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Most theories of the binding of molecules to surfaces or for the association between molecules treat the binding species as structureless entities and neglect their rigidity and the changes in their stiffness induced by the binding process. The binding species are also taken to be "ideal," meaning that the existence of van der Waals interactions and changes in these interactions upon molecular binding are also neglected. An understanding of the thermodynamics of these multifunctional molecular binding processes has recently come into focus in the context of the molecular binding of complex molecules, such as dendrimers and DNA grafted nanoparticles, to surfaces where the degree of binding cooperativity and selectivity, as well as the location of the binding transition, are found to be sensitive to the number of binding units constrained to a larger scale polymeric scaffold. We address the fundamental problem of molecular binding by extending classical Langmuir theory to describe the particular example of the reversible binding of semiflexible polymer chains to a solid substrate under melt conditions. The polymer chains are assumed to have a variable number N of binding units (segments) and to exhibit variable bending energies and van der Waals interactions in the bulk and on the surface, in addition to strong directional interactions with the surface. The resulting generalized Langmuir theory is applied to the examination of the influence of the chain connectivity of ideal polymers on the surface coverage Θ, transition binding temperature T 1/2 at which Θ = 1/2, and on the derivative |dΘ/dT| T=T 1/2 and the constant volume specific heat of binding, C v , measures of the cooperativity and "sharpness" of the binding transition, respectively. Paper II is devoted to the impact of the van der Waals attractive interactions and chain stiffness on the reversible binding of nonideal polymer chains to a solid surface, including the enthalpy-entropy compensation phenomenon observed experimentally in many molecular and particle binding processes.bind , measures of the cooperativity and "sharpness" of the binding transition, respectively. Paper II is devoted to the impact of the van der Waals attractive interactions and chain stiffness on the reversible binding of nonideal polymer chains to a solid surface, including the enthalpy-entropy compensation phenomenon observed experimentally in many molecular and particle binding processes.

The confinement of a polymer to volumes whose characteristic linear dimensions are comparable to or smaller than its bulk radius of gyration RG,bulk can produce significant changes in its static and dynamic properties, with important implications for the understanding of single-molecule processes in biology and chemistry. In this paper, we present calculations of the effects of a narrow rectangular slit of thickness d on the scaling behavior of the diffusivity D and relaxation time τr of a Gaussian chain of polymerization index N and persistence length l0. The calculations are based on the Rouse-Zimm model of chain dynamics, with the pre-averaged hydrodynamic interaction being obtained from the solutions to Stokes equations for an incompressible fluid in a parallel plate geometry in the limit of small d. They go beyond de Gennes' purely phenomenological analysis of the problem based on blobs, which has so far been the only analytical route to the determination of chain scaling behavior for this particular geometry. The present model predicts that D ∼ dN-1ln (N/d2) and τr ∼ N2d-1[ln (N/d2)]-1 in the regime of moderate confinement, where l0 < d < RG,bulk. The corresponding results for the blob model have exactly the same power law behavior, but contain no logarithmic corrections; the difference suggests that segments within a blob may actually be partially draining and not non-draining as generally assumed. [ABSTRACT FROM AUTHOR]

Nonlinear dynamics of a simple bead-spring glass-forming polymer were studied with molecular dynamics simulations. The energy response to sinusoidal variations in the temperature was tracked in order to evaluate the dynamic heat capacity. The amplitude dependence of the response is the focus of the current paper where pronounced nonlinear behavior is observed for large amplitudes in the temperature 'driving force.' We generalize the usual linear response analysis to the nonlinear regime so that higher order terms in the Fourier series of the energy response can be compactly analyzed. This is done by grouping all Fourier terms contributing to entropy generation into a 'loss' contribution and the remainder yields the 'storage' term. Finally, the bead-spring system is mapped onto three simpler models. First is a potential energy inspired 'trap' model consisting of interconnected potential energy meta-basins and barriers. Second is the Tool-Narayanaswamy-Moynihan (TNM) model. Third is a version of the TNM model with a temperature dependent heat capacity. Qualitatively similar nonlinear behaviors are observed in all cases. [ABSTRACT FROM AUTHOR]

The growing importance of microfluidic and nanofluidic devices to the study of biological processes has highlighted the need to better understand how confinement affects the behavior of polymers in flow. In this paper we explore one aspect of this question by calculating the steady-state extension of a long polymer chain in a narrow capillary tube in the presence of simple shear. The calculation is carried out within the framework of the Rouse-Zimm approach to chain dynamics, using a variant of a nonlinear elastic model to enforce finite extensibility of the chain, and assuming that the only effect of the confining surface is to modify the pre-averaged hydrodynamic interaction. The results, along with results from the corresponding calculations of finitely extensible versions of both the Rouse and Rouse-Zimm models, are compared with data from experiments on the flow-induced stretching of λ-phage DNA near a non-adsorbing glass surface [L. Fang, H. Hu, and R. G. Larson, J. Rheol. 49, 127 (2005)]. The comparison suggests that close to a surface hydrodynamic screening is significant, and causes the chains to become effectively free-draining. [ABSTRACT FROM AUTHOR]

This paper presents the exact formula for the bivariate probability distribution function of a Brownian particle as a function of its position and velocity, whose orbit makes a specified number of turns around an infinite straight line. In the limit of large friction constant, the solution reduces to the well-known results for random Wiener paths. Topological entanglements of stiff polymers are discussed on the basis of this solution. The method to find the solution is applied to the velocity space of a Brownian motion, and the probability to find a closed path with a specified winding number is obtained. Hence, closed two-dimensional Brownian orbits are classified into regular homotopy classes, whose statistical weight is derived as a function of the total length and the friction constant. [ABSTRACT FROM AUTHOR]

In this paper, the cooperative effect of halogen bond with hydrogen bond has been used to make a halogen bond in FCl-CNH dimer vary from a chlorine-shared one to an ion-pair one. The halogen bond is strengthened in FCl-CNH-CNH trimer and its maximal interaction energy equals to -76 kJ/mol when the number of CNH in FCl-CNH-(CNH)n polymer approaches infinity. Once the free H atom in FCl-CNH-CNH trimer is replaced with alkali metals, the halogen bond becomes strong enough to be an ion-pair one in FCl-CNH-CNLi and FCl-CNH-CNNa trimers. An introduction of a Lewis acid in FCl-CNH dimer has a more prominent effect on the type of halogen bond. A prominent cooperative effect is found for the halogen bond and hydrogen bond in the trimers. FH-FCl-CNH-CNH and FH-FCl-CNH-CNLi tetramers have also been studied and the interaction energy of halogen bonding in FH-FCl-CNH-CNLi tetramer is about 12 times as much as that in the FCl-CNH dimer. The atoms in molecules and natural bond orbital analyses have been carried out for these complexes to understand the nature of halogen bond and the origin of the cooperativity. [ABSTRACT FROM AUTHOR]

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time tc of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when d is much smaller than the size of the chain, tc ∼ Nd2, and that in case (b), tc ∼ N2/(2 - 2H), H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), tc ∼ N3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium. [ABSTRACT FROM AUTHOR]

Two different experimental studies of polymer dynamics based on single-molecule fluorescence imaging have recently found evidence of heterogeneities in the widths of the putative tubes that surround filaments of F-actin during their motion in concentrated solution. In one [J. Glaser, D. Chakraborty, K. Kroy, I. Lauter, M. Degawa, N. Kirchesner, B. Hoffmann, R. Merkel, and M. Giesen, Phys. Rev. Lett. 105, 037801 (2010)], the observations were explained in terms of the statistics of a worm-like chain confined to a potential determined self-consistently by a binary collision approximation, and in the other [B. Wang, J. Guan, S. M. Anthony, S. C. Bae, K. S. Schweizer, and S. Granick, Phys. Rev. Lett. 104, 118301 (2010)], they were explained in terms of the scaling properties of a random fluid of thin rods. In this paper, we show, using an exact path integral calculation, that the distribution of the length-averaged transverse fluctuations of a harmonically confined weakly bendable rod (one possible realization of a semiflexible chain in a tube), is in good qualitative agreement with the experimental data, although it is qualitatively different in analytic structure from the earlier theoretical predictions. We also show that similar path integral techniques can be used to obtain an exact expression for the time correlation function of fluctuations in the tube cross section. [ABSTRACT FROM AUTHOR]

Recently, we developed a formalism for the scattering from linear and acyclic branched structures build of mutually non-interacting sub-units. [C. Svaneborg and J. S. Pedersen, J. Chem. Phys. 136, 104105 (2012)] We assumed each sub-unit has reference points associated with it. These are well-defined positions where sub-units can be linked together. In the present paper, we generalize the formalism to the case where each reference point can represent a distribution of potential link positions. We also present a generalized diagrammatic representation of the formalism. Scattering expressions required to model rods, polymers, loops, flat circular disks, rigid spheres, and cylinders are derived, and we use them to illustrate the formalism by deriving the generic scattering expression for micelles and bottle-brush structures and show how the scattering is affected by different choices of potential link positions and sub-unit choices. [ABSTRACT FROM AUTHOR]

Exciton dissociation and charge recombination processes in organic semiconductors, with thermal effects taken into account, are described in this paper. Here, we analyzed the mechanisms of polaron-excitons dissociation into free charge carriers and the consequent recombination of those carriers under thermal effects on two parallel π-conjugated polymers chains electronically coupled. Our results suggest that exciton dissociation in a single molecule give rise to localized, polaron-like charge carrier. Besides, we concluded that in the case of interchain processes, the bimolecular polaron recombination does not lead to an usual exciton state. Rather, this type of recombination leads to an oscillating dipole between the two chains. The recombination time obtained here for these processes are in agreement with the experimental results. Finally, our results show that temperature effects are essential to the relaxation process leading to polaron formation in a single chain, as in the absence of temperature, this process was not observed. In the case of two chains, we conclude that temperature effects also help the bimolecular recombination process, as observed experimentally. [ABSTRACT FROM AUTHOR]

Cargo transport through the nuclear pore complex continues to be a subject of considerable interest to experimentalists and theorists alike. Several recent studies have revealed details of the process that have still to be fully understood, among them the apparent nonlinearity between cargo size and the pore crossing time, the skewed, asymmetric nature of the distribution of such crossing times, and the non-exponentiality in the decay profile of the dynamic autocorrelation function of cargo positions. In this paper, we show that a model of pore transport based on subdiffusive particle motion is in qualitative agreement with many of these observations. The model corresponds to a process of stochastic binding and release of the particle as it moves through the channel. It suggests that the phenylalanine-glycine repeat units that form an entangled polymer mesh across the channel may be involved in translocation, since these units have the potential to intermittently bind to hydrophobic receptor sites on the transporter protein. [ABSTRACT FROM AUTHOR]

In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7Tc), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water. [ABSTRACT FROM AUTHOR]

In efforts to produce polymeric materials with tailored physical properties, significant interest has grown around the ability to control the spatial organization of nanoparticles in polymer nanocomposites. One way to achieve controlled particle arrangement is by grafting the nanoparticle surface with polymers that are compatible with the matrix, thus manipulating the interfacial interactions between the nanoparticles and the polymer matrix. Previous work has shown that the molecular weight of the grafted polymer, both at high grafting density and low grafting density, plays a key role in dictating the effective inter-particle interactions in a polymer matrix. At high grafting density nanoparticles disperse (aggregate) if the graft molecular weight is higher (lower) than the matrix molecular weight. At low grafting density the longer grafts can better shield the nanoparticle surface from direct particle-particle contacts than the shorter grafts and lead to the dispersion of the grafted particles in the matrix. Despite the importance of graft molecular weight, and evidence of non-trivial effects of polydispersity of chains grafted on flat surfaces, most theoretical work on polymer grafted nanoparticles has only focused on monodisperse grafted chains. In this paper, we focus on how bidispersity in grafted chain lengths affects the grafted chain conformations and inter-particle interactions in an implicit solvent and in a dense homopolymer polymer matrix. We first present the effects of bidispersity on grafted chain conformations in a single polymer grafted particle using purely Monte Carlo (MC) simulations. This is followed by calculations of the potential of mean force (PMF) between two grafted particles in a polymer matrix using a self-consistent Polymer Reference Interaction Site Model theory-Monte Carlo simulation approach. Monte Carlo simulations of a single polymer grafted particle in an implicit solvent show that in the bidisperse polymer grafted particles with an equal number of short and long grafts at low to medium grafting density, the short grafts are in a more coiled up conformation (lower radius of gyration) than their monodisperse counterparts to provide a larger free volume to the longer grafts so they can gain conformational entropy. The longer grafts do not show much difference in conformation from their monodisperse counterparts at low grafting density, but at medium grafting density the longer grafts exhibit less stretched conformations (lower radius of gyration) as compared to their monodisperse counterparts. In the presence of an explicit homopolymer matrix, the longer grafts are more compressed by the matrix homopolymer chains than the short grafts. We observe that the potential of mean force between bidisperse grafted particles has features of the PMF of monodisperse grafted particles with short grafts and monodisperse grafted particles with long grafts. The value of the PMF at contact is governed by the short grafts and values at large inter-particle distances are governed by the longer grafts. Further comparison of the PMF for bidisperse and monodisperse polymer grafted particles in a homopolymer matrix at varying parameters shows that the effects of matrix chain length, matrix packing fraction, grafting density, and particle curvature on the PMF between bidisperse polymer grafted particles are similar to those seen between monodisperse polymer grafted particles. [ABSTRACT FROM AUTHOR]

In this paper, Brownian dynamics simulation (BDS) studies are executed to demonstrate the distinctive influences of the extent of confinement on the collapsing mechanism and kinetics of a flexible hydrophobic polymer chain in a poor solvent. The collapsing behavior is quantified by the time of collapse, which below a critical dimension of the confinement (hc), encounters a drastic reduction with a further strengthening in the degree of confinement. For dimensions greater than this critical one, the collapse occurs through the well-known hydrodynamic interaction (HI) controlled multiple-globule-mediated mechanisms. However, for channel dimensions less than this critical one, the collapse mechanism is drastically altered. Under such circumstances, the collapse gets predominantly controlled by the confinement effects (with negligible contribution of the HIs) and occurs via the formation of a single central globule. This central globule rapidly engulfs the noncondensed polymer segments, and in the process largely hastens up the collapsing event. Under such circumstances, the collapse time is found to decrease linearly with decrements in the channel height. On the contrary, for channel heights greater than hc, the multiple-globule-mediated collapse is characterized by a collapse time that shows an exponential dependence on the channel height, rapidly attaining a state in which the confinement effect becomes inconsequential and HIs dictate the entire collapsing behavior. We further propose detailed arguments based on physical reasoning as well as free energy estimations to conclusively support the qualitative and quantitative nature of influences of the confinement on the polymer collapse. [ABSTRACT FROM AUTHOR]

Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling procedure is presented for the efficient calculation of the static structural properties of binary homopolymer blends. The procedure combines computer simulations of polymer chains on two different length scales, using a united atom representation for the finer structure and a highly coarse-grained approach on the mesoscale, where chains are represented as soft colloidal particles interacting through an effective potential. A method for combining the structural information by inverse mapping is discussed, allowing for the efficient calculation of partial correlation functions, which are compared with results from full united atom simulations. The structure of several polymer mixtures is obtained in an efficient manner for several mixtures in the homogeneous region of the phase diagram. The method is then extended to incorporate thermal fluctuations through an effective χ parameter. Since the approach is analytical, it is fully transferable to numerous systems. [ABSTRACT FROM AUTHOR]

In this paper, we examine the second-harmonic generation (SHG) from spin-cast films of the conjugated polymer poly(2-methoxy-5-(2′-ethylhexyloxy)para-phenylenevinylene) (MEH-PPV). We find that the SHG intensity depends strongly on the speed used to spin cast the films. Two-dimensional grazing incidence x-ray diffraction (XRD) experiments show that the bulk crystallinity of the MEH-PPV films varies in the same way with spin speed as the SHG intensity. This strongly suggests that instead of being interface specific, the second-harmonic signal from conjugated polymer films is dominated by the crystalline domains in the bulk. The nonmonotonic dependence of both the SHG intensity and the degree of MEH-PPV crystallinity results from a competition between the shear forces and the solvent evaporation rate during spin coating, which produces a maximum degree of crystallinity for MEH-PPV films spin cast at around 1400 rpm. We also use XRD to show that thermal annealing produces MEH-PPV films with a single degree of bulk crystallinity, independent of how they were originally cast. This allows us to model the angle- and thickness-dependent SHG from annealed MEH-PPV films with a single polarizability tensor. We find that the SHG from MEH-PPV films fits best to a bulk-allowed electric quadrupole mechanism, consistent with the bulk SHG seen in other π-stacked aromatic molecules. Thus, rather than providing information about conjugated polymer interfaces, SHG can be used as a sensitive probe of the local degree of crystallinity in the bulk of conjugated polymer films. [ABSTRACT FROM AUTHOR]

The structural and dynamical properties of macromolecules in confining or crowded environments are different from those in simple bulk liquids. In this paper, both the conformational and diffusional dynamics of globular polymers are studied in solutions containing fixed spherical obstacles. These properties are studied as a function of obstacle volume fraction and size, as well as polymer chain length. The results are obtained using a hybrid scheme that combines multiparticle collision dynamics of the solvent with molecular dynamics that includes the interactions among the polymer monomers and between the polymer beads and obstacles and solvent molecules. The dynamics accounts for hydrodynamic interactions among the polymer beads and intermolecular forces with the solvent molecules. We consider polymers in poor solvents where the polymer chain adopts a compact globular structure in solution. Our results show that the collapse of the polymer chain to a compact globular state is strongly influenced by the obstacle array. A nonmonotonic variation in the radius of gyration with time is observed and the collapse time scale is much longer than that in simple solutions without obstacles. Hydrodynamic interactions are important at low obstacle volume fractions but are screened at high volume fractions. The diffusion of the globular polymer chain among the obstacles is subdiffusive in character on intermediate time scales where the dynamics explores the local structure of the heterogeneous environment. For large polymer chains in systems with high obstacle volume fractions, the chain adopts bloblike conformations that arise from trapping of portions of the chain in voids among the obstacles. [ABSTRACT FROM AUTHOR]

Calculating phase diagrams and measuring the properties of multiple phases in equilibrium is one of the most common applications of field-theoretic simulations. Such a simulation often attempts to simulate two phases in equilibrium with each other in the same simulation box. This is a computationally demanding approach because it is necessary to perform a large enough simulation so that the interface between the two phases does not affect the estimate of the bulk properties of the phases of interest. In this paper, we describe an efficient method for performing field-theoretic simulations in the Gibbs ensemble, a familiar construct in particle-based simulations where two phases in equilibrium with each other are simulated in separate simulation boxes. Chemical and mechanical equilibrium is maintained by allowing the simulation boxes to swap both chemical species and volume. By fixing the total number of each chemical species and the total volume, the Gibbs ensemble allows for the efficient simulation of two bulk phases at equilibrium in the canonical ensemble. After providing the theoretical framework for field-theoretic simulations in the Gibbs ensemble, we demonstrate the method on two two-dimensional model polymer test systems in both the mean-field limit (self-consistent field theory) and in the fluctuating field theory. [ABSTRACT FROM AUTHOR]

The classical bond-fluctuation model (BFM) is an efficient lattice Monte Carlo algorithm for coarse-grained polymer chains where each monomer occupies exclusively a certain number of lattice sites. In this paper we propose a generalization of the BFM where we relax this constraint and allow the overlap of monomers subject to a finite energy penalty [variant_greek_epsilon]. This is done to vary systematically the dimensionless compressibility g of the solution in order to investigate the influence of density fluctuations in dense polymer melts on various static properties at constant overall monomer density. The compressibility is obtained directly from the low-wave vector limit of the static structure factor. We consider, e.g., the intrachain bond-bond correlation function P(s) of two bonds separated by s monomers along the chain. It is shown that the excluded volume interactions are never fully screened for very long chains. If distances smaller than the thermal blob size are probed (s≤g) the chains are swollen according to the classical Fixman expansion where, e.g., P(s)∼g-1s-1/2. More importantly, the polymers behave on larger distances (s>g) like swollen chains of incompressible blobs with P(s)∼g0s-3/2. [ABSTRACT FROM AUTHOR]

The structural and dynamical properties of polymer nanocomposites are investigated using stochastic molecular dynamics simulations. For spherical nanoparticles dispersed in a polymer matrix, the results indicate that the polymer-nanoparticle interaction strength and the overall system temperature are primarily responsible for the type of dispersed state (clustering and homogeneous dispersion) achieved. A systematic study probing temperature, polymerization, and polymer-nanoparticle and nanoparticle-nanoparticle interaction strengths has been performed. In this paper, however, we focus the discussion on the results for varying polymer-nanoparticle interaction strengths at different temperatures. By examining the structure and dynamics, we show that there are two kinds of “clustering transitions:” one due to thermodynamic and another due to the dynamical response of the system. From these results, a representative phase diagram is developed that captures the entire simulated space and allows the easy identification of the highly dispersed and the clustered states. [ABSTRACT FROM AUTHOR]

We report in this paper experimental data on steady state and transient photoluminescence of poly-p-phenylene vinylene in the form of nanofibers prepared with a template method and converted at 110 °C. Results are compared to those obtained from films of different thicknesses converted at the same temperature. Data are analyzed by a model of bimodal distribution of conjugation lengths and the photoluminescence band shapes, evaluated in the framework of this model, are also presented. [ABSTRACT FROM AUTHOR]

In this paper, we construct an effective model for the dynamics of an excluded-volume chain under confinement by extending the formalism of Rouse modes. We make specific predictions about the behavior of the modes for a single polymer confined to a tube. The results are tested against Monte Carlo simulations using the bond-fluctuation algorithm which uses a lattice representation of the polymer chain with excluded-volume effects. [ABSTRACT FROM AUTHOR]

Molecular mechanisms of crystal growth and homogeneous nucleation from the melt of polyethylene-like linear polymer are investigated by molecular dynamics simulations. The present paper is aimed at extending our previous work with respect to the system size and the boundary condition, thereby enabling detailed studies on the structures of sufficiently large lamellae and fully equilibrated melt. Lamellae of uniform thickness but with marked tapered edges are found to grow at constant velocity from the substrate. Three-dimensional shape of the growing lamellae exhibits peculiar undulation at the growth front, the origin of which is suggested to be the inhomogeneous thickness distribution within the lamellae. Trajectories of chains crystallizing onto the growth front reveal an unexpected pathway for chain folding, where a partially attached chain stem forms a new fold by plunging its head back into a neighboring stem position through slithering snake motions of the chain. Detailed statistics of folds and cilia show that the folds are rather neat and mostly make re-entries into the nearest or the second or third nearest neighboring stem positions, whereas the cilia are generally short but with a small number of longer cilia forming thick amorphous layers. Structure of supercooled melt investigated versus temperature reveals that, at moderate degree of supercooling, the overall chain conformation remains Gaussian random coil but the persistent length of chains increases monotonically with increasing supercooling. Exceptions are at the largest supercooling where homogeneous nucleation takes place; usual melt structure becomes rapidly unstable and emerges many crystallites of random orientations. During early 10–20 ns after the quench, density of melt, radius of gyration of chains, and fraction of kinked bonds show marked alterations. These structural changes are highly cooperative and are considered simply due to the emergence of many embryonic crystals in the melt. Conformations of the chains forming nuclei are also traced to reveal that the homogeneous nuclei are fringed micelle like aggregates of chains, but the chains as a whole have folded conformations, which are similar to those reported in previous simulations on a single polyethylene in a vacuum. [ABSTRACT FROM AUTHOR]

In this paper we present theoretical analysis of the electron transport in conducting polymers being in a metal-like state. We concentrate on the study of the effects of temperature on characteristics of the transport. We treat a conducting polymer in the metal state as a network of metalliclike grains embedded in poorly conducting environment, which consists of randomly distributed polymeric chains. We carry out the present studies assuming that the intergrain conduction is mostly provided by electron quantum tunneling via intermediate states localized on polymer chains between the grains. To analyze the effects of temperature on this kind of electron intergrain transport we represent the thermal environment as a phonon bath coupled to the intermediate state. The electron transmission is computed using the Buttiker model within the scattering matrix formalism. This approach is further developed, and the dephasing parameter is expressed in terms of relevant energies including the thermal energy. It is shown that temperature dependencies of both current and conductance associated with the above transport mechanism differ from those typical for other conduction mechanisms in conducting polymers. This could be useful to separate out the contribution from the intergrain electron tunneling to the net electric current in transport experiments on various polymer nanofibers. The proposed model could be used to analyze inelastic electron transport through molecular junctions. [ABSTRACT FROM AUTHOR]

Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers. [ABSTRACT FROM AUTHOR]

Monte Carlo simulations of a model fluid in which the particles interact via a continuous potential that has a logarithmic divergence at a pair separation of σ, which we introduced in J. G. Powles et al., Proc. R. Soc. London, Ser. A 455, 3725 (1999), have been carried out. The potential has the form, [lowercase_phi_synonym](r)=-ε ln(f(r)), where ε sets the energy scale and f(r)=1-(σ/r)m. The value of m chosen was 12 but the qualitative trends depend only weakly on the value of m, providing it is greater than 3. The potential is entirely repulsive and has a logarithmic divergence as ∼-ln(r/σ-1) in the r→σ limit. Predictions of the previous paper that the internal energy can be computed at all temperatures using the standard statistical mechanics formula for continuous potentials are verified here. The pressure can be calculated using the usual virial expression for continuous potentials, although there are practical limitations in resolving the increasingly important contribution from the r→σ limit at reduced temperatures greater than ∼5. The mean square force ≤F2≥ and infinite frequency shear G∞ and bulk K∞ moduli are only finite for T*=kBT/ε<1. The logarithmic fluid’s physical properties become increasingly more like that of the hard sphere fluid with increasing temperature, showing a sharp transition in the behavior of the mean square force and infinite frequency elastic constants at T*=1. The logarithmic fluid is shown to exhibit a solid-fluid phase transition. [ABSTRACT FROM AUTHOR]

In this paper, we combine variable cell shape method with dynamic self-consistent field theory and extend to study structure and dynamics under shear for triblock copolymer melts. Due to shear, the calculation cell shape is variable and no longer orthogonal. Pseudospectral method is employed to solve the diffusion equation for chain propagator on the nonorthogonal coordinate and the shear periodical condition can be easily designed in terms of the variable cell shape method. By using this strategy, the shear induced morphology evolution is investigated for topologically complex polymeric systems such as linear and star triblock copolymers; the morphology of linear ABC triblock copolymers is more shear sensitive than that of star triblocks. In particular, once the chain propagator is obtained, the microscopic elastic stress and spatial stress distribution can be derived and thus the dynamic mechanical property can be calculated under shear. By imitating the dynamic storage modulus G′ corresponding to any given morphology in the oscillatory shear measurements, we explore the relationship between the morphology and the storage modulus G′ and extend to study the mechanism of phase separation dynamics as well as order-disorder transition (ODT) for linear and star triblock copolymers. The results show that the chain architecture can be easily distinguished by investigating the ODT, though the systems such as AB symmetric diblock and ABA triblock copolymers by coupling AB precursors almost exhibit similar microstructures. In addition, the storage modulus G′ and loss modulus G″ can be simultaneously determined in frequency sweeps of oscillatory shear measurements and the dependence of the moduli on phase separated patterns and the chain topology is investigated. The simulation findings are in qualitatively agreement with the experimental results. [ABSTRACT FROM AUTHOR]

Proteins contain many voids, which are unfilled spaces enclosed in the interior. A few of them have shapes compatible to ligands and substrates and are important for protein functions. An important general question is how the need for maintaining functional voids is influenced by, and affects other aspects of proteins structures and properties (e.g., protein folding stability, kinetic accessibility, and evolution selection pressure). In this paper, we examine in detail the effects of maintaining voids of different shapes and sizes using two-dimensional lattice models. We study the propensity for conformations to form a void of specific shape, which is related to the entropic cost of void maintenance. We also study the location that voids of a specific shape and size tend to form, and the influence of compactness on the formation of such voids. As enumeration is infeasible for long chain polymer, a key development in this work is the design of a novel sequential Monte Carlo strategy for generating large number of sample conformations under very constraining restrictions. Our method is validated by comparing results obtained from sampling and from enumeration for short polymer chains. We succeeded in accurate estimation of entropic cost of void maintenance, with and without an increasing number of restrictive conditions, such as loops forming the wall of void with fixed length, with additionally fixed starting position in the sequence. Additionally, we have identified the key structural properties of voids that are important in determining the entropic cost of void formation. We have further developed a parametric model to predict quantitatively void entropy. Our model is highly effective, and these results indicate that voids representing functional sites can be used as an improved model for studying the evolution of protein functions and how protein function relates to protein stability. [ABSTRACT FROM AUTHOR]

Amphiphilic block copolymers of the type poly(ethylenepropylene)-co-poly(ethyleneoxide) dramatically enhance the solubilisation efficiency of non-ionic surfactants in microemulsions that contain equal volumes of water in oil. Consequently, the length scale of the microstructure of such bicontinuous microemulsions is dramatically increased up to the order of a few 100 nm. In this paper, we show that this so-called efficiency boosting effect can also be applied to water-in-oil microemulsions with droplet microstructure. Such giant water-in-oil microemulsions would provide confined compartments in which chemical reactions of biological macromolecules can be performed on a single molecule level. With this motivation we investigated the phase behavior and the microstructure of oil-rich microemulsions containing D2O, n-decane(d22), C10E4 and the amphiphilic block copolymer PEP5-PEO5 [poly(ethylenepropylene)-co-poly(ethyleneoxide), weight per block of 5000 g/mol]. We found that 15 wt % of water can be solubilised by 5 wt % of surfactant and block copolymer when about 6 wt % of surfactant is replaced by the block copolymer. Small-angle-neutron-scattering experiments were performed to determine the length scales and microstructure topologies of the oil-rich microemulsions. To analyze the scattering data, we derived a novel form factor that also takes into account the scattering contribution of the hydrophobic part of the block copolymer molecules that reside in the surfactant shell. The quantitative analysis of the scattering data with this form factor shows that the radius of the largest droplets amounts up to 30 nm. The novel form factor also yielded qualitative information on the stretching of the polymer chains in dependence on the polymer surface density and the droplet radius. [ABSTRACT FROM AUTHOR]

A dynamic Monte Carlo simulation of the collapse transition of polymer chains is presented. The chains are represented as self-avoiding walks on the simple cubic lattice with a nearest-neighbor contact potential to model the effect of solvent quality. The knot state of the chains is determined using the knot group procedure presented in the accompanying paper. The equilibrium knot spectrum and the equilibrium rms radius of gyration as functions of the chain length and the contact potential are reported. The collapse transition was studied following quenches from good-to poor-solvent conditions. Our results confirm the prediction that the newly formed globule is not yet at equilibrium, since it has not yet achieved its equilibrium knot spectrum. For our model system, the relaxation of the knot spectrum is about an order of magnitude slower than that of the radius of gyration. The collapse transition is also studied for a model in which both ends of the chain remain in good-solvent conditions. Over the time scale of these simulations, knot formation is frustrated in this inhomogeneous model, verifying that the mechanism of knotting is the tunneling of chain ends in and out of the globule. [ABSTRACT FROM AUTHOR]

Polymers are naturally polydisperse. Polydispersity may have a large effect on the phase behavior of polymer solutions, in particular, on the liquid-liquid phase equilibria. In this paper, we determine the cloud and shadow curves bounded by lower critical solution temperatures for a number of polymer+solvent systems where the polymer is polydisperse in terms of molecular weight (chain length). The moment method [P. Sollich, P. B. Warren, and M. E. Cates, Adv. Chem. Phys. 116, 265 (2001)] is applied with the SAFT approach to determine cloud and shadow curves with continuous Schulz-Flory distributions. It is seen that chain length polydispersity always enhances the extent of liquid-liquid phase equilibria. The predicted cloud curves obtained for continuous distributions are very similar to those obtained for simple ternary mixtures with the same polydispersity index, while the corresponding shadow curves can be very different depending on the composition of the parent distribution. The ternary phase behavior can be used to provide an understanding of the shape of the cloud and shadow curves. Regions of phase equilibria between three liquid phases are found for ternary systems when the chain length distribution is very asymmetrical; such regions are not observed for Schulz-Flory distributions even in the case of a large degree of polydispersity. [ABSTRACT FROM AUTHOR]

We present in this work a new model to describe the component segmental dynamics in miscible polymers blends as a function of pressure, temperature, and composition. The model is based on a combination of the Adam-Gibbs (AG) theory and the concept of the chain connectivity. In this paper we have extended our previous approach [D. Cangialosi et al. J. Chem. Phys. 123, 144908 (2005)] to include the effects of pressure in the component dynamics of miscible polymer blends. The resulting model has been tested on poly(vinyl methyl ether) (PVME)/polystyrene (PS) blends at different concentrations and in the temperature range where the system is in equilibrium. The results show an excellent agreement between the experimental and calculated relaxation times using only one fitting parameter. Once this parameter is known the model allows calculating the size of the relevant length scale where the segmental relaxation of the dielectrically active component takes place, i.e., the so called cooperative rearrangement region (CRR) in the AG framework. Thus the size of the CRR for PVME in the blends with PS has been determined as well as its dependence with pressure, temperature, and concentration. [ABSTRACT FROM AUTHOR]

Many of the (ideal) infinite conjugated hydrocarbon polymers do not present a gap at the Fermi level in tight-binding calculations. However, due to the bielectronic interaction the excitation energy from the ground state to the lowest triplet state may be nonzero for some lattices (called spin gapped), while other lattices will keep a singlet-triplet degeneracy (spin-gapless lattices). This difference results in qualitative differences in their magnetic properties. Making use of the relevance of Heisenberg Hamiltonians for the study of the lowest states of conjugated hydrocarbons, this paper presents some qualitative arguments to predict the spin-gap character of various classes of such polymers. The arguments are based on real space renormalization group procedures, which considers fragments of the polymers as effective spins. Numerical evaluations, based on a renormalized excitonic method, confirm the qualitative predictions. [ABSTRACT FROM AUTHOR]

We present a computer simulation model of polymer melts representing each chain as one single particle. Besides the position coordinate of each particle, we introduce a parameter nij for each pair of particles i and j within a specified distance from each other. These numbers, called entanglement numbers, describe the deviation of the system of ignored coordinates from its equilibrium state for the given configuration of the centers of mass of the polymers. The deviations of the entanglement numbers from their equilibrium values give rise to transient forces, which, together with the conservative forces derived from the potential of mean force, govern the displacements of the particles. We have applied our model to a melt of C800H1602 chains at 450 K and have found good agreement with experiments and more detailed simulations. Properties addressed in this paper are radial distribution functions, dynamic structure factors, and linear as well as nonlinear rheological properties. [ABSTRACT FROM AUTHOR]

It is the purpose of this paper to establish a bottom-up multiscale approach for dendronized polymers. Based on our understanding of the phenomenology of an atomistic model for this class of polymers, we introduce a “Janus chain” (JC) model which adds a vectorial degree of freedom (Janus vector)—related to the sectorial amphiphilicity—to each segment of the linear backbone of a (classical) uncharged, semiflexible, and multibead chain representation of a polymer. The JC features induced polymeric curvature and ultimately triggers complexation. JC parameters related to the topology and chemical details are obtained from the atomistic level. Available experimental observations including the formation of superstructures and double helical conformations are well reproduced by the JC model. JC is efficiently solved via Brownian dynamics simulation and can be seen as a member of a universality class which is one (two) level(s) above the magnetic (semiflexible) chain model. It therefore should allow to model not only dendronized polymers but also structures belonging to the same class—exhibiting induced (or spontaneous) curvature—such as single stranded DNA and actin filaments. [ABSTRACT FROM AUTHOR]

A hierarchical electron-phonon coupling model is applied to describe the ultrafast decay of a photogenerated exciton at a donor-acceptor polymer heterojunction, via a vibronic coupling mechanism by which a charge-localized interfacial state is created. Expanding upon an earlier Communication [H. Tamura et al., J. Chem. Phys. 126, 021103 (2007)], we present a quantum dynamical analysis based on a two-state linear vibronic coupling model, which accounts for a two-band phonon bath including high-frequency C==C stretch modes and low-frequency ring torsional modes. Building upon this model, an analysis in terms of a hierarchical chain of effective modes is carried out, whose construction is detailed in the present paper. Truncation of this chain at the order n (i.e., 3n+3 modes) conserves the Hamiltonian moments (cumulants) up to the (2n+3)rd order. The effective-mode analysis highlights (i) the dominance of the high-frequency modes in the coupling to the electronic subsystem and (ii) the key role of the low-frequency modes in the intramolecular vibrational redistribution process that is essential in mediating the decay to the charge-localized state. Due to this dynamical interplay, the effective-mode hierarchy has to be carried beyond the first order in order to obtain a qualitatively correct picture of the nonadiabatic process. A reduced model of the dynamics, including a Markovian closure of the hierarchy, is presented. Dynamical calculations were carried out using the multiconfiguration time-dependent Hartree method. [ABSTRACT FROM AUTHOR]

According to linear response theory, all relaxation functions in the linear regime can be obtained using time correlation functions calculated under equilibrium. In this paper, we demonstrate that the cross correlations make a significant contribution to the partial stress relaxation functions in polymer melts. We present two illustrations in the context of polymer rheology using (1) Brownian dynamics simulations of a single chain model for entangled polymers, the slip-spring model, and (2) molecular dynamics simulations of a multichain model. Using the single chain model, we analyze the contribution of the confining potential to the stress relaxation and the plateau modulus. Although the idea is illustrated with a particular model, it applies to any single chain model that uses a potential to confine the motion of the chains. This leads us to question some of the assumptions behind the tube theory, especially the meaning of the entanglement molecular weight obtained from the plateau modulus. To shed some light on this issue, we study the contribution of the nonbonded excluded-volume interactions to the stress relaxation using the multichain model. The proportionality of the bonded/nonbonded contributions to the total stress relaxation (after a density dependent “colloidal” relaxation time) provides some insight into the success of the tube theory in spite of using questionable assumptions. The proportionality indicates that the shape of the relaxation spectrum can indeed be reproduced using the tube theory and the problem is reduced to that of finding the correct prefactor. [ABSTRACT FROM AUTHOR]

This paper reports the first computational estimation of the comb polymers’ third virial coefficients. The number of the chains in the comb polymers range from 5 to 11. An algorithm that counts the contributing terms of the third virial coefficients in an accelerated manner is presented along with its efficiency dependence on the polymers’ size. In addition, the second virial coefficients are estimated for the comb polymers and compared to previously reported results. [ABSTRACT FROM AUTHOR]

In this paper, the authors have systematically studied the microphase separation and crystallization during spin coating of an ABC triblock copolymer, polystyrene-b-poly(2-vinylpyridine)-b-poly(ethylene oxide) (PS-b-P2VP-b-PEO). The microphase separation of PS-b-P2VP-b-PEO and the crystallization of PEO blocks can be modulated by the types of the solvent and the substrate, the spinning speed, and the copolymer concentration. Ordered microphase-separated pattern, where PEO and P2VP blocks adsorbed to the substrate and PS blocks protrusions formed hexagonal dots above the P2VP domains, can only be obtained when PS-b-P2VP-b-PEO is dissolved in N,N-dimethylformamide and the films are spin coated onto the polar substrate, silicon wafers or mica. The mechanism of the formation of regular pattern by microphase separation is found to be mainly related to the inducement of the substrate (middle block P2VP wetting the polar substrate), the quick vanishment of the solvent during the early stage of the spin coating, and the slow evaporation of the remaining solvent during the subsequent stage. On the other hand, the probability of the crystallization of PEO blocks during spin coating decreases with the reduced film thickness. When the film thickness reaches a certain value (3.0 nm), the extensive crystallization of PEO is effectively prohibited and ordered microphase-separated pattern over large areas can be routinely prepared. When the film thickness exceeds another definite value (12.0 nm), the crystallization of PEO dominates the surface morphology. For films with thickness between these two values, microphase separation and crystallization can simultaneously occur. [ABSTRACT FROM AUTHOR]

This paper reports results of quantitative comparison between dynamic structure factors obtained experimentally and those calculated by using the Doi and Onuki (DO) theory for semidilute polymer solutions. The authors obtained the dynamic structure factors with dynamic light scattering (DLS) experiment while the dynamic structure factors were calculated by using DO theory with osmotic compressibility, viscoelastic relaxation function, and friction coefficient which are obtained independently of DLS experiment. Calculated dynamic structure factors agree with experimental ones well and can express the q-dependent fast modes and the q-insensitive slow mode which experimental ones show. The authors estimated the characteristic parameters, interdiffusion coefficient and cooperative diffusion coefficient, from experimental and calculated results by using the procedure proposed by Einaga and Fujita [Polymer 40, 565 (1999)]. The estimated parameters for the DLS experiment agree with those for the calculation. These agreements in dynamic structure factors and the parameters indicate that DO theory can describe well the relaxation processes of semidilute polymer solutions. [ABSTRACT FROM AUTHOR]

In the present paper the authors present a theoretical model to explain the kinetics involving the induction period observed by Irie et al. [Nature (London) 420, 759 (2002)] for photoisomerization of diarylethene derivatives dispersed on polymer films at a single molecular level. In the model we assume that both ground state and excited state free energy landscapes which result from the interaction between the photochromic molecule and the surrounding polymer are rugged and have several local minima along the pathway to the critical point at which isomerization actually occurs. We assume that after one photoexcitation a fraction of the photochromic molecule moves to a new local minimum and stays there, although the other fraction returns to the original local minimum. The former effect is referred to as the memory effect. After repeated photoexcitations the photochromic molecule moves gradually from one local minimum to another in the pathway to the isomerization point. It finally reaches the isomerization point, where isomerization occurs. Their model successfully reproduces the kinetics of photoisomerization of diarylethene derivatives dispersed on polymer films observed experimentally. [ABSTRACT FROM AUTHOR]

Conformational disorder of conjugated polymers is an important issue to be understood and quantified. In this paper we present a new method to assess the chain conformation of conjugated polymers based on measurements of intrachain energy transfer. The chain conformation is modeled on the basis of monomer-monomer interactions, such as torsion, bending, and stretching of the connecting bond. The latter two potentials are assumed to be harmonic, while the torsional potential was calculated by density functional theory using B3-LYP functional with the SVP basis set. The energy transfer dynamics of excitons on these chains are quantitatively simulated using Förster-type line-dipole energy transfer. This allows us to compare the simulated ground state conformation of single polymer chains to ultrafast depolarization experiments of poly [3-(2,5-dioctylphenyl)thiophene] in solution. We identify torsional rotation as the main contributor to conformational disorder and find that this disorder is mainly controlled by the energy difference between syn and anti bonds. [ABSTRACT FROM AUTHOR]

Global measures of structural diversity within a distribution of biopolymers, such as the radius of gyration and percent native contacts, have proven useful in the analysis of simulation data for protein folding. In this paper we describe a statistical-based methodology to quantify the local structural variability of a distribution of biopolymers, applied to 46- and 69-“residue” off-lattice, three-color model proteins. Each folds into β-barrel structures. First we perform a principal component analysis of all interbead distance variables for a large number of independent, converged Boltzmann-distributed samples of conformations collected at each of a wide range of temperatures. Next, the principal component vectors are subjected to orthogonal (varimax) rotation. The results are displayed on so-called “squared-loading” plots. These provide a quantitative measure of the contribution to the sample variance of the position of each residue relative to the others. Dominant structural elements, those having the largest structural diversity within the sampled distribution, are responsible for peaks and shoulders observed in the specific heat versus temperature curves, generated using the weighted histogram analysis method. The loading plots indicate that the local-structural diversity of these systems changes gradually with temperature through the folding transition but radically changes near the collapse transition temperature. The analysis of the structural overlap order statistic suggests that the 46-mer thermodynamic folding transition involves the native state and at least three other nearly native intermediates. In the case of the 46-mer protein model, data are generated at sufficiently low temperatures that squared-loading plots, coupled with cluster analysis, provide a local and energetic description of its glassy state. [ABSTRACT FROM AUTHOR]

The approach to asymptotic critical behavior in polymer solutions is governed by a competition between the correlation length of critical fluctuations diverging at the critical point of phase separation and an additional mesoscopic length scale, the radius of gyration. In this paper we present a theory for crossover between two universal regimes: a regime with Ising (fluctuation-induced) asymptotic critical behavior, where the correlation length prevails, and a mean-field tricritical regime with theta-point behavior controlled by the mesoscopic polymer chain. The theory yields a universal scaled description of existing experimental phase-equilibria data and is in excellent agreement with our light-scattering experiments on polystyrene solutions in cyclohexane with polymer molecular weights ranging from 2×105 up to 11.4×106. The experiments demonstrate unambiguously that crossover to theta-point tricriticality is controlled by a competition of the two mesoscales. The critical amplitudes deduced from our experiments depend on the polymer molecular weight as predicted by de Gennes [Phys. Lett. 26A, 313 (1968)]. Experimental evidence for the presence of logarithmic corrections to mean-field tricritical theta-point behavior in the molecular-weight dependence of the critical parameters is also presented. [ABSTRACT FROM AUTHOR]

In earlier theoretical studies, it has been widely noticed that the electron correlation effect played an important role in determining the excitation energies of low-lying π→π* excited states for neutral polyenes and their radical cations and dications. In this paper, neutral and doped polyene oligomers of medium to large sizes are investigated with the Pariser-Parr-Pople model, and the π-electron correlation effect is fully taken into consideration by virtue of the density-matrix renormalization group method. The excitation properties in the polymer limit are also obtained by exponential extrapolation from the finite oligomers. The reasonable agreement of our results with the available experimental observations and advanced ab initio calculations is witnessed. It is also observed that while charge doping can significantly lower the exciting energy, the odd-charged oligomers show lower excitation energies than the even-charged ones. [ABSTRACT FROM AUTHOR]

This paper is aimed to develop a Brownian dynamics simulation method for strongly confined semiflexible polymers where numerical simulation plays an indispensable role in complementing theory and experiments. A wormlike chain under strong confinement is modeled as a string of virtual spherical beads connected by inextensible rods with length varying according to the confinement intensity of the chain measured by the Odijk deflection length. The model takes hydrodynamic interactions into account. The geometrical constraints associated with the inextensible rods are realized by the so-called linear constraint solver. The model parameters are studied by quantitatively comparing the simulated properties of a double-stranded DNA chain with available experimental data and theoretical predictions. [ABSTRACT FROM AUTHOR]

We propose a simulation method for infinitely dilute polymer solutions. In this method, an effective Hamiltonian of the solvated polymer chain is introduced to eliminate the degree of freedom of the solvent particle. The effective Hamiltonian is coupled with the density-functional theory (DFT) that we have developed for a polymer-solvent pair correlation function. All the equations proposed in this paper are derived from the first principle. This simulation method was applied to polymer chains in supercritical solvents. We observed anomalous behaviors of polymer chains near the liquid-vapor critical point: both solvophilic and solvophobic polymers expand significantly near the critical point; this is in contrast to the behavior of polymer chains in vacuum. This expansion can be interpreted as a cooperative phenomenon, which enhances the large long-wavelength density fluctuation of the solvent. [ABSTRACT FROM AUTHOR]

We expand upon the results for the force-extension behavior of single-collapsed polymer chains to consider the mechanical response of networks of cross-linked globular polymers in poor solvent. Force-strain curves are obtained under the affine deformation approximation for networked globules with both disordered and ordered globule conformations. Due to their large stored lengths, these networks would be capable of reaching extremely large strains. They also show anomalous nonmonotonic force-strain response, as a consequence of the nonmonotonic force-extension curves of their constituent globules. Finally, we consider the stability of ordered and disordered globules in these networks and propose means taken from biological and colloid science to stabilize networked globules. [ABSTRACT FROM AUTHOR]

We present a new method for efficient total-energy calculation of biopolymers using the density-matrix (DM) scheme based on the molecular fractionation with conjugate caps (MFCC) approach. In this MFCC-DM method, a biopolymer such as a protein is partitioned into properly capped fragments whose density matrices are calculated by conventional ab initio methods which are then assembled to construct the full system density matrix. The assembled full density matrix is then employed to calculate the total energy and dipole moment of the protein using Hartree–Fock or density-functional theory methods. Using this MFCC-DM method, the self-consistent-field procedure for solving the full Hamiltonian problem is avoided and an efficient approach for ab initio energy calculation of biopolymers is achieved. Two implementations of the approach are presented in this paper. Systematic numerical studies are carried out on a series of extended polyglycines CH3CO–(GLY)n–NHCH3(n=3–25) and excellent results are obtained. [ABSTRACT FROM AUTHOR]

It has been suggested that, due to topological constraints, rings in the melt may assume a more compact shape than Gaussian chains. In this paper, we exploit the availability of narrow fractions of perdeuterated linear and cyclic polydimethylsiloxane (PDMS) and, through the analysis of the small angle neutron scattering (SANS) profiles, demonstrate the difference in scattering properties of linear and cyclic PDMS molecules. As expected for Gaussian chains, for the H/D linear PDMS samples, log-log plots of the scattered intensity versus scattering vector Q display a Q(-2) dependence. However, for H/D cyclic blends, the scaling exponent is higher than 2, as predicted by computer simulations reported in the literature. We show that cyclic molecules in bulk display the characteristic maximum in plots of scattered intensity versus Q(-2) that is expected on the basis of Monte Carlo calculations and from the Casassa equation [E. F. Casassa, J. Polym. Sci. A 3, 605 (1965)]. It is also shown that, for rings, the Debye equation [P. Debye, J. Appl. Phys. 15, 338 (1944)] is no longer appropriate to describe the SANS profiles of H/D cyclic blends, at least up to Mw≈10 000. For these samples, the Casassa form factor gives a better representation of the SANS data and we show that this function which was developed for monodisperse cyclics is still adequate to describe our slightly polydisperse samples. Deviations from all above observations are noted for Mw>11 000 and are attributed to partial contamination of cyclic samples with linear chains. The failure of both the Debye and the Casassa form factors could be due to contamination of the cyclic fractions by linear polymers or to a real conformational change. [ABSTRACT FROM AUTHOR]