arXiv subjects

Eugene M. Terentjev

Publications and source records attributed to Eugene M. Terentjev.

34 records · Page 2Linked to original sources

arXiv2016

Stress relaxation, dynamics and plasticity of transient polymer networks

We propose a theoretical framework for dealing with a transient polymer network undergoing small deformations, based on the rate of breaking and re-forming of network crosslinks and the evolving elastic reference state. In this framework, the characteristics of the deformed transient network at microscopic and macroscopic scales are naturally unified. Microscopically, the breakage rate of the crosslinks is affected by the local force acting on the chain. Macroscopically, we use the classical continuum model for rubber elasticity to describe the structure of the deformation energy, whose reference state is defined dynamically according to when crosslinks are broken and formed. With this, the constitutive relation can be obtained. We study three applications of the theory in uniaxial stretching geometry: for the stress relaxation after an instantaneous step strain is imposed, for the stress overshoot and subsequent decay in the plastic regime when a strain ramp is applied, and for the cycle of stretching and release. We compare the model predictions with experimental data on stress relaxation and stress overshoot in physically bonded thermoplastic elastomers and in vitrimer networks.

cond-mat.soft↗

arXiv2015

Mechanosensitivity of the IInd kind: TGFb mechanism of cell sensing the substrate stiffness

Cells can sense forces applied to them, but also the stiffness of their environment. These are two different phenomena, and here we investigate the mechanosensitivity of the IInd kind: how the cell can measure an elastic modulus at a single point of adhesion -- and how the cell can receive and interpret the chemical signal released from the sensor. Our model uses the example of large latent complex of TGFb as a sensor. Stochastic theory gives the rate of breaking of latent complex, which initiates the signaling feedback loop after the active TGFb release and leads to a change of cell phenotype driven by the smooth muscle actin. We investigate the dynamic and steady-state behaviours of the model, comparing them with experiments. In particular, we analyse the timescale of approach to the steady state, the stability of the non-linear dynamical system, and how the steady-state concentrations of the key markers vary depending on the elasticity of the substrate. We discover a crossover region for values of substrate elasticity closely corresponding to that of the fibroblast to myofibroblast transition. We suggest that the cell could actively vary the parameters of its dynamic feedback loop to `choose' the position of the transition region and the range of substrate elasticity that it can detect. In this way, the theory offers the unifying mechanism for a variety of phenomena, such as the myofibroblast conversion in fibrosis of wounds and lungs and smooth muscle cell dysfunction in cardiac disease.

q-bio.CB↗

arXiv2014

How cells feel: stochastic model for a molecular mechanosensor

Understanding mechanosensitivity, i.e. how cells sense the stiffness of their environment is very important, yet there is a fundamental difficulty in understanding its mechanism: to measure an elastic modulus one requires two points of application of force - a measuring and a reference point. The cell in contact with substrate has only one (adhesion) point to work with, and thus a new method of measurement needs to be invented. The aim of this theoretical work is to develop a self-consistent physical model for mechanosensitivity, a process by which a cell detects the mechanical stiffness of its environment (e.g. a substrate it is attached to via adhesion points) and generates an appropriate chemical signaling to remodel itself in response to this environment. The model uses the molecular mechanosensing complex of latent TGF-$β$ attached to the adhesion point as the biomarker. We show that the underlying Brownian motion in the substrate is the reference element in the measuring process. The model produces the closed expression for the rate of release of active TGF-$β$, which depends on the substrate stiffness and the pulling force coming from the cell in a subtle and non-trivial way. It is consistent with basic experimental data showing an increase in signal for stiffer substrates and higher pulling forces. In addition, we find that for each cell there is a range of stiffness where a homeostatic configuration of the cell can be achieved, outside of which the cell either relaxes its cytoskeletal forces and detaches from the very weak substrate, or generates an increasingly strong pulling force through stress fibers with a positive feedback loop on very stiff substrates. In this way, the theory offers the underlying mechanism for the myofibroblast conversion in wound healing and smooth muscle cell dysfunction in cardiac disease.

q-bio.CB↗

arXiv2014

Arrested spinodal decomposition in polymer brush collapsing in poor solvent

We study the Brownian dynamics of flexible and semiflexible polymer chains densely grafted on a flat substrate, upon rapid quenching of the system when the quality of solvent becomes poor and chains attempt collapse into a globular state. The collapse process of such a polymer brush differs from individual chains, both in its kinetics and its structural morphology. We find that the resulting collapsed brush does not form a homogeneous dense layer, in spite of all chain monomers equally attracting each other via a model Lennard-Jones potential. Instead, a very distinct inhomogeneous density distribution in the plane forms, with a characteristic length scale dependent on the quenching depth (or equivalently, the strength of monomer attraction) and the geometric parameters of the brush. This structure is identical to the spinodal-decomposition structure, however, due to the grafting constraint we find no subsequent coarsening: the established random bundling with characteristic periodicity remains as the apparently equilibrium structure. We compare this finding with a recent field-theoretical model of bundling in a semiflexible polymer brush.

cond-mat.soft↗

arXiv2013

Bundling in brushes of directed and semiflexible polymers

We explore the effect of an attractive interaction between parallel-aligned polymers, which are perpendicularly grafted on a substrate. Such an attractive interaction could be due to, e.g., reversible cross-links. The competition between permanent grafting favoring a homogeneous state of the polymer brush and the attraction, which tends to induce in-plane collapse of the aligned polymers, gives rise to an instability of the homogeneous phase to a bundled state. In this latter state the in-plane translational symmetry is spontaneously broken and the density is modulated with a finite wavelength, which is set by the length scale of transverse fluctuations of the grafted polymers. We analyze the instability for two models of aligned polymers: directed polymers with a line tension and weakly bending chains with a bending stiffness.

cond-mat.soft↗

arXiv2013

Ratcheted diffusion transport through crowded nanochannels

The problem of transport through nanochannels is one of the major questions in cell biology, with a wide range of applications. Brownian ratchets are fundamental in various biochemical processes, and are roughly divided into two categories: active (usually ATP-powered) molecular motors and passive constructions with a directional bias, where the transport is driven by thermal motion. In this paper we discuss the latter process, of spontaneous translocation of molecules (Brownian particles) by ratcheted diffusion with no external energy input: a problem relevant for protein translocation along bacterial flagella or injectosome complex, or DNA translocation by bacteriophages. We use molecular dynamics simulations and statistical theory to identify two regimes of transport: at low rate of particles injection into the channel the process is controlled by the individual diffusion towards the open end (the first passage problem), while at a higher rate of injection the crowded regime sets in. In this regime the particle density in the channel reaches a constant saturation level and the resistance force increases substantially, due to the osmotic pressure build-up. To achieve a steady-state transport, the apparatus that injects new particles into a crowded channel has to operate with an increasing power consumption, proportional to the length of the channel and the required rate of transport. The analysis of resistance force, and accordingly -- the power required to inject the particles into a crowded channel to oversome its clogging, is also relevant for many microfluidics applications.

cond-mat.soft↗

arXiv2012

Disorder-assisted melting and the glass transition in amorphous solids

The mechanical response of solids depends on temperature because the way atoms and molecules respond collectively to deformation is affected at various levels by thermal motion. This is a fundamental problem of solid state science and plays a crucial role in metallurgy, aerospace engineering, energy. In glasses the vanishing of rigidity upon increasing temperature is the reverse process of the glass transition. It remains poorly understood due to the disorder leading to nontrivial (nonaffine) components in the atomic displacements. Our theory explains the basic mechanism of the melting transition of amorphous (disordered) solids in terms of the lattice energy lost to this nonaffine motion, compared to which thermal vibrations turn out to play only a negligible role. It predicts the square-root vanishing of the shear modulus $G\sim\sqrt{T_{c}-T}$ at criticality observed in the most recent numerical simulation study. The theory is also in good agreement with classic data on melting of amorphous polymers (for which no alternative theory can be found in the literature) and offers new opportunities in materials science.

cond-mat.soft↗

arXiv2012

Theory of molecular crowding in Brownian hard-sphere liquids with application to the polymer coil-globule transition

We derive an analytical pair potential of mean force for Brownian molecules in the liquid-state. Our approach accounts for many-particle correlations of crowding particles of the liquid, and for diffusive transport across the spatially modulated local density of crowders in the dense environment. Specializing on the limit of equal-size particles, we show that this diffusive transport leads to additional density- and structure-dependent terms in the interaction potential, and to a much stronger attraction (by a factor ~4 at average volume fraction of crowders 0.25) than in the standard depletion interaction where the diffusive effects are neglected. As an illustration of the theory, we use it to study the size of a polymer chain in a solution of inert crowders. Even in the case of athermal background solvent, when a classical chain should be fully swollen, we find a sharp coil-globule transition of the ideal chain collapsing at a critical value of the crowder volume fraction ~0.145.

cond-mat.soft↗

arXiv2012

Kramers rate theory of 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, ionized plasma, or biomolecular complexes). We solve this classical problem by accounting for entropic memory 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 Sun in excellent agreement with experiments. In biology, the new theory accounts for crowding in receptor-ligand kinetics and protein aggregation.

cond-mat.stat-mech↗

arXiv2012

Network disorder and nonaffine deformations in marginal solids

The most profound effect of disorder on the elastic response of solids is the nonaffinity of local displacements whereby the atoms (particles, network junctions) do not simply follow the macroscopic strain, as they do in perfect crystals, but undergo additional displacements which result in a softening of response. Whether disorder can produce further effects has been an open and difficult question due to our poor understanding of nonaffinity. Here we present a systematic analysis of this problem by allowing both network disorder and lattice coordination to vary continuously under account of nonaffinity. In one of its limits, our theory, supported by numerical simulations, shows that in lattices close to the limit of mechanical stability the elastic response stiffens proportionally to the degree of disorder. This result has important implications in a variety of areas: from understanding the glass transition problem to the mechanics of biological networks such as the cytoskeleton.

cond-mat.soft↗

arXiv2011

A constrained random-force model for weakly bending semiflexible polymers

The random-force (Larkin) model of a directed elastic string subject to quenched random forces in the transverse directions has been a paradigm in the statistical physics of disordered systems. In this brief note, we investigate a modified version of the above model where the total transverse force along the polymer contour and the related total torque, in each realization of disorder, vanish. We discuss the merits of adding these constraints and show that they leave the qualitative behavior in the strong stretching regime unchanged, but they reduce the effects of the random force by significant numerical prefactors. We also show that a transverse random force effectively makes the filament softer to compression by inducing undulations. We calculate the related linear compression coefficient in both the usual and the constrained random force model.

cond-mat.soft↗

arXiv2010

Stretching semiflexible filaments with quenched disorder

We study the effect of quenched randomness in the arc-length dependent spontaneous curvature of a wormlike chain under tension. In the weakly bending approximation in two dimensions, we obtain analytic results for the force-elongation curve and the width of transverse fluctuations. We compare quenched and annealed disorder and conclude that the former cannot always be reduced to a simple change in the stiffness of the pure system. We also discuss the effect of a random transverse force on the stretching response of a wormlike chain without spontaneous curvature.

cond-mat.soft↗

arXiv2010

Stretching weakly bending filaments with spontaneous curvature in two dimensions

Some important biomolecules (for instance, bacterial FtsZ and eukaryotic DNA) are known to posses spontaneous (intrinsic) curvature. Using a simple extension of the wormlike chain model, we study the response of a weakly bending filament in two dimensions to a pulling force applied at its ends (a configuration common in classical in-vitro experiments and relevant to several in-vivo cell cases). The spontaneous curvature of such a chain or filament can in general be arc-length dependent and we study a case of sinusoidal variation, from which an arbitrary case can be reconstructed via Fourier transformation. We obtain analytic results for the force-extension relationship and the width of transverse fluctuations. We show that spontaneous-curvature undulations can affect the force-extension behavior even in relatively flexible filaments with a persistence length smaller than the contour length.

cond-mat.soft↗

arXiv2008

Non-linear dynamics of absorption and photo-bleaching of dyes

The celebrated Lambert-Beer law of light absorption in photochromic media is only valid at low intensities of incident light and low concentration of chromophore. Here we address the generic problem of photo-absorption dynamics, experimentally studying the case of azobenzene isomerization. We show that the non-linear regime is very common and easy to achieve in many practical situations, especially in thick samples where the light depletes the chromophore in the first layers and can propagate through the medium with a sub-exponential law. Importantly, the crossover into the non-linear absorption regime only weakly depends on the dye concentration and solution viscosity. We experimentally quantify the characteristics of this peculiar optical response and determine the key transition rate constants.

cond-mat.other↗

arXiv1995

Mean-Field Nematic--Smectic-{\sl A} Transition in a Random Polymer Network

Liquid crystal elastomers present a rich combination of effects associated with orientational symmetry breaking and the underlying rubber elasticity. In this work we focus on the effect of the network on the nematic--smectic-{\sl A} transition, exploring the additional translational symmetry breaking in these elastomers. We incorporate the crosslinks as a random field in a microscopic picture, thus expressing the degree to which the smectic order is locally frozen with respect to the network. We predict a modification of the NA transition, notably that it can be treated at the mean-field level (type-I system), due to the coupling with elastic degrees of freedom. There is a shift in the transition temperature $T_{\scriptscriptstyle NA}$, a suppression of the Halperin-Lubensky-Ma (HLM) effect (thus recovering the mean-field continuous transition to the smectic state), and a new tri-critical point, depending on the conditions of network formation. When the nematic phase possesses `soft elasticity', the NA transition becomes of first order due to the coupling with soft phonons in the network. We also discuss the microscopic origin of phenomenological long-wavelength coupling between smectic phase and elastic strain.

cond-mat↗

arXiv1995

Some properties of membranes in nematic solvents

The fluctuation spectrum of membranes in nematic solvents is altered by the boundary condition imposed on the bulk nematic director by the curved membrane. We discuss some properties of single and multi-membrane systems in nematic solvents, primarily based on the Berreman-de~Gennes model. We show that: membranes in nematic solvents are more rigid and less rough than in their isotropic counterparts; have a different Helfrich steric stabilization energy, proportional to $d^{-3}$, and hence a different compression modulus in the lamellar state; and can exhibit phase separation via unbinding during a quench into the nematic state. We also discuss the preparation and possible experimental effects of nematic-mediated surfactant membrane system.

cond-mat↗