We analyze the statistics of work generated by a gradient flow to stretch a nonlinear polymer. We obtain the Large Deviation Function (LDF) of the work in the full range of appropriate parameters by combining analytical and numerical tools. The LDF shows two distinct asymptotes: "near tails" are linear in work and dominated by coiled polymer configurations, while "far tails" are quadratic in work and correspond to preferentially fully stretched polymers. We find the extreme value statistics of work for several singular elastic potentials, as well as the mean and the dispersion of work near the coil-stretch transition. The dispersion shows a maximum at the transition.
We compute the distribution of the work done in stretching a Gaussian polymer, made of N monomers, at a finite rate. For a one-dimensional polymer undergoing Rouse dynamics, the work distribution is a Gaussian and we explicitly compute the mean and width. The two cases where the polymer is stretched, either by constraining its end or by constraining the force on it, are examined. We discuss connections to Jarzynski's equality and the fluctuation theorems.
How hydrodynamic interactions alter polymer stretching in turbulence
IITB-Monash Research Academy, Indian Institute of Technology Bombay（印度孟买理工学院-蒙纳士大学联合研究院）；Indian Institute of Technology Bombay（印度孟买理工学院）；Monash University（蒙纳士大学）；Université Côte d’Azur（蔚蓝海岸大学）
Polymers in a turbulent flow are stretched out by the fluctuating velocity gradient; the stationary probability distribution function (p.d.f.) of extensions $R$ has a power-law tail with an exponent that increases with the Weissenberg number $Wi$, a nondimensional measure of polymer elasticity. This study addresses the following questions: (i) What is the role of the non-Gaussian statistics of the turbulent velocity gradient on polymer stretching? (ii) How does the p.d.f. of $R$ evolve to its asymptotic stationary form? Our analysis is based on simulations of the dynamics of finitely-extensibl…
Using molecular dynamic simulation, we study the stretching of an adsorbed homopolymer in a poor solvent with one end held at a distance $z_e$ from the substrate. We measure the vertical force $f$ on the end of the chain as a function of the extension $z_e$ and the substrate interaction energy $w$. The force reaches a plateau value at large extensions. In the strong adsorption limit, we show that the plateau value increase linearly in $w$ in good agreement with a theoretical model. In the weak adsorption limit, a polymer globule with a layered structure is formed and elastically deformed when …
We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the simplest representation of biopolymers in a cell. We show the existence of intermediate states during stretching arising as a consequence of molecular crowding. In the constant distance ensemble the force-extension curves exhibit oscillations. We observe the emergence of two or more peaks in the probability distribution curves signaling the coexistence of d…
The way tension propagates along a chain is a key to govern many of anomalous dynamics in macromolecular systems. After introducing the weak and the strong force regimes of the tension propagation, we focus on the latter, in which the dynamical fluctuations of a segment in a long polymer during its stretching process is investigated. We show that the response, i.e., average drift, is anomalous, which is characterized by the nonlinear memory kernel, and its relation to the fluctuation is nontrivial. These features are discussed on the basis of the generalized Langevin equation, in which the rol…
The recently proposed fluctuation relation in unfolding forces [Phys. Rev. E ${\bf 84}$, $060101$(R) $(2011)$] is re-examined taking into account the explicit time dependence of the force distribution. The stretching of a tethered Rouse polymer is exactly solved and the ratio of the probabilities of positive to negative forces is shown to be an exponential in force. Extensive steered molecular dynamics simulations of unfolding of deca alanine peptide confirm the form of fluctuation relation proposed earlier, but with explicit correct time dependence of unfolding forces taken into account. From…
In this paper we present simulations of a surface-adsorbed polymer subject to an elongation force. The polymer is modelled by a self-avoiding walk on a regular lattice. It is confined to a half-space by an adsorbing surface with attractions for every vertex of the walk visiting the surface, and the last vertex is pulled perpendicular to the surface by a force. Using the recently proposed flatPERM algorithm, we calculate the phase diagram for a vast range of temperatures and forces. The strength of this algorithm is that it computes the complete density of states from one single simulation. We …
The stretching of a polymer chain by a large scale chaotic flow is considered. The steady state which emerges as a balance of the turbulent stretching and anharmonic resistance of the chain is quantitatively described, i.e. the dependency on the flow parameters (Lyapunov exponent statistics) and the chain characteristics (the number of beads and the inter-bead elastic potential) is made explicit.
The unfolding of a polymer below the $θ$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple steps, corresponding to transitions between different minima, in both cases. In the infinite length limit, these intermediate minima have a qualitative effect only in $d=2$. The phase diagram in d=2 is determined using transfer matrix techniques. Energy-entropy and renormalization group arguments are given which predict a qualitatively correct phase diagram and …
We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve depends on the polymer structural parameters: its thickness and granularity (spacing of the monomers). The expression is used to analyze experimental data for the stretching of various different types of biopolymers: polypeptides, polysaccharides and nucleic acids. Besides recovering elastic parameters (such as the persistence length) that are consistent with tho…
We investigate the properties of a system of semi-diluted polymers in the presence of charged groups and counter-ions, by means of self-consistent field theory. We study a system of polyelectrolyte chains grafted to a similarly, as well as an oppositely charged surface, solving a set of saddle-point equations that couple the modified diffusion equation for the polymer partition function to the Poisson-Boltzmann equation describing the charge distribution in the system. A numerical study of this set of equations is presented and comparison is made with previous studies. We then consider the cas…
We compare the Rubinstein-Duke model for reptation to a model where the boundary dynamics is modified by calculating the viscosity of polymer melts. The question is investigated whether the viscosity is determined by details of the dynamics of the polymer ends or by the stretching of the polymer. To this end the dependence of the viscosity on the particle density of the lattice gas models which can be identified by the stretching is determined. We show that the influence of the stretching of the polymer on the absolute value of the viscosity in the scaling limit of of very long chains is much …
While stretching of a polymer along a flat surface is hardly different from the classical Pincus problem of pulling chain ends in free space, the role of curved geometry in conformational statistics of the stretched chain is an exciting open question. Here by means of the scaling analyses and computer simulations we examine stretching of a fractal polymer chain around a disc in 2D (or a cylinder in 3D) of radius $R$. Surprisingly, we reveal that the typical excursions of the polymer away from the surface scale as $Δ\sim R^β$, with the Kardar-Parisi-Zhang (KPZ) growth exponent $β=1/3$, for any …
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is self-interacting and can therefore undergo a collapse transition. We show that this model can be solved and we obtain the force-temperature phase diagrams which, for the case of flexible polymers, agree with that of Brak et al obtained using a different method. At sufficiently low temperatures, the polymer conformation changes from compact to coil state as the …
We present Monte Carlo data for a linear chain with excluded volume subjected to a uniform stretching. Simulation of long chains (up to 6000 beads) at high stretching allows us to observe the signature of tensile blobs as a crossover in the scaling behavior of the chain scattering function for wave vectors perpendicular to stretching. These results and corresponding ones in the stretching direction allow us to verify for the first time Pincus prediction on scaling inside blobs. Outside blobs, the scattering function is well described by the Debye function for a stretched ideal chain.
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account the three elastic degrees of freedom, namely stretching, bending and torsion of the polymer. By integrating out these external variables, the conformational entropy contributes to bubble nucleation (opening of base-pairs), which sheds light on the DNA melting mechanism. Because the values of monomer length, bending and torsional moduli differ significantly in …
Theories of strongly stretched polymer brushes, particularly the parabolic brush theory, are valuable for providing analytically tractable predictions for the thermodynamic behavior of surface-grafted polymers in a wide range of settings. However, the parabolic brush limit fails to describe polymers grafted to convex, curved substrates, such as the surfaces of spherical nanoparticles or the interfaces of strongly segregated block copolymers. It has been previously shown that strongly-stretched, curved brushes require a boundary layer devoid of free chain ends, requiring modifications of the th…
We present a theory for the elasticity of cross-linked stiff polymer networks. Stiff polymers, unlike their flexible counterparts, are highly anisotropic elastic objects. Similar to mechanical beams stiff polymers easily deform in bending, while they are much stiffer with respect to tensile forces (``stretching''). Unlike in previous approaches, where network elasticity is derived from the stretching mode, our theory properly accounts for the soft bending response. A self-consistent effective medium approach is used to calculate the macroscopic elastic moduli starting from a microscopic charac…
We use the recently introduced small-world networks (SWN) to model cross-linked polymers, as an extension of the linear Rouse-chain. We study the SWN-dynamics under the influence of external forces. Our focus is on the structurally and thermally averaged SWN stretching, which we determine both numerically and analytically using a psudo-gap ansatz for the SWN-density of states. The SWN stretching is related to the probability of a random-walker to return to its origin on the SWN. We compare our results to the corresponding ones for Cayley trees.
The stretching of brushes of long polymers grafted to a planar surface is investigated byMonte Carlo simulations in the limit of very high grafting densities, as achieved in recent experiments. The monomer density profiles are shown to deviate considerably from the parabolic limiting form predicted by self-consistent field theory. A rapid transition is observed from parabolic to fully stretched polymers, characterized by a dramatic change in the end-monomer height distribution and by a clear cross-over in the slope of the brush height versus scaled grafting density.
Whether turbulence intermittencies shall be described by a log-Poisson, a log-stable pdf or other distributions is still debated nowadays. In this paper, a bridge between polymer physics, self-avoiding walk and random vortex stretching is established which may help in getting a new insight on this topics. Actually a very simple relationship between stability index of the stable law and the well known Flory exponent stemming from polymer physics is established. Moreover the scaling of turbulence intermittencies with Reynolds number is also obtained and the overall picture is very close to Tenne…
We study conformations and dynamics of active star polymers. The analysis shows that active star polymers stretching behaviour is quite different from that of active linear chains. The visual inspection of conformations and bond-bond correlations reveal a better coordination for the alignment and coordination of bonds for the star polymers than for the linear counterparts. The architecture substantially affects the chain extension transition at high values of active force. The scaling laws for the shape factor and the arm asphericity ratio established for the passive star polymers coincide wit…
We construct a three-dimensional lattice model for biological gels in which straight lines of bonds correspond to filamentous semi-flexible polymers and lattice sites, which are exactly four-fold coordinated, to crosslinks. With only stretching central forces between nearest neighbors, this lattice is sub-isostatic with an extensive number of zero modes; but all of its elastic constants are nonzero, and its elastic response is affine. Removal of bonds with probability $1-p$ leads to a lattice with average coordination number less than four and a distribution of polymer lengths. When bending fo…
We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. By performing simulations of single chains in a shear flow, we identify which of these phenomena are of collective nature and arise through interchain interactions and which are already present in dilute systems. Building upon these microscopic simulations we identify by m…
The growing importance of microfluidic and nanofluidic devices to the study of biological processes has highlighted the need to better understand how confinement affects the behavior of polymers in flow. In this paper we explore one aspect of this question by calculating the steady-state extension of a long polymer chain in a narrow capillary tube in the presence of simple shear. The calculation is carried out within the framework of the Rouse-Zimm approach to chain dynamics, using a variant of a nonlinear elastic model to enforce finite extensibility. Under the assumption that the sole effect…
We study the behavior of threads and polymers in a turbulent flow. These objects have finite spatial extension, so the flow along them differs slightly. The corresponding drag forces produce a finite average stretching and the thread is stretched most of the time. Nevertheless, the probability of shrinking fluctuations is significant and is known to decay only as a power-law. We show that the exponent of the power law is a universal number independent of the statistics of the flow. For polymers the coil-stretch transition exists: the flow must have a sufficiently large Lyapunov exponent to ove…
