Adsorption of Semiflexible Polymers in Cylindrical Tubes.

Conformations of wormlike chains in cylindrical pores with attractive walls are explored for varying pore radius and strength of the attractive wall potential by molecular dynamics simulations of a coarse-grained model. Local quantities such as the fraction of monomeric units bound to the surface and the bond-orientational order parameter as well as the radial density distribution are studied, as well as the global chain extensions parallel to the cylinder axis and perpendicular to the cylinder surface. A nonmonotonic convergence of these properties to their counterparts for adsorption on a planar substrate is observed due to the conflict between pore surface curvature and chain stiffness. Also the interpretation of partially adsorbed chains in terms of trains, loops, and tails is discussed.

How does stiffness of polymer chains affect their adsorption transition?

The adsorption transition and the structure of semiflexible adsorbed macromolecules are studied by a molecular dynamics simulation of a coarse-grained, bead-spring type model. Varying chain length N and stiffness κ (which is proportional to the persistence length ℓp in d = 3 dimensions) as well as the strength ϵwall of the adsorption potential, the adsorbed monomer fraction, orientational bond order parameter, and chain linear dimensions are studied. In the simulations, excluded volume interactions normally are included but can be "switched off," and thus, the influence of excluded volume (leading to deviations from predictions of the wormlike chain model) can be identified. It is shown that the variation in the adsorption threshold ϵwall cr with ℓp is compatible with the predicted law ϵwall cr∝ℓp -1/3. In the vicinity of the adsorption threshold, the coils are still three-dimensional, and for large ℓp, the effect of the excluded volume is almost negligible, while for strongly adsorbed chains it is always felt. Near the transition, the decay length of orientational correlations along the chain contour increases gradually from ℓp to 2ℓp. While the latter value is expected for strictly two-dimensional chains from the Kratky-Porod model, this model is inaccurate for the description of lateral chain dimensions of long, strongly adsorbed, semiflexible polymers due to its neglect of excluded volume. The significance of these findings for the interpretation of pertinent experiments is briefly discussed.

Detachment of semiflexible polymer chains from a substrate: a molecular dynamics investigation.

Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force ⟨f⟩ vs height D of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the ⟨f⟩-D profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and dissipative particle dynamics-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the ⟨f⟩-D profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio ε(s)(B)/ε(s)(A) of the binding energies of A- and B-segments in the detachment of an AB-copolymer from adhesive surface strongly changes the ⟨f⟩-D profile whereby the B-spikes vanish when ε(s)(B)/ε(s)(A)<0.15. Eventually, performing an atomistic simulation of (bio)-polymers, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.

A case of synchronous bleeding from esophageal varices and appendixin a patient with decompensated liver cirrhosis.

UNLABELLED: Lower gastrointestinal bleeding is defined as any bleeding localized distally to Treitz's ligament. The massive bleeding from the appendix is extremely rare and only 21 cases described in the English literature. CASE PRESENTATION: We present a 61-years-old patient with decompensated liver cirrhosis and bleeding from esophageal varices. He underwent band ligation by Six Shooter (Cook Medical, USA). Due to a massive bleeding from the lower gastrointestinal tract and a rapid decline of hemoglobin level to 3 g/dL, angiography was performed. It revealed a bleeding from distal branches of ileocolic artery, confirmed by the followed computed tomography angiography. The patient underwent appendectomy and was discharged in a good condition on the 6th postoperative day. CONCLUSION: The synchronous bleeding from upper and lower GIT should be considered, especially in the cases with portal hypertension. The angiography and computed tomography angiography are valuable diagnostic methods, able to localize the bleeding a thus to reduce the morbidity and mortality.

Star polymers rupture induced by constant forces.

In this work, we study the breakage process of an unknotted three-arm star-shaped polymer when it is pulled from its free ends by a constant force. The star polymer configuration is described through an array of monomers coupled by anharmonic bonds, while the rupture process is tracked in three-dimensional space by means of Langevin Molecular Dynamics simulations. The interaction between monomers is described by a Morse potential, while a Weeks-Chandler-Anderson energetic contribution accounts for the excluded volume interaction. We explore the effect of the molecular architecture on the distributions of rupture times over a broad interval of pulling forces and star configurations. It was found that the rupture time distribution of the individual star arms is strongly affected by the star configuration imposed by the pulling forces and the length of the arms. We also observed that for large pulling forces the rupture time distributions resemble the dominant features observed for linear polymer chains. The model introduced here provides the basic ingredients to describe the effects of tensile forces on stress-induced degradation of branched macromolecules and polymer networks.

Efficient Separation of Long Polymer Chains by Contour Length and Architecture.

On the basis of theoretical considerations and computer experiment, we suggest a new technique for separation of polymer molecules. The method is based on filling an array of nanochannels with macromolecules whereby the subsequent ejection time depends strongly on small differences in the end-to-end distances of elongated configurations inside the nanotubes. In contrast to conventional methods for chromatographic separation, the efficiency of the proposed method increases with growing molecular length of the chains. The method appears promising also for the separation of ring from linear polymer chains.

Structure and dynamics of a polymer melt at an attractive surface.

We study the structural and dynamic properties of a polymer melt in the vicinity of an adhesive solid substrate by means of Molecular Dynamics simulation at various degrees of surface adhesion. The properties of the individual polymer chains are examined as a function of the distance to the interface and found to agree favorably with theoretical predictions. Thus, the adsorbed amount at the adhesive surface is found to scale with the macromolecule length as Γ is proportional to √N, regardless of the adsorption strength. For chains within the range of adsorption we analyze in detail the probability size distributions of the various building blocks: loops, tails and trains, and find that loops and tails sizes follow power laws while train lengths decay exponentially thus confirming some recent theoretical results. The chain dynamics as well as the monomer mobility are also investigated and found to depend significantly on the proximity of a given layer to the solid adhesive surface with onset of vitrification for sufficiently strong adsorption.

Thermal decomposition of a honeycomb-network sheet: a molecular dynamics simulation study.

The thermal degradation of a graphene-like two-dimensional honeycomb membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that at lower temperature the probability distribution of breaking bonds is highly peaked at the rim of the membrane sheet whereas at higher temperature bonds break at random everywhere in the hexagonal flake. The mean breakage time τ is found to decrease with the total number of network nodes N by a power law τ ∝ N(-0.5) and reveals an Arrhenian dependence on temperature T. Scission times are themselves exponentially distributed. The fragmentation kinetics of the average number of clusters can be described by first-order chemical reactions between network nodes n(i) of different coordination. The distribution of fragments sizes evolves with time elapsed from initially a δ-function through a bimodal one into a single-peaked again at late times. Our simulation results are complemented by a set of 1st-order kinetic differential equations for n(i) which can be solved exactly and compared to data derived from the computer experiment, providing deeper insight into the thermolysis mechanism.

Forced translocation of a polymer: Dynamical scaling versus molecular dynamics simulation.

We suggest a theoretical description of the force-induced translocation dynamics of a polymer chain through a nanopore. Our consideration is based on the tensile (Pincus) blob picture of a pulled chain and the notion of a propagating front of tensile force along the chain backbone, suggested by Sakaue [Phys. Rev. E 76, 021803 (2007); Phys. Rev. E 81, 041808 (2010); Eur. Phys. J. E 34, 135 (2011)]. The driving force is associated with a chemical potential gradient that acts on each chain segment inside the pore. Depending on its strength, different regimes of polymer motion (named after the typical chain conformation: trumpet, stem-trumpet, etc.) occur. Assuming that the local driving and drag forces are equal (i.e., in a quasistatic approximation), we derive an equation of motion for the tensile front position X(t). We show that the scaling law for the average translocation time 〈τ〉 changes from <τ> ∼ N2ν/f1/ν to <τ> ∼ N^1+ν/f (for the free-draining case) as the dimensionless force f[over ̃]R=aNνf/T (where a, N, ν, f, and T are the Kuhn segment length, the chain length, the Flory exponent, the driving force, and the temperature, respectively) increases. These and other predictions are tested by molecular-dynamics simulation. Data from our computer experiment indicate indeed that the translocation scaling exponent α grows with the pulling force f[over ̃]R, albeit the observed exponent α stays systematically smaller than the theoretically predicted value. This might be associated with fluctuations that are neglected in the quasistatic approximation.

Semiflexible polymers grafted to a solid planar substrate: changing the structure from polymer brush to "polymer bristle".

Monte Carlo simulations are presented for a coarse-grained model of polymer brushes with polymers having a varying degree of stiffness. Both linear chains and ring polymers grafted to a flat structureless non-adsorbing substrate surface are considered. Applying good solvent conditions, it is shown that with growing polymer stiffness the brush height increases significantly. The monomer density profiles for the case of ring polymers (chain length N(R) = 64) are very similar to the case of corresponding linear chains (N(L) = 32, grafting density larger by a factor of two) in the case of flexible polymers, while slight differences appear with increasing stiffness. Evidence is obtained that the chain dynamics in brushes is slowed down dramatically with increasing stiffness. Very short stiff rings (N(R) ≤ 16) behave like disks, grafted to the substrate such that the vector, perpendicular to the disk plane, is oriented parallel to the substrate surface. It is suggested that such systems can undergo phase transitions to states with liquid crystalline order.

Force-induced breakdown of flexible polymerized membrane.

We consider the fracture of a free-standing two-dimensional (2D) elastic-brittle network to be used as protective coating subject to constant tensile stress applied on its rim. Using a molecular-dynamics simulation with a Langevin thermostat, we investigate the scission and recombination of bonds, and the formation of cracks in the 2D graphenelike hexagonal sheet for different pulling force f and temperature T. We find that bond rupture occurs almost always at the sheet periphery, and the first mean breakage time <τ> of bonds decays with membrane size as <τ> ∝N(-ß), where ß≈0.50±0.03 and N denotes the number of atoms in the membrane. The probability distribution of bond scission times t is given by a Poisson function W(t)∝t(1/3)exp(-t/<τ>). The mean failure time <τ(r)> necessary to rip off the sheet declines with growing size N as a power law <τ(r)>∝N(-φ(f)). We also find <τ(r)>∝exp(ΔU(0)/k(B)T), where the nucleation barrier for crack formation ΔU(0)∝f(-2), in agreement with Griffith's theory. <τ(r)> displays an Arrhenian dependence of <τ(r)> on temperature T. Our results indicate a rapid increase in crack spreading velocity with growing external tension f.

Thermal degradation of unstrained single polymer chain: non-linear effects at work.

We examine the thermally induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of molecular dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped dynamics are investigated, and a comparison with recent studies of bond scission in model polymers with harmonic interactions is performed. We find that the polymer degradation changes qualitatively between the inertial regime and that of heavily damped dynamics. The role of bond healing (recombination) is also studied and probability distributions for the recombination times and overstretched bond lengths are obtained. Our extensive simulations reveal many properties of the scission dynamics in agreement with the notion of random breakdown of independent bonds, e.g., the mean time of chain rupture, <τ> follows an Arrhenian behavior with temperature T, and depends on the number of bonds N in the polymer as <τ> ∝ N(-1). In contrast, the rupture rates of the individual bonds along the polymer backbone indicate clearly the presence of self-induced inhomogeneity resulting from the interplay of thermal noise and nonlinearity. Eventually we examine the fragmentation kinetics during thermolysis. We demonstrate that both the probability distribution function of fragment sizes as well as the mean length of fragments at subsequent times t characterize degradation as predominantly a first order reaction.

Fractional Brownian motion approach to polymer translocation: the governing equation of motion.

We suggest a governing equation that describes the process of polymer-chain translocation through a narrow pore and reconciles the seemingly contradictory features of such dynamics: (i) a Gaussian probability distribution of the translocated number of polymer segments at time t after the process has begun, and (ii) a subdiffusive increase of the distribution variance Δ(t) with elapsed time Δ(t)∝t(α). The latter quantity measures the mean-squared number s of polymer segments that have passed through the pore Δ(t)=([s(t)-s(t=0)](2)), and is known to grow with an anomalous diffusion exponent α<1. Our main assumption [i.e., a Gaussian distribution of the translocation velocity v(t)] and some important theoretical results, derived recently, are shown to be supported by extensive Brownian dynamics simulation, which we performed in 3D. We also numerically confirm the predictions made recently that the exponent α changes from 0.91 to 0.55 to 0.91 for short-, intermediate-, and long-time regimes, respectively.

Polymer brushes with nanoinclusions under shear: A molecular dynamics investigation.

We use molecular dynamics simulations with a dissipative particle dynamics thermostat to study the behavior of nanosized inclusions (colloids) in a polymer brush under shear whereby the solvent is explicitly included in the simulation. The brush is described by a bead-spring model for flexible polymer chains, grafted on a solid substrate, while the polymer-soluble nanoparticles in the solution are taken as soft spheres whose diameter is about three times larger than that of the chain segments and the solvent. We find that the brush number density profile, as well as the density profiles of the nanoinclusions and the solvent, remains insensitive to strong shear although the grafted chains tilt in direction of the flow. The thickness of the penetration layer of nanoinclusions, as well as their average concentration in the brush, stays largely unaffected even at the strongest shear. Our result manifests the remarkable robustness of polymer brushes with embedded nanoparticles under high shear which could be of importance for technological applications.

Thermal breakage and self-healing of a polymer chain under tensile stress.

We consider the thermal breakage of a tethered polymer chain of discrete segments coupled by Morse potentials under constant tensile stress. The chain dynamics at the onset of fracture is studied analytically by Kramers-Langer multidimensional theory and by extensive molecular dynamics simulations in one dimension (1D) and three dimension (3D) space. Comparison with simulation data in one and three dimensions demonstrates that the Kramers-Langer theory provides good qualitative description of the process of bond scission as caused by a collective unstable mode. We derive distributions of the probability for scission over the successive bonds along the chain which reveal the influence of chain ends on rupture in good agreement with theory. The breakage time distribution of an individual bond is found to follow an exponential law as predicted by theory. Special attention is focused on the recombination (self-healing) of broken bonds. Theoretically derived expressions for the recombination time and distance distributions comply with MD observations and indicate that the energy barrier position crossing is not a good criterion for true rupture. It is shown that the fraction of self-healing bonds increases with rising temperature and friction.

Method for wettability characterization based on contact line pinning.

We demonstrate an efficient and reliable method for wettability characterization by determining the contact angle theta which a liquid-vapor interface makes with a solid wall. The purpose is to overcome the difficulties, related to the curvature of the liquid-vapor interface, which make measurements of theta rather uncertain, especially on the micro- and nanoscale. The method employs a specially designed slitlike channel in contact with a reservoir whereby the wettability of one of the slit walls is to be examined whereas the other (auxiliary) wall is separated by half into a lyophilic and a lyophobic part so as to pin the incoming fluid and fix the one end of the liquid-vapor interface. In the present work, the physical background of the method is elucidated theoretically while the method's applicability is demonstrated by molecular-dynamics simulation of a typical Lennard-Jones fluid, in contact with an atomistic wall. The wettability of the latter, as described by the corresponding contact angle theta, is accurately determined by variation of the liquid-wall interaction in a very broad interval.

Capillary filling in microchannels with wall corrugations: a comparative study of the Concus-Finn criterion by continuum, kinetic, and atomistic approaches.

We study the impact of wall corrugations in microchannels on the process of capillary filling by means of three broadly used methods: computational fluid dynamics (CFD), lattice Boltzmann equations (LBE), and molecular dynamics (MD). The numerical results of these approaches are compared and tested against the Concus-Finn (CF) criterion, which predicts pinning of the contact line at rectangular ridges perpendicular to flow for contact angles of theta > 45 degrees . Whereas for theta = 30, 40 (no flow), and 60 degrees (flow) all methods are found to produce data consistent with the CF criterion, at theta = 50 degrees the numerical experiments provide different results. Whereas the pinning of the liquid front is observed both in the LB and CFD simulations, MD simulations show that molecular fluctuations allow front propagation even above the critical value predicted by the deterministic CF criterion, thereby introducing a sensitivity to the obstacle height.

Scaling exponents of forced polymer translocation through a nanopore.

We investigate several properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulations in three dimensions (3D). Motivated by several recent theoretical and numerical studies that are apparently at odds with each other, we estimate the exponents describing the scaling with chain length (N) of the average translocation time , the average velocity of the center of mass , and the effective radius of gyration during the translocation process defined as approximately Nalpha, approximately N(-delta), and Rg approximately Nnu respectively, and the exponent of the translocation coordinate (s-coordinate) as a function of the translocation time approximately tbeta. We find alpha = 1.36 +/- 0.01, beta = 1.60+/- 0.01 for approximately taubeta and beta = 1.44 +/- 0.02 for approximately taubeta, delta = 0.81 +/- 0.04, and nu congruent with nu = 0.59 +/- 0.01, where nu is the equilibrium Flory exponent in 3D. Therefore, we find that approximately N1.36 is consistent with the estimate of approximately /. However, as observed previously in Monte Carlo (MC) calculations by Kantor and Kardar (Y. Kantor, M. Kardar, Phys. Rev. E 69, 021806 (2004)) we also find the exponent alpha = 1.36 +/- 0.01 < 1 + nu. Further, we find that the parallel and perpendicular components of the gyration radii, where one considers the "cis" and "trans" parts of the chain separately, exhibit distinct out-of-equilibrium effects. We also discuss the dependence of the effective exponents on the pore geometry for the range of N studied here.

Pulling an adsorbed polymer chain off a solid surface.

The thermally assisted detachment of a self-avoiding polymer chain from an adhesive surface by an external force applied to one of the chain-ends is investigated. We perform our study in the "fixed height" statistical ensemble where one measures the fluctuating force, exerted by the chain on the last monomer when a chain-end is kept fixed at height h over the solid plane at different adsorption strength [Formula: see text]. The phase diagram in the h-[Formula: see text] plane is calculated both analytically and by Monte Carlo simulations. We demonstrate that in the vicinity of the polymer desorption transition a number of properties like fluctuations and probability distribution of various quantities behave differently, if h rather than f is used as an independent control parameter.

Polymer translocation through a nanopore: a showcase of anomalous diffusion.

We investigate the translocation dynamics of a polymer chain threaded through a membrane nanopore by a chemical potential gradient that acts on the chain segments inside the pore. By means of diverse methods (scaling theory, fractional calculus, and Monte Carlo and molecular dynamics simulations), we demonstrate that the relevant dynamic variable, the transported number of polymer segments, s(t), displays an anomalous diffusive behavior, both with and without an external driving force being present. We show that in the absence of drag force the time tau, needed for a macromolecule of length N to thread from the cis into the trans side of a cell membrane, scales as tauN(2/alpha) with the chain length. The anomalous dynamics of the translocation process is governed by a universal exponent alpha= 2/(2nu + 2 - gamma(1)), which contains the basic universal exponents of polymer physics, nu (the Flory exponent) and gamma(1) (the surface entropic exponent). A closed analytic expression for the probability to find s translocated segments at time t in terms of chain length N and applied drag force f is derived from the fractional Fokker-Planck equation, and shown to provide analytic results for the time variation of the statistical moments and . It turns out that the average translocation time scales as tau proportional, f(-1)N(2/alpha-1). These results are tested and found to be in perfect agreement with extensive Monte Carlo and molecular dynamics computer simulations.