlorella sorokiniana (UTEX #1230) and Neochloris oleoabundans (UTEX #1185), were chosen for this study. Both species were considered to be candidates for biofuel production. Raman signals due to storage lipids (specifically triglycerides) were clearly identified in the nitrogen-starved C. sorokiniana and N. oleoabundans, but not in their healthy counterparts. On the other hand, signals resulting from the carotenoids were found to be present in all of the samples. Composition mapping was conducted in which Raman spectra were acquired from a dense sequence of locations over a small region of interest. The spectra obtained for the mapping images were filtered for the wavelengths of characteristic peaks that correspond to components of interest (i.e., triglyceride or carotenoid). The locations of the components of interest could be identified by the high intensity areas in the composition maps. Finally, the time evolution of fluorescence background was observed while acquiring Raman signals from the algae. The time dependence of fluorescence background is characterized by a general power law decay interrupted by sudden high intensity fluorescence events. The decreasing trend is likely a result of photo-bleaching of cell pigments due to prolonged intense laser exposure, while the sudden high intensity fluorescence events are not understood.

Effects of water on aggregation and stability of monoglycerides in hydrophobic solutions.

We apply a set of different techniques to analyze the physical properties and phase transitions of monoglyceride (MG)-oil-water ternary systems. The effect of MGs on water absorption in food-grade hazelnut oil and in pure hydrocarbon oil (decane) is reported. Comparison between decane and hazelnut oil backgrounds indicates that the effect of water absorption is significant and universal in different MG ternary systems. Adding small amounts of cosurfactant (stearic acid) is necessary to stabilize the MGs in oil-water combinations by enhancing the swelling capacity of lamellar layers; as a result, the structures become sensitive to the pH of the aqueous phase used. The dramatic changes on increasing the aqueous content are recorded by the calorimetry. In samples with small quantities of water, the phase behavior is almost independent of the pH. Once the proportion of water increases, the effect of pH is prominent. At low pH, the solubility of MG in water is limited, and the ternary system retains key features of the oil-dominated environment, such as the sequence of two transitions on cooling, with the low-temperature sub-alpha crystalline phase. At high pH and a sufficient amount of water, the MG layers remain properly swollen, and the crystalline phase disappears from the phase diagram. We spend considerable effort identifying the inverse lamellar phase of MGs in an oil-dominated environment with the so-called alpha-gel phase that is well-established in water-dominated systems, and distinguishing "demixing" from water and from oil. The rheology is examined in different fluid and gel phases; the storage modulus generally decreased on increasing the water proportion, but a gel-like response is found in the high-temperature lamellar phase over a wide range of water dilution. We then focus on aging phenomena in the inverse lamellar (or alpha-gel) phase and show that the rearranging of hydrogen bonds is slowed down and disrupted by the presence of water, giving the lamellar gel longer life times.

Rheology of hard glassy materials.

Glassy solids may undergo a fluidization (yielding) transition upon deformation whereby the material starts to flow plastically. It has been a matter of debate whether this process is controlled by a specific time scale, from among different competing relaxation/kinetic processes. Here, two constitutive models of cage relaxation are examined within the microscopic model of nonaffine elasto-plasticity. One (widely used) constitutive model implies that the overall relaxation rate is dominated by the fastest between the structural (α) relaxation rate and the shear-induced relaxation rate. A different model is formulated here which, instead, assumes that the slowest (global) relaxation process controls the overall relaxation. We show that the first model is not compatible with the existence of finite elastic shear modulus for quasistatic (low-frequency) deformation, while the second model is able to describe all key features of deformation of 'hard' glassy solids, including the yielding transition, the nonaffine-to-affine plateau crossover, and the rate-stiffening of the modulus. The proposed framework provides an operational way to distinguish between 'soft' glasses and 'hard' glasses based on the shear-rate dependence of the structural relaxation time.

Deuterium NMR study of mobility and fluctuations in nematic and isotropic elastomers.

Orientational ordering in polydomain nematic and isotropic elastomers with identical polysiloxane backbone and different deuterium-labeled side groups is studied by D-NMR. In the nematic elastomer the orientational order parameter grows in a critical fashion on crossing the I-N transition implying a continuous phase transition driven by critical fluctuations of local director. The orientational (nematic) ordering occurs on the background of the polymer dynamics exhibited by the backbone, which is similar in the nematic and the analogous isotropic elastomers. The temperature dependence of NMR linewidths is compatible with a Vogel-Fulcher glassy dynamics.

Universal kinetics of helix-coil transition in gelatin.

By covering a much wider concentration range than previous studies we find a very unusual exponential dependence of the rate of helix formation on concentration of gelatin in water and ethylene glycol solutions. By applying a procedure of concentration-temperature superposition we build a master curve describing the initial renaturation rates in both solvents. The growth of the normalized helical fraction chi(t) is a first-order process, with a rate constant consistent with cis-trans isomerization, in most situations. We propose that association of three separate chains to form a triple helical nucleus occurs rapidly and contributes less to the helical onset than previously thought. The measured helix content is a result of lengthening of the triple helix after nucleation, by zipping from the associated nuclei.

Semisoft elastic response of nematic elastomers to complex deformations.

We consider a relaxed semisoft elastomer with its director oriented along the z axis that is first subjected to a large stretch in the x direction then to a slight x-z shear. We give a general argument that in any theory including director rotation, at the onset and end of the director rotation induced by these large stretches, there will be kinks in the stress-large strain curve (forming a stress-strain plateau) and zeros in the x-z shear modulus (C5) associated with small shears imposed on top of the stretches. We then find the analytical forms of the C5 -strain curves for a particular model of semisoftness (arising from compositional fluctuations) and show that it, together with the known stress-strain curve, provides the basis for a strong test of this theory. Finally, we consider the scope for other semisoft models and show that the compositional fluctuations model in fact yielded a generic form, that is, it is the most general quadratic free energy that does not explicitly include a final state direction other than the director. By introducing such additional directions, a large range of alternative models could be developed.

Nematic-isotropic transition with quenched disorder.

Nematic elastomers do not show the discontinuous, first-order, phase transition that the Landau-De Gennes mean field theory predicts for a quadrupolar ordering in three dimensions. We attribute this behavior to the presence of network crosslinks, which act as sources of quenched orientational disorder. We show that the addition of weak random anisotropy results in a singular renormalization of the Landau-De Gennes expression, adding an energy term proportional to the inverse quartic power of order parameter Q. This reduces the first-order discontinuity in Q. For sufficiently high disorder strength the jump disappears altogether and the phase transition becomes continuous, in some ways resembling the supercritical transitions in external field.

Chirality transfer and stereoselectivity of imprinted cholesteric networks.

Imprinting of cholesteric textures in a polymer network is a method of preserving a macroscopically chiral phase in a system with no molecular chirality. By modifying the elastic properties of the network, the resulting stored helical twist can be manipulated within a wide range since the imprinting efficiency depends on the balance between the elastic constants and twisting power at network formation. One spectacular property of phase chirality imprinting is the created ability of the network to adsorb preferentially one stereo component from a racemic mixture. In this paper we explore this property of chirality transfer from a macroscopic to a molecular scale. In particular, we focus on the competition between the phase chirality and the local nematic order. We demonstrate that it is possible to control the subsequent release of a chiral solvent component from the imprinting network and the reversibility of the stereo-selective swelling by racemic solvents.

Local structure controls the nonaffine shear and bulk moduli of disordered solids.

Paradigmatic model systems, which are used to study the mechanical response of matter, are random networks of point-atoms, random sphere packings, or simple crystal lattices; all of these models assume central-force interactions between particles/atoms. Each of these models differs in the spatial arrangement and the correlations among particles. In turn, this is reflected in the widely different behaviours of the shear (G) and compression (K) elastic moduli. The relation between the macroscopic elasticity as encoded in G, K and their ratio, and the microscopic lattice structure/order, is not understood. We provide a quantitative analytical connection between the local orientational order and the elasticity in model amorphous solids with different internal microstructure, focusing on the two opposite limits of packings (strong excluded-volume) and networks (no excluded-volume). The theory predicts that, in packings, the local orientational order due to excluded-volume causes less nonaffinity (less softness or larger stiffness) under compression than under shear. This leads to lower values of G/K, a well-documented phenomenon which was lacking a microscopic explanation. The theory also provides an excellent one-parameter description of the elasticity of compressed emulsions in comparison with experimental data over a broad range of packing fractions.

F1 rotary motor of ATP synthase is driven by the torsionally-asymmetric drive shaft.

F1F0 ATP synthase (ATPase) either facilitates the synthesis of ATP in a process driven by the proton moving force (pmf), or uses the energy from ATP hydrolysis to pump protons against the concentration gradient across the membrane. ATPase is composed of two rotary motors, F0 and F1, which compete for control of their shared γ -shaft. We present a self-consistent physical model of F1 motor as a simplified two-state Brownian ratchet using the asymmetry of torsional elastic energy of the coiled-coil γ -shaft. This stochastic model unifies the physical concepts of linear and rotary motors, and explains the stepped unidirectional rotary motion. Substituting the model parameters, all independently known from recent experiments, our model quantitatively reproduces the ATPase operation, e.g. the 'no-load' angular velocity is ca. 400 rad/s anticlockwise at 4 mM ATP. Increasing the pmf torque exerted by F0 can slow, stop and overcome the torque generated by F1, switching from ATP hydrolysis to synthesis at a very low value of 'stall torque'. We discuss the motor efficiency, which is very low if calculated from the useful mechanical work it produces - but is quite high when the 'useful outcome' is measured in the number of H(+) pushed against the chemical gradient.

Shape instability on swelling of a stretched nematic elastomer filament.

Liquid crystalline elastomers combine the ordering properties of liquid crystals with elasticity of crosslinked polymer networks. In monodomain (permanently aligned) elastomers, altering the orientational (nematic) order causes changes in the equilibrium sample length, which is the basis of the famous effect of large-amplitude reversible mechanical actuation. The stimulus for this effect could be a change in temperature, or illumination by light in photosensitized elastomers, but equally the nematic order changes by mixing with a solvent. This work theoretically investigates a competition between the spontaneous contraction on swelling of a monodomain nematic elastomer and the externally imposed stretching. We find that this competition leads to bistability in the system and allows a two-phase separation between a nematic state with lower swelling and an isotropic state with higher solvent concentration. We calculated the conditions in which the instability occurs as well as the mechanical and geometric parameters of equilibrium states. Being able to predict how this instability arises will provide opportunities for exploiting nematic elastomer filaments.

Cholesteric elastomers: deformable photonic solids.

A mechanical strain applied to a monodomain cholesteric elastomer modulates and eventually unwinds the helical director distribution. There are similarities with the classical problem of an electric field applied to a cholesteric liquid crystal, but also differences. Frank elasticity is of minor importance unless the gel is very weak. The interplay is rather between the director being helically anchored to the rubber elastic matrix and the external mechanical field. Stretching perpendicular to the helix axis induces the uniform unwound state via the elimination of sharp, pinned twist walls above a critical strain. Below the critical strain the coarsening of the director distribution is not accompanied by an increase but rather by an affine decrease in the pitch. Unwinding through conical director states occurs when the elastomer is stretched along the helical axis. Finally we consider cholesteric elastomers in a classical device geometry with an electric field applied along the pitch axis and hence transverse to the director orientation.