Tribology of polymer brush: microscale modelling and simulation

In order to examine the tribological behaviour of the polymer brush, we constructed a mesoscale particle model of a polymer brush system, based on a Brownian dynamics scheme. The polymer model consists of coarse-grained beads connected with harmonic springs. The Lennard-Jones type interaction is assumed between beads. The flow velocity is affected by the local packing fraction of beads. With this model, we executed a series of molecular dynamics simulation to investigate the mechanical responses of brush to shear flow.     

Velocity of polymer translocation through a pore

We theoretically study the translocation time and the mean velocity of a long polymer threading a long nanopore on an external electric field. Theoretical method, which explicitly takes into account the nucleation theory, is presented based on the built polymer expanded model. We overcame the previous theory's defect which did not consider the real length of the pore. The present model implies that the length scale of a pore plays a very important role in the process of polymer translocation. Our calculation results are in agreement with those of previous experiments.     

Investigation of interfacial mechanical properties of graphene-polymer nanocomposites

A series of graphene (GR) pull-out simulations based on molecular dynamics (MD) were carried out to investigate the interfacial mechanical properties between GR and a polymer matrix (polyethylene: PE). The effects of pull-out velocity, number of vacancy defect in GR and temperature on the interfacial mechanical properties of a GR/PE nanocomposite system were explored. The obtained results showed that the pull-out velocity and the temperature have significant influences on the interfacial mechanical properties for a perfect GR. Moderate vacancy defects in GR can effectively enhance the interfacial mechanical properties in GR-based polymer nanocomposites.     

Steady-state gel electrophoresis of long polymer molecules: a theoretical study

The velocity of long polymer molecules in a gel and the liquid flow profile in the vicinity of a molecule's surface were studied theoretically by combining the Navier-Stokes equation with the Poisson-Boltzmann equation. The electrophoretic mobility has been calculated in dependence of the ionic strength of the electrolyte solution, its viscosity, the gels' volume friction coefficient, the surface charge and the radius of the polymer molecule. The results are presented in a non-dimensional form and depend on two dimensionless parameters only. The first parameter is the radius of the polymer molecule in units of the Debye length. The second is a parameter comprising the electrolyte's viscosity and the gel density. Thus, by similarity theory, the results apply to any given experimental arrangement. Received: 10 May 1999 / Revised version: 17 November 1999 / Accepted: 6 December 1999     

Instability in pressure-dependent sedimentation of monomer-polymer systems

The possibility of convection in velocity sedimentation studies on pressure dependent associating systems is known both experimentally and theoretically. We present accurate numerical solutions to the Lamm equation to illustrate this phenomenon for monomer–polymer systems. An approximate theory based on the absence of diffusion is then developed to predict the onset of convection. Comparison of the theory with the numerical solutions shows it to be quite accurate.     

Electrophoresis of long DNA molecules in linear polyacrylamide solutions

Electrophoresis of long DNA (T4 DNA; 166 kb, S. pombe chromosomal DNA; 3-6 Mb) in linear polyacrylamide solutions was investigated by fluorescence microscopy and capillary electrophoresis. In the past studies on electrophoresis of long DNA in a polymer solution, it was reported that DNA migrates in 'U-shape conformation'. We found that at higher polymer concentrations, the shape of the migrating DNA changes from U shape to linear shape ('I-shape conformation'). In the migration mode with the I-shape conformation, the DNA moves with almost constant velocity and constant shape. However, the migration velocity does depend on the DNA size, and it is possible to separate DNAs under this I-shape motion. Actually, Mb-sized DNAs are well separated within 5 min in the region for the I-shape motion by means of capillary electrophoresis with a DC field. Considering that it takes 20 h to separate Mb-sized DNAs by standard pulsed-field gel electrophoresis (PFGE), this results will be useful for the separation of giant DNAs.     

Optical peroxide biosensor using the electrically controlled-release technique

An optical biosensor using an electrically controlled-release system was developed for the measurement of peroxide concentration. The electrically controlled-release system consisted of a current-supplying system and a polymer complex by hydrogen bonding between the carboxylic and oxazoline group. The polymer complex was formed below pH 5.0 and was degraded above pH 5.4. The local pH change near the surface of the polymer complex could be controlled by applying the electric current to release an enzyme reaction reagent, 4-hydroxyphenylacetic acid (HPA), in the polymer complex. The releasing rate of HPA was proportional to the electric current applied to the polymer complex. The model of the controlled-release system was proposed to predict the degradation velocity of the polymer complex, which is equivalent to the releasing rate of HPA. The released HPA and analyte, peroxide, flowed into the reactor with the immobilized enzyme and then reacted with the enzyme. The peroxide concentration was measured based on the fluorescence detection of enzyme reaction product, 6,6'-dihydroxy (1,1'-biphenyl) 3,3'-diacetic acid (DBDA). The proposed biosensor had the linear analytical range of 0.025 approximately 1.0 mM with a response time of 20 min, good repeatability, and reproducibility.     

Dynamical Properties of Condensed Charged Polymer Melts

Abstract

Dynamical properties of condensed charged polymer melts are studied with a two-dimensional model and molecular dynamics simulation. Screened Coulombic interactions are assumed for the interactions between the monomer charges as well as the counterions which were introduced to neutralize the total monomer charges of polymer chains. Through molecular dynamics calculations, we have obtained the radial distribution function and velocity auto-correlation function, and their density dependences. As a structural characteristics in condensed charged polymer melts, we find that the monomers tend to form triangular structures locally. The radial distribution function for the center monomers implies that the polymer chains on our two-dimensional model are not entangled. The diffusion properties for both the counter-ions and innermost monomers are studied in detail. In this paper, we have also computed neutral polymer melts to study the effects of the presence of the long-range Coulombic interactions on the dynamical properties of polymer melts. We find that the Coulombic interactions significantly reduce the self diffusion. Snapshots analyses obtained from the molecular dynamics simulation suggest that the reptation model is not a proper model for two-dimensional polymer-chain melts, in which there are little entanglement effects in agreement with the result of the analyses for the radial distribution function.     

Characterisation of interchain association in polysaccharide solutions by ultrasonic relaxation and velocity

The amplitude of ultrasonic relaxation in aqueous solutions of disordered polysaccharides shows a marked increase with increasing degree of coil overlap and, at comparatively low concentrations, attains values comparable to those observed in polysaccharide gels. Mechanical spectroscopy studies indicate that, on the ultrasonic timescale, dynamic networks formed by polymer entanglement in solution are indistinguishable from true gels. In both cases the intense relaxations observed are attributed predominantly to motion of solvent within the polymer network. Due to the inherent stiffness of most polysaccharides, formation of a highly entangled network structure (with consequent enhancement of ultrasonic relaxation) occurs at much lower concentrations than for typical synthetic polymers. The onset of coil overlap (c¹ transition) is accompanied by an abrupt change in the concentration dependence of ultrasonic velocity. Results for the conformationally rigid polysaccharide xanthan, suggest that velocity measurements may offer a convenient method for determination of c¹ in systems where the normal viscometric characterisation is impossible.     

Silanized surfaces for in vitro studies of actomyosin function and nanotechnology applications

We have previously shown that selective heavy meromyosin (HMM) adsorption to predefined regions of nanostructured polymer resist surfaces may be used to produce a nanostructured in vitro motility assay. However, actomyosin function was of lower quality than on conventional nitrocellulose films. We have therefore studied actomyosin function on differently derivatized glass surfaces with the aim to find a substitute for the polymer resists. We have found that surfaces derivatized with trimethylchlorosilane (TMCS) were superior to all other surfaces tested, including nitrocellulose. High-quality actin filament motility was observed up to 6 days after incubation with HMM and the fraction of motile actin filaments and the velocity of smooth sliding were generally higher on TMCS than on nitrocellulose. The actomyosin function on TMCS-derivatized glass and nitrocellulose is considered in relation to roughness and hydrophobicity of these surfaces. The results suggest that TMCS is an ideal substitute for polymer resists in the nanostructured in vitro motility assay. Furthermore, TMCS derivatized glass also seems to offer several advantages over nitrocellulose for HMM adsorption in the ordinary in vitro motility assay.     

Radial migration of DNA molecules in cylindrical flow. II. The non-draining model and possible application to fractionation

The radial-migration calculation of the preceding paper is extended to the non-draining polymer. The results show an inward radial velocity that depends on the 5/2 power of the molecular weight, assuming gaussian statistics for the chain. This sensitivity to size serves as the basis for a method of separating DNA molecules in solution according to their size. Normal stress (Weissenberg) effects are also discussed.     

The lateral separation of contacts on erythrocytes agglutinated by polylysine.

The form of contact seam (whether a continuous parallel seam or membranes in spatially periodic contact) has been characterized for normal and for neuraminidase pretreated human erythrocytes following adhesion in solutions of polylysine in the molecular mass range 10-225 kDa at concentrations from 0.5 to 1.0 mg/mL. The adhesion contact seam was spatially periodic for all normal control cells in polylysine. The lateral separation of contacts decreased from 1.6 to 0.8 microns as the concentration of 225 kDa polylysine was increased threefold from the adhesion threshold value. The separation distance did not change further even at high polymer concentrations that increased the electrophoretic velocity to positive values over twice the modulus of the velocity of control cells. The probability of cell adhesion decreased at these high polymer concentrations. The lateral contact separation increased and cell adhesion decreased for cells pretreated with neuraminidase. Cell adhesion did not occur when neuraminidase reduced the cell electrophoretic velocity modulus by 30%. Following neuraminidase pretreatments that allowed a small amount of adhesion, the cell contact seam was continuous rather than spatially periodic. The results show that a procedure that increases (e.g., polymer concentration increase) or decreases (e.g., enzyme removal of polycation crosslinking site) attraction leads to shorter (to a limiting value) or longer lateral contact separation, respectively.     

Statistical modeling and optimization of biomass granulation and COD removal in UASB reactors treating low strength wastewaters

The aim of this work was to study the influence of influent chemical oxygen demand (COD), upflow velocity of wastewater, and cationic polymer additives in inoculum, on biomass granulation and COD removal efficiency in upflow anaerobic sludge blanket (UASB) reactor for treating low strength wastewater. Statistical models were formulated based on these three variables to optimize the biomass granulation and COD removal efficiency in UASB reactors using a two-level, full factorial design. For the thick inoculum used in this study, having suspended solids (SS) >80 g/l and volatile suspended solids (VSS) to SS ratio <0.3, cationic polymer additives in the inoculum showed adverse effect on biomass granulation and COD removal efficiency. It is concluded that for such thick inoculum, granulation can be obtained while treating low strength wastewaters in UASB reactor by selecting proper combination of influent COD and liquid upflow velocity so as to represent the organic loading rate (OLR) greater than 1.0 kg COD/m(3) d. Validation of model predictions for treatment of synthetic wastewater and actual sewage reveals the efficacy of these models for enhancing granulation and COD removal efficiency.     

Langevin dynamics simulations of genome packing in bacteriophage

We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general.     

Volume and sound velocity changes accompanying the -helix to -form and coil to -helix transitions in aqueous solution

The volume increment per amino acid residue for the α-helix to β-form transition of uncharged poly-L -lysine in aqueous solution was 3.8 ml in water and 4.3 ml in 0.2M and 1M NaBr solutions at 26°C, respectively. The sound velocity of the polymer solution was greater with the β-helix than with the β-form, but the difference was less in dilute salt solutions and disappeared in 1 or 2M NaBr solution. Thus, the β poly-L -lysine solution was slightly more compressible than the α-polymer solution, but this difference was diminished with increasing salt concentration. Both the volume change and the change in adiabatic compressibility of the polymer solution suggest that hydrophobic interactions among the lysyl groups in the β-form reduce the amount of “icebergs” surrounding the polymer molecules as compared with the amount originally present with the α-helix. The coil-to-helix transition of poly-L -glutamic acid in aqueous solution was also accompanied by a decrease in sound velocity. This can be attributed to the reduction of the water of hydration which is less compressible than free water.     

Kinetic Analysis of Analyte Binding by Optical Biosensors: Hydrodynamic Penetration of the Analyte Flow into the Polymer Matrix Reduces the Influence of Mass Transport

I examined the penetration of the hydrodynamic flow into a polymer matrix immobilized by grafting to a surface, such as used in optical biosensors designed to measure binding reactions in real time. I show that the flow penetrates with an appreciable velocity into a region located at the tip of such a polymer brush, corresponding to about 10 to 15% of the total mass of the grafted polymer. Furthermore, under the conditions recommended for kinetic measurements, the concentrations of both polymer and immobilized ligands are low in these regions of the matrix, where crowding effects are negligible. Under such conditions, the hydrodynamic flow penetrating into the dextran matrix flow will bring the analytes close to their targets, thus considerably reducing transport problems.     

Hydrodynamic theory of swimming of flagellated microorganisms.

A theory of the type commonly used in polymer hydrodynamics is developed to calculate swimming properties of flagellated microorganisms. The overall shape of the particle is modeled as an array of spherical beads which act, at the same time, as frictional elements. The fluid velocity field is obtained as a function of the forces acting at each bead through Oseen-type, hydrodynamic interaction tensors. From the force and torque equilibrium conditions, such quantities as swimming velocity, angular velocity, and efficiency can be calculated. Application is made to a spherical body propelled by a helical flagellum. A recent theory by Lighthill, and earlier formulations based on tangential and normal frictional coefficients of a curved cylinder, CT and CN, are analyzed along with our theory. Although all the theories predict similar qualitative characteristics, such as optimal efficiency and the effect of fluid viscosity, they lead to rather different numerical values. In agreement with Lighthill, we found the formalisms based on CN and CT coefficients to be somewhat inaccurate, and head-flagellum interactions are shown to play an important role.     

Miscibility studies of HPMC/PEG blends in water by viscosity,density, refractive index and ultrasonic velocity method

Hydroxy propyl methyl cellulose (HPMC)/polyethylene glycol (PEG) blends are edible polymer films used for food packing and directly in foodstuffs. However, they are water-soluble in ordinary temperature and have good mechanical properties. The miscibility of HPMC/PEG blend in water was studied by viscosity, ultrasonic velocity, density and refractive index techniques at 30 and 50 °C. Using viscosity data, the interaction parameters μ and α were calculated. These values revealed that HPMC/PEG blend is miscible when the HPMC content is more than 60 wt.% in the blend at 30 and 50 °C, below which is immiscible. Further the result was also confirmed by ultrasonic velocity, density, refractive index measurements, which also revealed that the change in temperature has no significant effect on the miscibility of HPMC/PEG polymer blend.     

The lateral separation of contacts on erythrocytes agglutinated by polylysine

The form of contact seam (whether a continuous parallel seam or membranes in spatially periodic contact) has been characterized for normal and for neuraminidase pretreated human erythrocytes following adhesion in solutions of polylysine in the molecular mass range 10–225 kDa at concentrations from 0.5 to 1.0 mg/mL. The adhesion contact seam was spatially periodic for all normal control cells in polylysine. The lateral separation of contacts decreased from 1.6 to 0.8 μm as the concentration of 225 kDa polylysine was increased threefold from the adhesion threshold value. The separation distance did not change further even at high polymer concentrations that increased the electrophoretic velocity to positive values over twice the modulus of the velocity of control cells. The probability of cell adhesion decreased at these high polymer concentrations. The lateral contact separation increased and cell adhesion decreased for cells pretreated with neuraminidase. Cell adhesion did not occur when neuraminidase reduced the cell electrophoretic velocity modulus by 30%. Following neuraminidase pretreatments that allowed a small amount of adhesion, the cell contact seam was continuous rather than spatially peridic. The results show that a procedure that increases (e.g., polymer concentration increase) or decreases (e.g., enzyme removal of polycation crosslinking site) attraction leads to shorter (to a limiting value) or longer lateral contact separation, respectively.     

Chaperone-assisted translocation

We investigate the translocation of a stiff polymer through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind reversibly to the polymer on both sides of the membrane. A bound chaperone covers one (univalent binding) or many (multivalent binding) binding sites. Assuming that the diffusion of the chaperones is fast compared to the rate of translocation we describe the process by a one-dimensional master equation. We expand previous models by a detailed study of the effective force in the master equation, which is obtained by the appropriate statistical mechanical average over the chaperone states. The dependence of the force on the degree of valency (the number of binding sites occupied by a chaperone) is studied in detail. We obtain finite size corrections (to the thermodynamical expression for the force), which, for univalent binding, can be expressed analytically. We finally investigate the mean velocity for translocation as a function of chaperone binding strength and size. For both univalent and multivalent binding simple results are obtained for the case of a sufficiently long translocating polymer.