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We consider a coarse-grained model in which polymers under good-solvent conditions are represented by soft spheres whose radii, which should be identified with the polymer radii of gyrations, are allowed to fluctuate. The corresponding pair potential depends on the sphere radii. This model is a single-sphere version of the one proposed in Vettorel et al. [Soft Matter 6, 2282 (2010)], and it is sufficiently simple to allow us to determine all potentials accurately from full-monomer simulations of two isolated polymers (zero-density potentials). We find that in the dilute regime (which is the expected validity range of single-sphere coarse-grained models based on zero-density potentials) this model correctly reproduces the density dependence of the radius of gyration. However, for the thermodynamics and the intermolecular structure, the model is largely equivalent to the simpler one in which the sphere radii are fixed to the average value of the radius of gyration and radii-independent potentials are used: for the thermodynamics there is no advantage in considering a fluctuating sphere size. [ABSTRACT FROM AUTHOR]

We present a numerical self-consistent field (SCF) method which describes freely jointed chains of spherical monomers applied to densely grafted polymer brushes. We discuss both the Flory-Huggins model and the Carnahan-Starling equation of state and show the latter being preferable within our model at polymer volume fractions above 10%. We compare the results of our numerical method with data from molecular dynamics (MD) simulations [G.-L. He, H. Merlitz, J.-U. Sommer, and C.-X. Wu, Macromolecules 40, 6721 (2007)] and analytical SCF calculations [P. M. Biesheuvel, W. M. de Vos, and V. M. Amoskov, Macromolecules 41, 6254 (2008)] and obtain close agreement between the density profiles up to high grafting densities. In contrast to prior numerical and analytical studies of densely grafted polymer brushes our method provides detailed information about chain configurations including fluctuation, depletion, and packing effects. Using our model we could study the recently discovered instability of densely grafted polymer brushes with respect to slight variations of individual chain lengths, driven by fluctuation effects [H. Merlitz, G.-L. He, C.-X. Wu, and J.-U. Sommer, Macromolecules 41, 5070 (2008)]. The obtained results are in very close agreement with corresponding MD simulations. [ABSTRACT FROM AUTHOR]

Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width R embedded in two dimensions, driven by a force proportional to the number of monomers in the channel. Such a setup mimics typical experimental situations in nano/microfluidics. During the translocation process if the monomers in the channel can sufficiently quickly assume steady state motion, we observe the scaling τ ∼ N/F of the translocation time τ with the driving force F per bead and the number N of monomers per chain. With smaller channel width R, steady state motion cannot be achieved, effecting a nonuniversal dependence of τ on N and F. From the simulations we also deduce the waiting time distributions under various conditions for the single segment passage through the channel entrance. For different chain lengths but the same driving force, the curves of the waiting time as a function of the translocation coordinate s feature a maximum located at identical smax, while with increasing the driving force or the channel width the value of smax decreases. [ABSTRACT FROM AUTHOR]

When two types of side chains (A,B) are densely grafted to a (stiff) backbone and the resulting bottlebrush polymer is in a solution under poor solvent conditions, an incompatibility between A and B leads to microphase separation in the resulting cylindrical brush. The possible types of ordering are reminiscent of the ordering of block copolymers in cylindrical confinement. Starting from this analogy, Leibler's theory of microphase separation in block copolymer melts is generalized to derive a description of the system in the weak segregation limit. Also molecular dynamics simulation results of a corresponding coarse-grained bead-spring model are presented. Using side chain lengths up to N = 50 effective monomers, the ratio of the Lennard-Jones energy parameter between unlike monomers ([variant_greek_epsilon]AB) and monomers of the same kind ([variant_greek_epsilon]AA = [variant_greek_epsilon]BB) is varied. Various correlation functions are analyzed to study the conditions when (local) Janus-cylinder-type ordering and when (local) microphase separation in the direction along the cylinder axis occurs. Both the analytical theory and the simulations give evidence for short-range order due to a tendency toward microphase separation in the axial direction, with a wavelength proportional to the side chain gyration radius, irrespective of temperature and grafting density, for a wide range of these parameters. [ABSTRACT FROM AUTHOR]

Using a lattice-based Monte Carlo code for simulating self-avoiding flexible polymers in three dimensions in the absence of explicit hydrodynamics, we study their Rouse modes. For self-avoiding polymers, the Rouse modes are not expected to be statistically independent; nevertheless, we demonstrate that numerically these modes maintain a high degree of statistical independence. Based on high-precision simulation data we put forward an approximate analytical expression for the mode amplitude correlation functions for long polymers. From this, we derive analytically and confirm numerically several scaling properties for self-avoiding flexible polymers, such as (i) the real-space end-to-end distance, (ii) the end-to-end vector correlation function, (iii) the correlation function of the small spatial vector connecting two nearby monomers at the middle of a polymer, and (iv) the anomalous dynamics of the middle monomer. Importantly, expanding on our recent work on the theory of polymer translocation, we also demonstrate that the anomalous dynamics of the middle monomer can be obtained from the forces it experiences, by the use of the fluctuation-dissipation theorem. [ABSTRACT FROM AUTHOR]

Monte Carlo simulations were performed on semiflexible polymer chains with the goal of delineating their isotropic-nematic (IN) and gas-liquid coexistence envelopes. The chain monomers are spherical beads that interact via a square-well potential with all other beads. Bonded beads are connected by strings chosen so that bond length varies between 1.01σ and 1.05σ (where σ is the hard sphere diameter). The stiffness of the molecules is controlled via a potential between beads separated by two bonds; this potential restricts the distance between these beads to be between 2.02σ and 2.1σ. The vapor-liquid coexistence and IN coexistence curves are obtained using computer simulations. An IN transition is found for 10≤=Nb≤30. Both the density at which the IN transition occurs and the location of the gas-liquid coexistence go through a maximum with increasing Nb. For longer chains, behavior expected from theory is found and both of these coexisting densities decrease with increasing length. [ABSTRACT FROM AUTHOR]

The depletion interaction between proteins caused by addition of either uncharged or partially charged oligomers was studied using the canonical Monte Carlo simulation technique and the integral equation theory. A protein molecule was modeled in two different ways: either as (i) a hard sphere of diameter 30.0 Å with net charge 0, or +5, or (ii) as a hard sphere with discrete charges (depending on the pH of solution) of diameter 45.4 Å. The oligomers were pictured as tangentially jointed, uncharged, or partially charged, hard spheres. The ions of a simple electrolyte present in solution were represented by charged hard spheres distributed in the dielectric continuum. In this study we were particularly interested in changes of the protein-protein pair-distribution function, caused by addition of the oligomer component. In agreement with previous studies we found that addition of a nonadsorbing oligomer reduces the phase stability of solution, which is reflected in the shape of the protein-protein pair-distribution function. The value of this function in protein-protein contact increases with increasing oligomer concentration, and is larger for charged oligomers. The range of the depletion interaction and its strength also depend on the length (number of monomer units) of the oligomer chain. The integral equation theory, based on the Wertheim Ornstein-Zernike approach applied in this study, was found to be in fair agreement with Monte Carlo results only for very short oligomers. The computer simulations for a model mimicking the lysozyme molecule (ii) are in qualitative agreement with small-angle neutron experiments for lysozyme-dextran mixtures. [ABSTRACT FROM AUTHOR]

We study polymer-polymer phase separation in a common good solvent by means of Monte Carlo simulations of the bond-fluctuation model. Below a critical, chain-length-dependent concentration, no phase separation occurs. For higher concentrations, the critical demixing temperature scales nonlinearly with the total monomer concentration, with a power law relatively close to a renormalization-group prediction based on “blob” scaling arguments. We point out that earlier simulations and experiments have tested this power-law dependence at concentrations outside the validity regime of the scaling arguments. The critical amplitudes of the order parameter and the zero-angle scattering intensity also exhibit chain-length dependences that differ from the conventional predictions but are in excellent agreement with the renormalization-group results. In addition, we characterize the variation of the average coil shape upon phase separation. [ABSTRACT FROM AUTHOR]

The native structure of fast-folding proteins, albeit a deep local free-energy minimum, may involve a relatively small energetic penalty due to nonoptimal, though favorable, contacts between amino acid residues. The weak energetic frustration that such contacts represent varies among different proteins and may account for folding behavior not seen in unfrustrated models. Minimalist model proteins with heterogeneous contacts—as represented by lattice heteropolymers consisting of three types of monomers—also give rise to weak energetic frustration in their corresponding native structures, and the present study of their equilibrium and nonequilibrium properties reveals some of the breadth in their behavior. In order to capture this range within a detailed study of only a few proteins, four candidate protein structures (with their cognate sequences) have been selected according to a figure of merit called the winding index—a characteristic of the number of turns the protein winds about an axis. The temperature-dependent heat capacities reveal a high-temperature collapse transition, and an infrequently observed low-temperature rearrangement transition that arises because of the presence of weak energetic frustration. Simulation results motivate the definition of a new measure of folding affinity as a sequence-dependent free energy—a function of both a reduced stability gap and high accessibility to non-native structures—that correlates strongly with folding rates. [ABSTRACT FROM AUTHOR]

Using a one-dimensional model for the translocation of a polymer through a nanopore, the effect of a 'sticky site' at which the polymer binds to the pore is explored via exact numerical techniques. Results for the mean translocation time and the probability of translocation on the insertion of the first monomer in the pore are generated across a wide range of driving forces and binding potential strengths (well depths). The balance between the driving force, diffusion, and well depth yields a rich set of dynamics that depend strongly on where the sticky site is located along the polymer. For example, when the sticky site is located near the head of the polymer, the translocation time is found to be a maximum at an intermediate driving force with events at lower driving forces taking less time. Additionally, the critical well depth at which the sticky site dominates the dynamics, is found to be a non-monotonic function of the driving force when the sticky site is located at the head or tail of the polymer, but not in the middle. Modeling of the process yields good agreement with simulation results. [ABSTRACT FROM AUTHOR]

The spatial correlations of the monomer displacements are studied via molecular-dynamics simulations of a melt of fully flexible, unentangled polymer chains with different length, interacting potential, density, and temperature. Both the scalar and the vector characters of the correlations are considered and their extension quantified in terms of suitable dynamical correlation lengths. Displacements performed at both short, i.e., vibrational, and long times, i.e., comparable to the structural relaxation time, are investigated. On both time scales the spatial correlations are modulated according to the radial distribution function g(r) to an extent which is determined by the character of the correlations, the time scale of the displacements and the structural slowing down. The spatial correlations of the short-time displacements have clear directional character. The modulus correlations of the long-time displacements are more marked, especially for sluggish states. Analogous findings are found by experiments on colloids. By inspecting the dynamical heterogeneities of states with slowed-down dynamics, it is observed that fast monomers exhibit correlations which are stronger and more differing from the bulk than the slow ones. It is shown that states with identical average vibrational monomer displacement exhibit identical spatial correlations of the monomer displacements pertaining to the subsets of the fast and the slow monomers characterizing both the short-time and the long-time dynamical heterogeneities. [ABSTRACT FROM AUTHOR]