Static and dynamic properties of tethered chains at adsorbing surfaces: a Monte Carlo study

We present extensive Monte Carlo simulations of tethered chains of length N on adsorbing surfaces, considering the dilute case in good solvents, and analyze our results using scaling arguments. We focus on the mean number M of chain contacts with the adsorbing wall, on the chain's extension (the radius of gyration) perpendicular and parallel to the adsorbing surface, on the probability distribution of the free end and on the density profile for all monomers. At the critical adsorption strength epsilon(c) one has M(c) approximately N(phi), and we find (using the above results) as best candidate phi to equal 0.59. However, slight changes in the estimation of epsilon(c) lead to large deviations in the resulting phi; this might be a possible reason for the difference in the phi values reported in the literature. We also investigate the dynamical scaling behavior at epsilon(c), by focusing on the end-to-end correlation function and on the correlation function of monomers adsorbed at the wall. We find that at epsilon(c) the dynamic scaling exponent a (which describes the relaxation time of the chain as a function of N) is the same as that of free chains. Furthermore, we find that for tethered chains the modes perpendicular to the surface relax quicker than those parallel to it, which may be seen as a splitting in the relaxation spectrum.     

Polymer translocation through a nanopore under an applied external field

We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength E, length of the chain N, and length of the pore L on forced translocation. As our main result, we find a crossover scaling for the translocation time tau with the chain length from tau approximately N2nu for relatively short polymers to tau approximately N1+nu for longer chains, where nu is the Flory exponent. We demonstrate that this crossover is due to the change in the dependence of the translocation velocity v on the chain length. For relatively short chains v approximately N-nu, which crosses over to v approximately N(-1) for long polymers. The reason for this is that with increasing N there is a high density of segments near the exit of the pore, which slows down the translocation process due to slow relaxation of the chain. For the case of a long nanopore for which R parallel, the radius of gyration Rg along the pore, is smaller than the pore length, we find no clear scaling of the translocation time with the chain length. For large N, however, the asymptotic scaling tau approximately N1+nu is recovered. In this regime, tau is almost independent of L. We have previously found that for a polymer, which is initially placed in the middle of the pore, there is a minimum in the escape time for R parallel approximately L. We show here that this minimum persists for weak fields E such that EL is less than some critical value, but vanishes for large values of EL.     

Langevin dynamics simulations of polymer translocation through nanopores

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of an external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau(e) required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that tau(e) scales with the chain length N as tau(e) approximately N(1+2nu), where nu is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient xi, the driving force E, and the length of the chain N on the translocation time tau, which is defined as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and tau approximately E(-1). The influence of xi depends on the ratio between the driving and frictional forces. For intermediate xi, we find a crossover scaling for tau with N from tau approximately N(2nu) for relatively short chains to tau approximately N(1+nu) for longer chains. However, for higher xi, only tau approximately N(1+nu) is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing xi increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveal additional features of dependency on friction.     

Polymer translocation through a nanopore: a two-dimensional Monte Carlo study

We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau required for the polymer to completely exit the pore on either end. We find numerically that tau scales with the chain length N as tau approximately N(1+2nu), where nu is the Flory exponent. This is the same scaling as predicted for the translocation time of a polymer which passes through the nanopore in one direction only. We examine the interplay between the pore length L and the radius of gyration R(g). For LR(g), we find tau approximately N. In addition, we numerically find the scaling function describing crossover between short and long pores. We also show that tau has a minimum as a function of L for longer chains when the radius of gyration along the pore direction R( parallel) approximately L. Finally, we demonstrate that the stiffness of the polymer does not change the scaling behavior of translocation dynamics for single-segment dynamics.     

Irreversible adsorption of tethered chains at substrates: Monte Carlo study

The irreversible adsorption of single chains grafted with one end to the surface is studied using scaling arguments and computer simulations. We introduce a two-phase model, in which the chain is described by an adsorbate portion and a corona portion formed by nonadsorbed monomers. The adsorption process can be viewed as consisting of a main stage, during which monomers join by "zipping" (along their order in the chain) the surface, and a late stage, in which the remaining corona collapses on the surface. Based on our model we derive a scaling relation for the time of adsorption t(M) as a function of the number M of adsorbed monomers; t(M) follows a power law, M(alpha), with alpha > 1. We find that alpha is related to the Flory exponent nu by alpha = 1 + nu. Using further scaling arguments we derive relations between the overall time of adsorption, the characteristic time of adsorption (given by the crossover time between the main and the last stage of adsorption), and the chain length. To support our analysis we perform Monte Carlo simulations using the bond fluctuation model. In particular, the sequence of adsorption events is very well reproduced by the simulations, and an analysis of the various density profiles supports our theoretical model. Especially the loop formation during adsorption clearly shows that the growth of the adsorbate is dominated by zipping. The simulations are also in almost quantitative agreement with our theoretical scaling analysis, showing that here the assumption of a linear relation between Monte Carlo steps and time is well obeyed. We conclude by also discussing the geometrical shape of the adsorbate.     

Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model

Dynamic Monte Carlo simulation of a bead-spring model of flexible macromolecules threading through a very narrow pore in a very thin rigid membrane are presented, assuming at the cis side of the membrane a purely repulsive monomer-wall interaction, while the trans side is attractive. Two choices of monomer-wall attraction epsilon are considered, one choice is slightly below and the other slightly above the "mushroom to pancake" adsorption threshold epsilon(c) for an infinitely long chain. Studying chain lengths N=32, 64, 128, and 256 and varying the number of monomers N(trans) (time t=0) that have already passed the pore when the simulation started, over a wide range, we find for epsilonepsilon(c) a finite number N(trans)(t=0) suffices that the translocation probability is close to unity. In the case epsilonepsilon(c), we find that the translocation time scales as tau proportional, variant N(1.65+/-0.08). We suggest a tentative scaling explanation for this result. Also the distribution of translocation times is obtained and discussed.     

Polymer chains in a soft nanotube: a Monte Carlo study

We study the equilibrium properties of flexible polymer chains confined in a soft tube by means of extensive Monte Carlo simulations. The tube wall is that of a single sheet six-coordinated self-avoiding tethered membrane. Our study assumes that there is no adsorption of the chain on the wall. By varying the length N of the polymer and the tube diameter D we examine the variation of the polymer gyration radius Rg and diffusion coefficient Ddiff in soft and rigid tubes of identical diameter and compare them to scaling theory predictions. We find that the swollen region of the soft tube surrounding the chain exhibits a cigarlike cylindrical shape for sufficiently narrow tubes with D相似文献   

A Monte Carlo algorithm to study polymer translocation through nanopores. II. Scaling laws

In the first paper of this series, we developed a new one-dimensional Monte Carlo approach for the study of flexible chains that are translocating through a small channel. We also presented a numerical scheme that can be used to obtain exact values for both the escape times and the escape probabilities given an initial pore-polymer configuration. We now present and discuss the fundamental scaling behaviors predicted by this Monte Carlo method. Our most important result is the fact that, in the presence of an external bias E, we observe a change in the scaling law for the translocation time tau as function of the polymer length N: In the general expression tau approximately N(beta)E, the exponent changes from beta=1 for moderately long chains to beta=1+nu or beta=2nu for very large values of N (for Rouse and Zimm dynamics, respectively). We also observe an increase in the effective diffusion coefficient due to the presence of entropic pulling on unbiased polymer chains.     

Concentration and saturation effects of tethered polymer chains on adsorbing surfaces

We consider end-grafted chains at an adsorbing surface under good solvent conditions using Monte Carlo simulations and scaling arguments. Grafting of chains allows us to fix the surface concentration and to study a wide range of surface concentrations from the undersaturated state of the surface up to the brushlike regime. The average extension of single chains in the direction parallel and perpendicular to the surface is analyzed using scaling arguments for the two-dimensional semidilute surface state according to Bouchaud and Daoud [J. Phys. (Paris) 48, 1991 (1987)]. We find good agreement with the scaling predictions for the scaling in the direction parallel to the surface and for surface concentrations much below the saturation concentration (dense packing of adsorption blobs). Increasing the grafting density we study the saturation effects and the oversaturation of the adsorption layer. In order to account for the effect of excluded volume on the adsorption free energy we introduce a new scaling variable related with the saturation concentration of the adsorption layer (saturation scaling). We show that the decrease of the single chain order parameter (the fraction of adsorbed monomers on the surface) with increasing concentration, being constant in the ideal semidilute surface state, is properly described by saturation scaling only. Furthermore, the simulation results for the chains' extension from higher surface concentrations up to the oversaturated state support the new scaling approach. The oversaturated state can be understood using a geometrical model which assumes a brushlike layer on top of a saturated adsorption layer. We provide evidence that adsorbed polymer layers are very sensitive to saturation effects, which start to influence the semidilute surface scaling even much below the saturation threshold.     

Confinement free energy and chain conformations of homopolymers confined between two repulsive walls

Lattice Monte Carlo simulations of polymer solutions confined between two parallel plates were performed. The confinement free energy Deltamicro(conf) per chain and the radius of gyrations of the chains parallel and perpendicular to the plates were obtained. When the concentration of the confined solution is above the overlap concentration, Deltamicro(conf) is found to scale with Na/D in a power law, betaDeltamicro(conf) approximately (Na/D)(m), with an exponent m=1.10+/-0.02 for athermal walls where N is the number of monomers in a chain, D is the slit width, and a is the lattice spacing. The presence of a weak attractive polymer/wall interaction epsilon(w) does not change the scaling variable, but the exponent m increases slightly. Extrapolating the results to melt would suggest that the predictions made by de Gennes [C. R. Acad. Sci. Paris II 305, 1181 (1987)] about the confinement free energy cost per chain in polymer melt is correct as far as the scaling variable is concerned, but is incorrect about the exponent m observed. The implication of this result on the predicted force between plates immersed in polymer melt is discussed. The parallel dimensions of the confined chain is expanded when the slit width D is narrow, however, the expansion is reduced at high concentration. It is conceivable that in melt the chain is not expanded when confined in a repulsive slit.     

Kinetics of loop formation in polymer chains

We investigate the kinetics of loop formation in ideal flexible polymer chains (the Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is tau(c) approximately tau(0)N(2) (where tau(0) is a microscopic time scale and N is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when a, the capture radius for contact formation, exceeds b, the average distance between two connected beads. Simulations also show that when a < b, tau(c) approximately N(alpha)(tau), where 1.5 < alpha(tau) < or = 2 in the range 7 < N < 200 used in the simulations. By using a diffusion coefficient that is dependent on the length scales a and b (with a < b), which captures the two-stage mechanism by which looping occurs when a < b, we obtain an analytic expression for tauc that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly effected when interactions between monomers are taken into account. Remarkably, for N < 100, the values of tau(c) decrease by more than 2 orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for tau(c) to a power law in N (tau(c) approximately N(alpha)(tau)) show that alpha(tau) varies from about 2.4 in a good solvent to about 1.0 in poor solvents. The effective exponent alpha(tau) decreases as the strength of the attractive monomer-monomer interactions increases. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain. The time for contact formation between beads that are interior to the chain in good solvents changes nonmonotonically as the loop length varies. In contrast, the variation in interior loop closure time is monotonic in poor solvents. The implications of our results for contact formation in polypeptide chains, RNA, and single-stranded DNA are briefly outlined.     

Adsorption and freezing of diblock copolymers on stripe-patterned surfaces: a scaling analysis

We present the results of scaling analysis of diblock copolymers adsorbed on stripe-patterned surfaces of various widths. Our previous studies [K. Sumithra and E. Straube, J. Chem. Phys. 125, 154701 (2006)] show that the adsorption of diblock copolymer on patterned surfaces yields two peaks in the specific heat capacity, thereby indicating two transition. In the current study, we characterize these two transitions. The scaling of the adsorption energy data proves that the first peak in the heat capacity curve is, in fact, associated with the adsorption transition. We found that for this transition the classical scaling laws are obeyed and that the critical crossover exponent is unaltered with respect to the case of homogeneous polymers. However, we found a change in the scaling exponent in the case of parallel component of the radius of gyration. It is evident from the scaling analysis of the parallel component of the radius of gyration that the chain is stretched along the direction of the stripes. The scaling plot shows, for (square root )/Nnu, an exponent of approximately 0.55 which is much different from that expected of a self-avoiding chain (nud=2-nu)/phi which is 0.25. The observed value is closer to an exponent of (nud=1-nu)/phi=0.69, for a completely stretched chain in one dimension. The perpendicular component of the radius of gyration shows deviation from the power law and the slope is steeper than the expected value of -2. We have also defined an order parameter to characterize the second transition and have found that it corresponds to a freezing transition where there are only a few dominant conformations. The perpendicular component of the radius of gyration also supports this information.     

Dynamics of propylene glycol and its oligomers confined to a single molecular layer

The dynamics of propylene glycol (PG) and its oligomers 7-PG and poly-propylene glycol (PPG), with M(w) = 4000 (approximately 70 monomers), confined in a Na-vermiculite clay have been investigated by quasielastic neutron scattering. The liquids are confined to single molecular layers between clay platelets, giving a true two-dimensional liquid. Data from three different spectrometers of different resolutions were Fourier transformed to S(Q,t) and combined to give an extended dynamical time range of 0.3-2000 ps. An attempt was made to distinguish the diffusive motion from the methyl group rotation and a fast local motion of hydrogen in the polymer backbone. The results show that the average relaxation time tau(d) of this diffusive process is, as expected, larger than the relaxation time tau averaged over all dynamical processes observed in the experimental time window. More interesting, it is evident that the severe confinement has a relatively small effect on tau(d) at T = 300 K, this holds particularly for the longest oligomer, PPG. The most significant difference is that the chain-length dependence of tau(d) is weaker for the confined liquids, although the slowing down in bulk PG due to the formation of a three-dimensional network of OH-bonded end groups reduces this difference. The estimated average relaxation time tau at Q = 0.92 Angstroms(-1) for all the observed processes is in excellent agreement with the previously reported dielectric alpha relaxation time in the studied temperature range of 260-380 K. The average relaxation time tau (as well as the dielectric alpha relaxation time) is also almost unaffected by the confinement to a single molecular layer, suggesting that the interaction with the clay surfaces is weak and that the reduced dimensionality has only a weak influence on the time scale of all the dynamical processes observed in this study.     

Study of the semidilute solutions of poly(N,N-dimethylacrylamide) by fluorescence and its implications to the kinetics of coil-to-globule transitions

The large scale motions of poly(N,N-dimethylacrylamide) chains randomly labeled with pyrene (Py-PDMA) were monitored by steady-state and time-resolved fluorescence in semidilute solutions of naked PDMA in acetone and DMF for polymer concentrations ranging from 0 to 550 g/L. Although increasing the polymer concentration of the solution led to a decrease of the mobility of the chromophore attached onto the PDMA backbone, this reduction was rather modest when compared to the large increase of the macroscopic viscosity. This result indicated that locally, the monomer constituting the chains experienced freedom of movement despite the high solution viscosity. The restricted mobility of the chromophore was characterized by the number of monomers occupying the volume probed by the excited chromophore during its lifetime, referred to as a fluorescence "blob". The number of monomers constituting a fluorescence blob, N(F)(-)(blob), and the volume of a fluorescence blob, V(F)(-)(blob), were found to decrease as the polymer concentration of the solution increased, reflecting the decreased mobility experienced by the chromophore. In DMF, the radius of an F-blob was found to scale as N(nu)(F)(-)blob, where nu equaled 0.66 +/- 0.03, very close to the expected value of the Flory exponent of 0.6 for a polymer in a good solvent. The combined knowledge of how N(F)(-)(blob) varies with the fluorescence lifetime of the chromophore and the coil density of the polymer was used to propose a new means of studying coil-to-globule transitions with potential implications for predicting the rate of protein folding.     

Theoretical study of the chemisorption of CO on Al2O3(0001)

Density functional molecular cluster calculations have been used to study the adsorption of CO on the alpha-Al2O3-(0001) surface. Substrate and adsorbate geometry modifications, adsorption enthalpies, and adsorbate vibrations are computed. Despite the rather small size of the employed cluster, relaxation phenomena evaluated for the clean surface agree well with experimental measurements and periodic slab calculations and mainly consist of an inward relaxation of the Lewis acid site (Lsa). Different adsorbate arrangements, perpendicular and parallel to the surface, have been considered. Among them, the most state CO chemisorption geometry (delta Hads approximately -13 kcal/mol) is that corresponding to the adsorbate perpendicular to the surface, atop Lsa and C-down oriented. The C-O stretching frequency (nu C-O) computed for such an arrangement is 2158 cm-1, i.e., blue shifted by 44 cm-1 with respect to the free adsorbate. The lack of experimental evidence pertaining to CO interacting with a well-defined alpha-Al2O3(0001) surface prevents the possibility of a direct check of the computed quantities. Nevertheless, low-temperature IR data for CO on alumina powders (Zecchina, A.; Escalona Platero, E.; Otero Areán, C. J. Catal. 1987, 107, 244) indicate for the chemisorbed species a delta nu = 12 cm-1. The adsorbate-substrate interaction relieves some of the Lsa relaxation, even if the Lsa electronic structure is only slightly affected upon chemisorption.     

Polymer chains confined into tubes with attractive walls: A Monte Carlo simulation

A bead-spring off-lattice model of a polymer chain with repulsive interactions among repeating units confined into straight tubes of various cross sections, D_T², is studied by Monte Carlo simulation. We are also varying the chain length from N = 16 to 128 and the strength of a short-range attractive interaction between the repeating units and the walls of the tube. Longitudinal and perpendicular static linear dimensions of the chains are analyzed, as well as the density profile of repeating units across the tube. These data are interpreted in terms of scaling concepts describing the crossover between three-dimensional and quasi-one-dimensional chain conformations and the adsorption transition of chains at flat infinite walls, respectively. We also study the time-dependent mean-square displacements of repeating units and obtain various relaxation times. It is shown that both relaxation times scaling proportional to N² and to N³ play a role in the reptative motion of the chain in the tubes.     

Equilibrium conformational dynamics of a polymer in a solvent

Molecular dynamics simulations were used to study the conformational dynamics of a bead-spring model polymer in an explicit solvent under good solvent conditions. The dynamics of the polymer chain were investigated using an analysis of the time autocorrelation functions of the Rouse coordinates of the polymer chain. We have investigated the variation of the correlation functions with polymer chain length N, solvent density rho, and system size. The measured initial decay rates gamma(p) of the correlation functions were compared with the predictions from a theory of polymer dynamics which uses the Oseen tensor to describe hydrodynamic interactions between monomers. Over the range of chain lengths considered (N = 30-60 monomers), the predicted scaling of gamma(p) proportional to N(-3nu) was observed at high rho, where nu is the polymer scaling exponent. The predicted gamma(p) are generally higher than the measured values. This discrepancy increases with decreasing rho, as a result in the breakdown in the conditions required for the Oseen approximation. The agreement between theory and simulation at high rho improves considerably if the theoretical expression for gamma(p) is modified to avoid sum-to-integral approximations, and if the values of (R(p)2), which are used in the theory, are taken directly from the simulation rather than being calculated using approximate scaling relations. The observed finite-size scaling of gamma(p) is not quantitatively consistent with the theoretical predictions.     

Translocation of α-helix chains through a nanopore

The translocation of α-helix chains through a nanopore is studied through Langevin dynamics simulations. The α-helix chains exhibit several different characteristics about their average translocation times and the α-helix structures when they transport through the nanopores under the driving forces. First, the relationship between average translocation times τ and the chain length N satisfies the scaling law, τ～N(α), and the scaling exponent α depends on the driving force f for the small forces while it is close to the Flory exponent (ν) in the other force regions. For the chains with given chain lengths, it is observed that the dependence of the average translocation times can be expressed as τ～f(-1/2) for the small forces while can be described as τ～f in the large force regions. Second, for the large driving force, the average number of α-helix structures N(h) decreases first and then increases in the translocation process. The average waiting time of each bead, especially of the first bead, is also dependent on the driving forces. Furthermore, an elasticity spring model is presented to reasonably explain the change of the α-helix number during the translocation and its elasticity can be locally damaged by the large driving forces. Our results demonstrate the unique behaviors of α-helix chains transporting through the pores, which can enrich our insights into and knowledge on biopolymers transporting through membranes.     

Structure, dynamics, and phase transitions of tethered membranes: a Monte Carlo simulation study

A coarse-grained model of a self-avoiding tethered membrane with hexagonal coordination, embedded in three-dimensional space, is studied by means of extensive Monte Carlo computer simulations. The simulations are performed at various temperatures for membranes with linear size 5< or =L< or =50. We find that the membrane undergoes several folding transitions from a high-temperature flat phase to multiple-folded structure as the temperature is steadily decreased. Using a suitable order parameter and finite size scaling analysis, these phase transitions are shown to be of first order. The equilibrium shape of the membranes is analyzed by calculating the eigenvalues lambda(max) (2)> or =lambda(med) (2)> or =lambda(min) (2) of the inertia tensor. We present a systematic finite size scaling analysis of the radius of gyration and the eigenvalues of the inertia tensor at different phases of the observed folding transitions. In the high-temperature flat phase, the radius of gyration R(g) grows with the linear size of the membrane L as R(g) proportional to L(nu), where the exponent nu is approximately equal to 1.0. The eigenvalues of the inertia tensor scale as lambda(max) proportional to lambda(med) proportional to L(nu) and lambda(min) proportional to L(nu(min) ), whereby the roughness exponent nu(min) is approximately equal to 0.7. We also find that the time tau(R) of a self-avoiding membrane to diffuse a distance R(g) scales as tau(R) proportional to L(2nu+2), which is in good agreement with the theoretical predictions.     

Rheological complexity in simple chain models

Dynamical properties of short freely jointed and freely rotating chains are studied using molecular dynamics simulations. These results are combined with those of previous studies, and the degree of rheological complexity of the two models is assessed. New results are based on an improved analysis procedure of the rotational relaxation of the second Legendre polynomials of the end-to-end vector in terms of the Kohlrausch-Williams-Watts (KWW) function. Increased accuracy permits the variation of the KWW stretching exponent beta to be tracked over a wide range of state points. The smoothness of beta as a function of packing fraction eta is a testimony both to the accuracy of the analytical methods and the appropriateness of (eta(0)-eta) as a measure of the distance to the ideal glass transition at eta(0). Relatively direct comparison is made with experiment by viewing beta as a function of the KWW relaxation time tau(KWW). The simulation results are found to be typical of small molecular glass formers. Several manifestations of rheological complexity are considered. First, the proportionality of alpha-relaxation times is explored by the comparison of translational to rotational motion (i.e., the Debye-Stokes-Einstein relation), of motion on different length scales (i.e., the Stokes-Einstein relation), and of rotational motion at intermediate times to that at long time. Second, the range of time-temperature superposition master curve behavior is assessed. Third, the variation of beta across state points is tracked. Although no particulate model of a liquid is rigorously rheologically simple, we find freely jointed chains closely approximated this idealization, while freely rotating chains display distinctly complex dynamical features.