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1.
J Phys Condens Matter ; 32(39): 395402, 2020 Jun 24.
Artículo en Inglés | MEDLINE | ID: mdl-32579542

RESUMEN

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.

2.
Phys Biol ; 15(2): 026008, 2018 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-29058683

RESUMEN

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.


Asunto(s)
Adhesión Celular , Adhesiones Focales/fisiología , Mecanotransducción Celular , Modelos Moleculares , Adhesiones Focales/química , Método de Montecarlo , Fosforilación , Procesos Estocásticos
3.
J Chem Phys ; 145(10): 105101, 2016 Sep 14.
Artículo en Inglés | MEDLINE | ID: mdl-27634278

RESUMEN

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.


Asunto(s)
Actinas/química , Amiloide/química , Modelos Moleculares , Multimerización de Proteína , Actinas/metabolismo , Amiloide/metabolismo , Cinética , Estructura Secundaria de Proteína , Temperatura
4.
Sci Rep ; 6: 28180, 2016 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-27321713

RESUMEN

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.


Asunto(s)
Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfato/metabolismo , Bacterias/metabolismo , Proteínas Motoras Moleculares/metabolismo , Proteínas de Transferencia de Fosfolípidos/metabolismo , ATPasas de Translocación de Protón/metabolismo , Torque
5.
Sci Rep ; 6: 18724, 2016 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-26732406

RESUMEN

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.

6.
Artículo en Inglés | MEDLINE | ID: mdl-26565260

RESUMEN

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.

7.
J Chem Phys ; 142(11): 114905, 2015 Mar 21.
Artículo en Inglés | MEDLINE | ID: mdl-25796264

RESUMEN

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.


Asunto(s)
Simulación por Computador , Modelos Moleculares , Elasticidad , Nanopartículas/química , Polimerizacion , Proteínas/química , Electricidad Estática , Termodinámica
8.
J Chem Phys ; 141(22): 224901, 2014 Dec 14.
Artículo en Inglés | MEDLINE | ID: mdl-25494767

RESUMEN

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.


Asunto(s)
Coloides/química , Transporte Biológico , Difusión , Diseño de Equipo , Cinética , Técnicas Analíticas Microfluídicas/instrumentación , Modelos Biológicos , Modelos Químicos
9.
Phys Rev Lett ; 112(9): 098101, 2014 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-24655282

RESUMEN

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.


Asunto(s)
Modelos Químicos , Proteínas/química , Difusión , Método de Montecarlo , Polimerizacion , Proteínas/metabolismo , Procesos Estocásticos
10.
Phys Rev Lett ; 108(3): 038302, 2012 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-22400791

RESUMEN

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.

11.
Nanotechnology ; 23(10): 105305, 2012 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-22362025

RESUMEN

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.


Asunto(s)
Nanocompuestos/química , Nanofibras/química , Nanotecnología/métodos , Nanotubos de Carbono/química , Dimetilpolisiloxanos/química , Impedancia Eléctrica , Microelectrodos , Nanocompuestos/ultraestructura , Nanofibras/ultraestructura , Polietilenglicoles/química , Resistencia a la Tracción
12.
Phys Rev Lett ; 104(15): 157801, 2010 Apr 16.
Artículo en Inglés | MEDLINE | ID: mdl-20482018

RESUMEN

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.

13.
Biotechnol Bioeng ; 105(5): 889-98, 2010 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-19998275

RESUMEN

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.


Asunto(s)
Eucariontes/química , Espectrometría Raman/métodos , Chlorella/química , Chlorophyta/química , Fluorescencia
14.
Langmuir ; 26(5): 3095-105, 2010 Mar 02.
Artículo en Inglés | MEDLINE | ID: mdl-19968297

RESUMEN

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.

15.
J Chem Phys ; 131(7): 074903, 2009 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-19708759

RESUMEN

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.

16.
Langmuir ; 25(12): 6717-24, 2009 Jun 16.
Artículo en Inglés | MEDLINE | ID: mdl-19449819

RESUMEN

Monoglyceride dispersed in oil acts as gel emulsifier to stabilize ordered lamellar structures; however, with time these phases age, leading to separation of oil and lipid. The aging of aggregated structures of monoglycerides in hydrophobic medium is described by a set of different techniques. Polarized microscopy was used to study the mesomorphic behavior as a function of time. Differential scanning calorimetry was utilized to quantitatively monitor changes in the latent heat in different phase transformations that take place in the aging system. The X-ray diffraction patterns fingerprinted the molecular arrangement in different emerging phases. Infrared spectroscopy was used to monitor the states of hydrogen bonding in the system. We conclude that in both inverted-lamellar and sub-alpha crystalline phases, monoglyceride molecules inevitably lose their emulsified ability in the hydrophobic solutions through the gradual change in hydrogen bonding patterns. On aging, the recombination of hydrogen bonding between glycerol groups causes the segregation of chiral (d and l) isomers within the bilayers. Therefore, all structures were eventually forced to reorder into the ground-state beta-crystalline phase. Accordingly, the highly ordered packing of aged structures weakened the emulsifying ability and finally led to the collapse of the percolating gel network.

17.
Phys Rev E Stat Nonlin Soft Matter Phys ; 80(5 Pt 1): 051701, 2009 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-20364992

RESUMEN

In this work we examine layer fluctuations in a smectic elastomer with quenched random disorder induced by crosslinks. The system is analyzed in a continuum model and crosslinks are introduced as a random field in a macroscopic picture. In the case of small deformations and replica symmetry the intensity profile for x-ray scattering along the layer normal was determined for layer displacements smaller than the layer separation. In this regime it is predicted that for large enough crosslink densities the first-order diffraction pattern of the solid assumes a characteristic squared-Lorentzian form, showing a decay of short-range order over a length scale of 20 nm. Crosslinks are observed to disorder the system by decreasing the correlation length, which we show not to be a consequence of the random field. The coupling to random crosslinks is predicted to retard the decrease in the correlation length and hence found to stabilize the one-dimensional periodic layer structure against thermal fluctuations. The dependence of the correlation length on the crosslink density leads us to propose an estimate for the percolation limit of a smectic elastomer network.


Asunto(s)
Elastómeros/química , Cristales Líquidos/química , Modelos Químicos , Modelos Estadísticos , Simulación por Computador , Dispersión del Ángulo Pequeño , Difracción de Rayos X
18.
Phys Rev E Stat Nonlin Soft Matter Phys ; 78(4 Pt 1): 041704, 2008 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-18999442

RESUMEN

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.

19.
Phys Rev E Stat Nonlin Soft Matter Phys ; 77(3 Pt 1): 031908, 2008 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-18517423

RESUMEN

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.


Asunto(s)
Biología Computacional/métodos , Gelatina/química , Glicol de Etileno/química , Cinética , Modelos Moleculares , Conformación Molecular , Conformación de Ácido Nucleico , Conformación Proteica , Pliegue de Proteína , Soluciones , Solventes/química , Temperatura , Termodinámica , Factores de Tiempo , Agua/química
20.
Eur Phys J E Soft Matter ; 25(1): 83-9, 2008 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-18217198

RESUMEN

Vertically aligned monodomain nematic liquid-crystal elastomers contract when heated. If a temperature gradient is applied across the width of such a cantilever, inhomogeneous strain distribution leads to bending motion. We modelled the kinetics of thermally induced bending in the limit of a long thin strip and the predicted time variation of curvature agreed quantitatively with experimental data from samples with a range of critical indices and nematic-isotropic transition temperatures. We also deduced a value for the thermal diffusion coefficient of the elastomer.


Asunto(s)
Algoritmos , Elastómeros/química , Cristales Líquidos/química , Fenómenos Biomecánicos , Difusión , Cinética , Modelos Químicos , Porosidad , Temperatura
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