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We propose a novel path sampling method based on the Onsager-Machlup (OM) action by generalizing the multiscale enhanced sampling technique suggested by Moritsugu and co-workers [J. Chem. Phys. 133, 224105 (2010)]. The basic idea of this method is that the system we want to study (for example, some molecular system described by molecular mechanics) is coupled to a coarse-grained (CG) system, which can move more quickly and can be computed more efficiently than the original system. We simulate this combined system (original + CG system) using Langevin dynamics where different heat baths are coupled to the two systems. When the coupling is strong enough, the original system is guided by the CG system, and is able to sample the configuration and path space with more efficiency. We need to correct the bias caused by the coupling, however, by employing the Hamiltonian replica exchange, where we prepare many path replicas with different coupling strengths. As a result, an unbiased path ensemble for the original system can be found in the weakest coupling path ensemble. This strategy is easily implemented because a weight for a path calculated by the OM action is formally the same as the Boltzmann weight if we properly define the path 'Hamiltonian.' We apply this method to a model polymer with Asakura-Oosawa interaction, and compare the results with the conventional transition path sampling method. [ABSTRACT FROM AUTHOR]

The protein folding problem has long represented a "holy grail" in statistical physics due to its physical complexity and its relevance to many human diseases. While past theoretical work has yielded apt descriptions of protein folding landscapes, recent large-scale simulations have provided insights into protein folding that were impractical to obtain from early theories. In particular, the role that non-native contacts play in protein folding, and their relation to the existence of misfolded, β-sheet rich trap states on folding landscapes, has emerged as a topic of interest in the field. In this paper, we present a modified model of heteropolymer freezing that includes explicit secondary structural characteristics which allow observations of "intramolecular amyloid" states to be probed from a theoretical perspective. We introduce a variable persistence length-based energy penalty to a model Hamiltonian, and we illustrate how this modification alters the phase transitions present in the theory. We find, in particular, that inclusion of this variable persistence length increases both generic freezing and folding temperatures in the model, allowing both folding and glass transitions to occur in a more highly optimized fashion. We go on to discuss how these changes might relate to protein evolution, misfolding, and the emergence of intramolecular amyloid states.

We study translocation dynamics of a semi-flexible polymer chain through a nanoscopic pore in two dimensions using Langevin dynamics simulation in presence of an external bias F inside the pore. For chain length N and stiffness parameter κb considered in this paper, we observe that the mean first passage time <τ> increases as <τ(κb)>~<τ(κb=0)>lp(aN) , where κb and lp are the stiffness parameter and persistence length, respectively, and aN is a constant that has a weak N dependence. We monitor the time dependence of the last monomer xN(t) at the cis compartment and calculate the tension propagation time (TP) ttp directly from simulation data for ~ t as alluded in recent nonequlibrium TP theory [T. Sakaue, Phys. Rev. E 76, 021803 (2007)] and its modifications to Brownian dynamics tension propagation theory [T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, Phys. Rev. E 85, 051803 (2012); and J. Chem. Phys. 137, 085101 (2012)] originally developed to study translocation of a fully flexible chain. We also measure ttp from peak position of the waiting time distribution W(s) of the translocation coordinate s (i.e., the monomer inside the pore), and explicitly demonstrate the underlying TP picture along the chain backbone of a translocating chain to be valid for semi-flexible chains as well. From the simulation data, we determine the dependence of ttp on chain persistence length lp and show that the ratio ttp∕<τ> is independent of the bias F.

The trapping process in polymer systems constitutes a fundamental mechanism for various other dynamical processes taking place in these systems. In this paper, we study the trapping problem in two representative polymer networks, Cayley trees and Vicsek fractals, which separately model dendrimers and regular hyperbranched polymers. Our goal is to explore the impact of trap location on the efficiency of trapping in these two important polymer systems, with the efficiency being measured by the average trapping time (ATT) that is the average of source-to-trap mean first-passage time over every staring point in the whole networks. For Cayley trees, we derive an exact analytic formula for the ATT to an arbitrary trap node, based on which we further obtain the explicit expression of ATT for the case that the trap is uniformly distributed. For Vicsek fractals, we provide the closed-form solution for ATT to a peripheral node farthest from the central node, as well as the numerical solutions for the case when the trap is placed on other nodes. Moreover, we derive the exact formula for the ATT corresponding to the trapping problem when the trap has a uniform distribution over all nodes. Our results show that the influence of trap location on the trapping efficiency is completely different for the two polymer networks. In Cayley trees, the leading scaling of ATT increases with the shortest distance between the trap and the central node, implying that trap's position has an essential impact on the trapping efficiency; while in Vicsek fractals, the effect of location of the trap is negligible, since the dominant behavior of ATT is identical, respective of the location where the trap is placed. We also present that for all cases of trapping problems being studied, the trapping process is more efficient in Cayley trees than in Vicsek fractals. We demonstrate that all differences related to trapping in the two polymer systems are rooted in their underlying topological structures.

In polymer blends where the glass transition temperatures of the two components differ greatly, the segmental α-relaxation and the chain dynamics of the faster component exhibit a number of anomalous properties not seen before in homopolymers, and not explainable by conventional theory of polymer dynamics. In the first part of this paper, these anomalous properties are collected altogether and made known. We show their interconnections and emphasize the necessity of explaining all of them together if the objective is to fully solve the problem. In the second part, the predictions from a single theoretical framework, namely, the coupling model, are applied to explain the anomalous properties in toto.

We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse graining affects entropy and dissipation, two factors enter the rescaling: inclusion of intramolecular vibrational degrees of freedom and rescaling of the friction coefficient. Because our approach is analytical, it is general and transferable. Translational and rotational diffusion of unentangled and entangled polyethylene melts, predicted from mesoscale simulations of coarse-grained polymer melts using our rescaling procedure, are in quantitative agreement with united-atom simulations and with experiments. [ABSTRACT FROM AUTHOR]

We employ self-consistent-field and density-functional theories to simulate the phase behaviors of diblock copolymer-nanoparticle mixtures confined in a two-dimensional circular pore. By varying the block ratio, the size of the pore, and the particle concentration, rich phase structures are discovered. It is shown that the structural frustration, the loss of conformational entropy of the polymer chains under confinement, the curvature of the pore, and the steric packing effect of the particles play important roles in determining the morphologies of the nanocomposites under circular confinement. It is found that the increase in the particle concentration can promote the transformation of concentric lamellas to the cylindrical domains. Our results suggest effective ways to stabilize the phase orderings of diblock copolymer-nanoparticle mixtures under two-dimensional circular confinement. [ABSTRACT FROM AUTHOR]

The process during which a polymer translocates through a nanopore depends on many physical parameters and fundamental mechanisms. We propose a new one-dimensional lattice Monte Carlo algorithm that integrates various effects such as the entropic forces acting on the subchains that are outside the channel, the external forces that are pulling the polymer through the pore, and the frictional effects that involve the chain and its environment. Our novel approach allows us to study the polymer as a single Brownian particle diffusing while subjected to a position-dependent force that includes both the external driving forces and the internal entropic bias. Frictional effects outside and inside the pore are also considered. This Monte Carlo method is much more efficient than other simulation methods, and it can be used to obtain scaling laws for various polymer translocation regimes. In this first part, we derive the model and describe a subtle numerical approach that gives exact results for both the escape probability and the mean translocation time (and higher moments of its distribution). The scaling laws obtained from this model will be presented and discussed in the second part of this series. [ABSTRACT FROM AUTHOR]

The paper shows the influence of the reaction mechanism on the time course of the entropy production σ in a closed system during reversible polymerization. We consider two different reaction mechanisms with (a) being a polycondensation and (b) a chain growth mechanism. For both mechanisms explicit expressions for the entropy production σ as a function of time t are derived. To demonstrate the application of these general expressions we consider two different polymerization experiments where the reaction starts (i) from monomer molecules polymerizing to a defined number average chain length xn,eq and (ii) from monodisperse polymer molecules reacting with each other under the constraint that xn is the same at the beginning and the end of the reaction. In both cases we treat the system to be ideal and describe the kinetics of the reversible polymerization reactions using two kinetic constants for the forward and backward reactions, respectively. Under these assumptions the difference in the curvature of the entropy production σ between a polycondensation and a chain growth mechanism is only marginal if the reaction starts from monomer molecules polymerizing to a defined number average chain length xn,eq. [ABSTRACT FROM AUTHOR]

We simulated the translocation process of a polymer chain from a source container to a drain container through a short nanochannel. We utilized the bond fluctuation model coupled with Monte Carlo dynamics in our simulations. The calculation results show that the excluded volume effect significantly affects the polymer’s translocation time τ. This time depends nonmonotonically on the polymer length N. For a fixed nanochannel length, τ decreases when the polymer length increases. τ, however, increases when the polymer length exceeds a certain threshold. This observation differs from those predicated for a Gaussian chain. In this paper, we will further present our findings to explain this phenomenon. The knowledge we gain from this research can enhance the understanding of complex transport processes in many biological systems. [ABSTRACT FROM AUTHOR]

Bounded potentials are good models to represent the effective two-body interaction in some colloidal systems, such as the dilute solutions of polymer chains in good solvents. The simplest bounded potential is that of penetrable spheres, which takes a positive finite value if the two spheres are overlapped, being 0 otherwise. Even in the one-dimensional case, the penetrable-rod model is far from trivial, since interactions are not restricted to nearest neighbors and so its exact solution is not known. In this paper the structural properties of one-dimensional penetrable rods are studied. We first derive the exact correlation functions of the penetrable-rod fluids to second order in density at any temperature, as well as in the high-temperature and zero-temperature limits at any density. It is seen that, in contrast to what is generally believed, the Percus-Yevick equation does not yield the exact cavity function in the hard-rod limit. Next, two simple analytic theories are constructed: a high-temperature approximation based on the exact asymptotic behavior in the limit T→∞ and a low-temperature approximation inspired by the exact result in the opposite limit T→0. Finally, we perform Monte Carlo simulations for a wide range of temperatures and densities to assess the validity of both theories. It is found that they complement each other quite well, exhibiting a good agreement with the simulation data within their respective domains of applicability and becoming practically equivalent on the borderline of those domains. A comparison with numerical solutions of the Percus-Yevick and the hypernetted-chain approximations is also carried out. Finally, a perspective on the extension of our two heuristic theories to the more realistic three-dimensional case is provided. [ABSTRACT FROM AUTHOR]

The presence of space charge in the polymeric insulation of high-voltage cables is thought to be correlated with electric breakdown. However, a direct link between molecular properties, space charge formation and eventual breakdown has still to be established. It is clear that both physical (e.g., conformational disorder) and chemical defects (e.g., broken bonds and impurities) are present in insulating materials and that both may trap electrons. We have shown that by defining the defect energy in terms of the molecular electron affinity, a relationship is established between the electron trap and the molecular properties of the material. In a recent paper [M. Meunier and N. Quirke, J. Chem. Phys. 113, 369 (2000)] we proposed methods that have made it possible to provide estimates of the energy, number and residence times of electrons in conformational traps in polyethylene. Typical physical trap energies are of the order of 0.15 eV and all are less than 0.3 eV. In the present paper we focus on the role of chemical defects, where we expect much deeper traps but at very low concentrations. Following the methodology used in our previous paper we have used density-functional theory to calculate trap energies for a set of chemical impurities and additives commonly found in polyethylene used for high-voltage cable insulation. In an extension of our approach we have estimated the effect of neighboring molecules on the trap energies of such defects. The resulting trap energy-trap density distribution reveals some very deep (>1 eV) traps presumably implicated in the formation of long-lived space charge in polymeric insulators and consequently to changes in the dielectric properties of the material. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy S and free energy F from a given MC trajectory developed recently and applied to liquid argon, TIP3P water, and peptides. In this paper HSMC is extended to random coil polymers by applying it to self-avoiding walks on a square lattice—a simple but difficult model due to strong excluded volume interactions. With HSMC the probability of a given chain is obtained as a product of transition probabilities calculated for each bond by MC simulations and a counting formula. This probability is exact in the sense that it is based on all the interactions of the system and the only approximation is due to finite sampling. The method provides rigorous upper and lower bounds for F, which can be obtained from a very small sample and even from a single chain conformation. HSMC is independent of existing techniques and thus constitutes an independent research tool. The HSMC results are compared to those obtained by other methods, and its application to complex lattice chain models is discussed; we emphasize its ability to treat any type of boundary conditions for which a reference state (with known free energy) might be difficult to define for a thermodynamic integration process. Finally, we stress that the capability of HSMC to extract the absolute entropy from a given sample is important for studying relaxation processes, such as protein folding. [ABSTRACT FROM AUTHOR]

The nonlinear rheological version of our barrier hopping theory for particle-polymer suspensions and gels has been employed to study the effect of steady shear and constant stress on the alpha relaxation time, yielding process, viscosity, and non-Newtonian flow curves. The role of particle volume fraction, polymer-particle size asymmetry ratio, and polymer concentration have been systematically explored. The dynamic yield stress decreases in a polymer-concentration- and volume-fraction-dependent manner that can be described as apparent power laws with effective exponents that monotonically increase with observation time. Stress- or shear-induced thinning of the viscosity becomes more abrupt with increasing magnitude of the quiescent viscosity. Flow curves show an intermediate shear rate dependence of an effective power-law form, becoming more solidlike with increasing depletion attraction. The influence of polymer concentration, particle volume fraction, and polymer-particle size asymmetry ratio on all properties is controlled to a first approximation by how far the system is from the gelation boundary of ideal mode-coupling theory (MCT). This emphasizes the importance of the MCT nonergodicity transition despite its ultimate destruction by activated barrier hopping processes. Comparison of the theoretical results with limited experimental studies is encouraging. [ABSTRACT FROM AUTHOR]

We review the force-extension behavior of polymers collapsed in poor solvent, modified to include the effects of semiflexibility and considered for globules with “ordered” and “disordered” internal structures. A series of ordered globules is used as a model for the unbinding of a disordered globule beneath its glass transition and for multiple-repeat proteins such as the poly-Ig-domain titin used in atomic force microscopy studies. These single-chain results form the foundation for the treatment of cross-linked networks of globular polymers. [ABSTRACT FROM AUTHOR]

We study the depletion, pair interaction, and phase behavioral characteristics of proteins in polymer solutions. We use a McMillan–Mayer-like approach [W. G. McMillan, Jr. and J. E. Mayer, J. Chem. Phys. 13, 276 (1945)] to suggest that the depletion characteristics should be studied at an effective polymer concentration which is a function of both the average polymer and the protein concentrations. In the protein limit, we show that the volume of the polymer depletion layers exceeds the size of the proteins, leading to effective polymer concentrations typically in the semidilute and concentrated regimes even when the average polymer concentrations are in the dilute regimes. We propose an approximate approach that accounts for the multibody depletion overlaps, and use an accurate numerical solution of polymer mean-field theory to address depletion characteristics in these regimes which are characterized by both the importance of polymer interactions as well as the curvature of the proteins relative to the correlation length of polymers. We show that the depletion characteristics of the protein-polymer mixture can be quite different when viewed in this framework, and this can have profound consequences for the phase behavior of the mixture. Our theoretical predictions for the phase diagram match semiquantitatively with published experimental results. [ABSTRACT FROM AUTHOR]

The presence of space charge in the polymeric insulation of high-voltage cables is correlated with electric breakdown. There is a vast literature concerned with the experimental characterization of space charge and with phenomenological models of space charge formation and discharge. However, a direct link between molecular properties, space charge formation and eventual breakdown has still to be established. In this paper, we suggest a new scheme that constitutes a first step in linking microscopic defects to the formation of space charge. Although our goal is to understand the role of defects at the molecular level in electron trapping and the formation of space charge in polyethylene, we start by considering a "model" material; the wax tridecane (n-C[sub 13]H[sub 28]). It is clear that both physical (e.g., conformational defects) and chemical defects (e.g., broken bonds) may be present in insulating materials and may both trap electrons. In the present paper, we focus on the role of physical defects. Our analysis suggests that by defining the defect energy in terms of the molecular electron affinity, a relationship is established between the electron trap and the molecular properties of the material. The electron affinity and its variation with wax molecule conformation have been calculated using density functional theory (DFT, as implemented in the code DMol). By performing molecular-dynamics simulations of amorphous waxes, we are able to determine likely conformational defects, and by using ab initio methods estimate the trapping energies. Conformational defects in these waxy materials are predicted to produce shallow traps with energies below 0.3 eV. These results are used to estimate the energy, number, and residence times of electrons in conformational traps in polyethylene. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

During fast diffusion-influenced polymerization, nonequilibrium behavior of the polymer chains and the surrounding reactive monomers has been reported recently. Based on the laws of thermodynamics, the emerging nonequilibrium structures should be characterizable by some "extra free energy" (excess over the equilibrium Helmholtz free energy). Here, we study the nonequilibrium thermodynamics of chain-growth polymerization of ideal chains in a dispersion of free reactive monomers, using off-lattice, reactive Brownian dynamics computer simulations in conjunction with approximative statistical mechanics and relative entropy (Gibbs–Shannon and Kullback–Leibler) concepts. In the case of fast growing polymers, we indeed report increased nonequilibrium free energies ΔFneq of several kBT compared to equilibrium and near-equilibrium, slowly growing chains. Interestingly, ΔFneq is a non-monotonic function of the degree of polymerization and thus also of time. Our decomposition of the thermodynamic contributions shows that the initial dominant extra free energy is stored in the nonequilibrium inhomogeneous density profiles of the free monomer gas (showing density depletion and wakes) in the vicinity of the active center at the propagating polymer end. At later stages of the polymerization process, we report significant extra contributions stored in the nonequilibrium polymer conformations. Finally, our study implies a nontrivial relaxation kinetics and "restoring" of the extra free energy during the equilibration process after polymerization. [ABSTRACT FROM AUTHOR]

The inclusion of nuclear quantum effects (NQEs) in molecular dynamics simulations is one of the major obstacles for an accurate modeling of molecular scattering processes involving more than a couple of atoms. An efficient method to incorporate these effects is ring polymer molecular dynamics (RPMD). Here, we extend the scope of our recently developed method based on non-equilibrium RPMD (NE-RPMD) from triatomic chemical reactions to reactions involving more atoms. We test the robustness and accuracy of the method by computing the integral cross sections for the H/F + CH4/CHD3 reactions where the methane molecule is either initially in its vibrational ground or excited state (C–H stretch). Furthermore, we analyze the extent to which NQEs are described by NE-RPMD. The method shows significant improvement over the quasiclassical trajectory approach while remaining computationally efficient. [ABSTRACT FROM AUTHOR]

Bottlebrush polymers are a class of highly branched macromolecules that show promise for applications such as self-assembled photonic materials and tunable elastomers. However, computational studies of bottlebrush polymer solutions and melts remain challenging due to the high computational cost involved in explicitly accounting for the presence of side chains. Here, we consider a coarse-grained molecular model of bottlebrush polymers where the side chains are modeled implicitly, with the aim of expediting simulations by accessing longer length and time scales. The key ingredients of this model are the size of a coarse-grained segment and a suitably coarse-grained interaction potential between the non-bonded segments. Prior studies have not focused on developing explicit forms of such potentials, instead, relying on scaling arguments to model non-bonded interactions. Here, we show how to systematically calculate an interaction potential between the coarse-grained segments of bottlebrush from finer grained explicit side chain models using Monte Carlo and Brownian dynamics and then incorporate it into an implicit side chain model. We compare the predictions from our coarse-grained implicit side chain model with those obtained from models with explicit side chains in terms of the potential of mean force, the osmotic second virial coefficient, and the interpenetration function, highlighting the range of applicability and limitations of the coarse-grained representation. Although presented in the context of homopolymer bottlebrushes in athermal solvents, our proposed method can be extended to other solvent conditions as well as to different monomer chemistries. We expect that our implicit side chain model will prove useful for accelerating large-scale simulations of bottlebrush solutions and assembly. [ABSTRACT FROM AUTHOR]

We investigate the morphology of microphase separated domains in diblock copolymers where each chain consists of a stiff rod block and a flexible coil block. A simplified phenomenological model system is introduced, which is coarse-grained in terms of the local concentration difference between the two blocks and the local director field of the rod part. Computer simulations of this set of time-evolution equations in two dimensions show in the weak segregation regime that the elastic energy in the rod-block rich domains affects drastically the structures of microphase separated domains. A coil-to-rod transition is incorporated into the model system to examine the elastic and anisotropic effects. The effects of the external electric field are also investigated to control the domain morphology. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We developed a simple time-dependent mean-field theory to describe the phase separation kinetics of either homopolymers or AB-diblock copolymers in supercritical (SC) fluids. The model, previously used to describe the phase behavior of AB-block copolymers under the assumption of strong solvent selectivity for just one copolymer chain, has been extended to study the kinetics of the phase separation process. Time resolved small angle x-ray scattering (TR–SAXS) measurements have been performed on different AB-diblock copolymers containing a perfluorinated chain and dissolved in SC–CO[sub 2]. The data obtained over a wide range of pressure and temperature confirm our theoretical predictions. Particularly interesting is the presence of two relaxation frequencies for the homogeneous solution→spherical aggregate transition, where the two relaxation processes depend on the depth of the pressure jump and on temperature. The whole phenomenon could be explained as an initial SC solvent/polymer phase separation followed by a slow reorientation process to form spherical aggregates driven by the copolymer solvophilic moiety. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The dynamics of protein folding result from both enthalpic and entropic contributions to the free energy. In this paper we focus on entropic volume exclusion effects. We carry out computer simulations using a model that allows us to independently change the size or biochemical properties of amino acid residues. To determine the importance of excluded volume effects, we investigate the effects of changing the size of side chains on the unfolding dynamics of a model four-helix bundle protein. In addition, we also investigate the effects of changing the thickness of the chain’s backbone. This has relevance to the behavior of synthetic polymers where the size of the constituent units can be varied. We find that entropic excluded volume effects are crucially important for stabilizing the organized native state relative to the molten globule. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The influence of thermal activation, chemical initiation, chain fragmentation, and chain stiffness on basic thermodynamic properties of equilibrium polymerization solutions is systematically investigated using a Flory–Huggins type lattice model. The properties treated include the average chain length L, extent of polymerization [uppercase_phi_synonym], Helmholtz free energy F, configurational entropy S, specific heat C[sub V], polymerization transition temperature T[sub p], osmotic pressure Π, and the second and third virial coefficients, A[sub 2] and A[sub 3]. The dependence of the critical temperature T[sub c] and critical composition [lowercase_phi_synonym][sub c] (volume fraction of associating species) on the enthalpy Δh[sub p] and entropy Δs[sub p] of polymerization and on the strength ε[sub FH] of the FH effective monomer–solvent van der Waals interaction (χ=ε[sub FH]/T) is also analyzed as an illustration of the strong coupling between phase separation and polymerization. For a given polymerization model, both T[sub c] and [lowercase_phi_synonym][sub c], normalized by their values in the absence of polymerization, are functions of the dimensionless “sticking energy” h[sub ε]≡(|Δh[sub p]|/R)/(2ε[sub FH]) (where R is the gas constant) and Δs[sub p]. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The polymer threading a membrane transition (PTM), which is a first-order thermodynamic phase transition for an isolated linear polymer in the limit of infinite molecular weight, is coupled to the other four phase transitions of the isolated polymer molecule. They are (1) the helix–random coil (HR) phase transition which can be diffuse (polypeptides), second-order (DNA) or first-order (collagen) depending on the number of strands, (2) the collapse (C) transition which is usually second-order but can be first-order for polymeric solvents, (3) adsorption onto a surface (SA) which is second-order, (4) a model of equilibrium polymerization (P) which is first-order. In each case an exact expression for the partition function of the coupled pair is given as a one-dimensional summation over products of the individual partition functions corresponding to sides 1 and 2. Using a procedure analogous to evaluation of the grand canonical ensemble the summation can be performed and the character of the transition elucidated in the limit of infinite molecular weight. Given that the solutions on either side are sufficiently diverse there are 15 possible translocation pair couplings. They are PTM–PTM, HR–HR, C–C, SA–SA, P–P, PTM–HR, PTM–C, PTM–SA, PTM–P, HR–C, HR–SA, HR–P, C–SA, C–P, SA–P. The PTM–P coupling is most interesting because one can create polymer in the PTM side even though the P side is in the depolymerization regime. For HR–HR there are eight possible translocation modes. For example, as we raise the temperature we can have H1→H2→R1→R2 in obvious notation. These exact model solutions provide a thermodynamic base for the study of the kinetics of significant technological problems such as the translocation of DNA through pores imbedded in membranes. They also throw light on the nature of polymer–membrane–pore interactions in living cells and viruses. [ABSTRACT FROM AUTHOR]

This paper extends previous methods for obtaining the probability distribution function of end-to-end distance for semiflexible polymers, and presents a general formalism that can generate conformational statistics of any continuum filament model of semiflexible chains with internal bends and twists. In particular, our focus is distribution functions for chains composed of straight or helical segments connected with discrete bends or twists. Prior polymer theories are not able to fully account for the effects of these internal shape discontinuities. We use the operational properties of the noncommutative Fourier transform for the group of rigid-body motions in three-dimensional space. This general method applies to various stiffness models of semiflexible chainlike macromolecules. Examples are given which apply the stiffness parameters defined in the Kratky–Porod model, Yamakawa helical wormlike chain model, and revised Marko–Siggia double-helix model to chains with intrinsic bends or twists in their undeformed (minimal energy) state. We demonstrate how the location and magnitude of internal bends in the chain affect the distribution of end-to-end distances for each of these models. This capability allows one to study the entropic effects of intrinsic shape changes (e.g., bend angle) in various models, and may lead to coarse-grained continuum mechanical models of processes that occur during transcription regulation. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A Monte Carlo (MC) study is made of the second virial coefficient A[SUB2] for polymers using two freely rotating chains, each of bond angle 109°, with the Lennard-Jones 6-12 intramolecular and intermolecular potentials between beads in a cutoff version for the number of bonds in the chain ranging from 6 to 1000 in the Θ and good-solvent conditions. It is found that effects of chain ends on A[SUB2] are appreciable for small molecular weight M, as was expected, and that the second virial coefficient A[SUB2,Θ] at the Θ temperature, at which the ratio 〈S[SUP2]〉/M of the mean-square radius of gyration 〈S[SUP2]〉 to M becomes a constant independent of M for very large M, remains slightly negative even for such large (but finite) M where the effects of chain ends disappear. Such behavior of A[SUB2,Θ], which cannot be explained within the framework of the binary cluster theory, is shown to be understandable if possible effects of three-segment interactions are considered. The present MC data for A[SUB2] (along with the previous ones for 〈S[SUP2]〉) may then be consistently explained by the existent theory based on the helical wormlike chain model only if a minor correction is made to the theoretical A[SUB2,Θ] in almost the same range where the effects of chain ends are appeciable. The present MC data are also compared with experimental data, and it is shown that the latter may also be similarly explained. [ABSTRACT FROM AUTHOR]

In this contribution, we theoretically investigate the isothermal mass transport of a simple fluid into a blend of two immiscible Newtonian polymers. Using internal state variables, we derive a nonlinear formulation that addresses the effects of the diffusion/interface coupling on both the mass transport as well as on the morphology of the interface. The approach uses a scalar and a second-order tensor to directly track the dynamic changes of the size and shape of the interface. The mass flux governing equation includes new terms that lead to non-Fickian behavior attributed to the viscoelatic contribution of the interface. In turn, the size and shape of the interface are modified by diffusion. In one-dimensional analysis, we examine the nature of propagation of both nonlinear hyperbolic and linear dispersive waves. Explicit formulas for the characteristic speed, phase velocity, and attenuation are provided. [ABSTRACT FROM AUTHOR]

Two improved versions of the pruned-enriched-Rosenbluth method (PERM) are proposed and tested on simple models of lattice heteropolymers. Both are found to outperform not only the previous version of PERM, but also all other stochastic algorithms which have been employed on this problem, except for the core directed chain growth method (CG) of Beutler and Dill. In nearly all test cases they are faster in finding low-energy states, and in many cases they found new lowest energy states missed in previous papers. The CG method is superior to our method in some cases, but less efficient in others. On the other hand, the CG method uses heavily heuristics based on presumptions about the hydrophobic core and does not give thermodynamic properties, while the present method is a fully blind general purpose algorithm giving correct Boltzmann-Gibbs weights, and can be applied in principle to any stochastic sampling problem. [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.

Dendrimers and regular hyperbranched polymers are two classic families of macromolecules, which can be modeled by Cayley trees and Vicsek fractals, respectively. In this paper, we study the trapping problem in Cayley trees and Vicsek fractals with different underlying geometries, focusing on a particular case with a perfect trap located at the central node. For both networks, we derive the exact analytic formulas in terms of the network size for the average trapping time (ATT)-the average of node-to-trap mean first-passage time over the whole networks. The obtained closed-form solutions show that for both Cayley trees and Vicsek fractals, the ATT display quite different scalings with various system sizes, which implies that the underlying structure plays a key role on the efficiency of trapping in polymer networks. Moreover, the dissimilar scalings of ATT may allow to differentiate readily between dendrimers and hyperbranched polymers.

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 t(c) 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, t(c) ~ Nd(2), and that in case (b), t(c) ~ N(2/(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), t(c) ~ N(3.4), the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium.

The photoelectric power conversion efficiency of polymer solar cells is till now, compared to conventional inorganic solar cells, still relatively low with maximum values ranging from 7% to 8%. This essentially relates to the existence of exciton and charge carrier loss phenomena, reducing the performance of polymer solar cells significantly. In this paper we introduce a new computer simulation technique, which permits to explore the causes of the occurrence of such phenomena at the nanoscale and to design new photovoltaic materials with optimized opto-electronic properties. Our approach consists in coupling a mesoscopic field-theoretic method with a suitable dynamic Monte Carlo algorithm, to model the elementary photovoltaic processes. Using this algorithm, we investigate the influence of structural characteristics and different device conditions on the exciton generation and charge transport efficiencies in case of a novel nanostructured polymer blend. More specifically, we find that the disjunction of continuous percolation paths leads to the creation of dead ends, resulting in charge carrier losses through charge recombination. Moreover, we observe that defects are characterized by a low exciton dissociation efficiency due to a high charge accumulation, counteracting the charge generation process. From these observations, we conclude that both the charge carrier loss and the exciton loss phenomena lead to a dramatic decrease in the internal quantum efficiency. Finally, by analyzing the photovoltaic behavior of the nanostructures under different circuit conditions, we demonstrate that charge injection significantly determines the impact of the defects on the solar cell performance.

The lattice cluster theory (LCT) for the thermodynamics of a wide array of polymer systems has been developed by using an analogy to Mayer's virial expansions for non-ideal gases. However, the high-temperature expansion inherent to the LCT has heretofore precluded its application to systems exhibiting strong, specific "sticky" interactions. The present paper describes a reformulation of the LCT necessary to treat systems with both weak and strong, "sticky" interactions. This initial study concerns solutions of linear telechelic chains (with stickers at the chain ends) as the self-assembling system. The main idea behind this extension of the LCT lies in the extraction of terms associated with the strong interactions from the cluster expansion. The generalized LCT for sticky systems reduces to the quasi-chemical theory of hydrogen bonding of Panyioutou and Sanchez when correlation corrections are neglected in the LCT. A diagrammatic representation is employed to facilitate the evaluation of the corrections to the zeroth-order approximation from short range correlations., (© 2012 American Institute of Physics)

In this paper a combined experimental and quantum chemical study of the geometry and opto-electronic properties of unsubstituted and dialkoxy-sustituted phenylene-vinylene oligomers (PV's) is presented. The optical absorption spectra for PV cations with different chain lengths and substitution patterns were measured using pulse radiolysis with time-resolved spectrophotometric detection from 1380 to 500 nm (0.9 to 2.5 eV). The geometries of the PV's studied were optimized using density functional theory (DFT) for both the neutral and singly charged molecule. The spectra for the PV radical cations were then calculated using singly excited configuration interaction with an intermediate neglect of differential overlap reference wave function method together with the DFT geometry. The agreement between experimental and theoretical absorption energies is excellent; most of the calculated radical cation absorption energies are within 0.15 eV of the experimental values. The pattern of dialkoxy-substitution is found to have a large effect on the optical absorption spectrum of the cation. Using the calculated charge distribution it is shown that the degree of delocalization of the charge correlates with the energy of the lowest absorption band. If alkoxy side chains are present on some of the rings the positive charge tends to localize at those sites. [ABSTRACT FROM AUTHOR]

We present a new real space Newton-based computational approach to computing the properties of inhomogeneous polymer systems with density functional theory (DFT). The DFT is made computationally efficient by modeling the polymers as freely jointed chains and obtaining direct correlation functions from polymer reference interaction site model calculations. The code we present can solve the DFT equations in up to three dimensions using a parallel implementation. In addition we describe our implementation of an arc-length continuation algorithm, which allows us to explore the phase space of possible solutions to the DFT equations. These numerical tools are applied in this paper to hard chains near hard walls and briefly to block copolymer systems. The method is shown to be accurate and efficient. Arc-length continuation calculations of the diblock copolymer systems illustrate the care required to obtain a complete understanding of the structures that may be found with this polymer-DFT approach. [ABSTRACT FROM AUTHOR]

Phase separated structure of ternary blends of A and B homopolymers and symmetric AB diblock copolymer is investigated using a lattice (real-space) self-consistent field theory. This paper includes the detailed description of our published results [Kodama, Komura, and Tamura, Europhys. Lett. 53, 46 (2001)] as well as more extended calculations. We consider the symmetric case, namely, (i) both A and B homopolymers have the same degree of polymerization N[sub A]=N[sub B]; (ii) AB diblock copolymer of length N[sub AB] is symmetric; (iii) average volume fractions of A and B homopolymers are equal. We looked into the influence of relative chain lengths α=N[sub A]/N[sub AB] on the phase separated structure. Our numerical simulations are performed in the real space without assuming the symmetry of the structure a priori. For the fixed copolymer length and α<1, the typical length scale of the microphase separated structure become smaller for relatively shorter homopolymer chains (small α). In other words, the homopolymers becomes more efficient to swell the microphase separated structure for longer homopolymer chains (large α). Detailed free-energy analysis revealed that the stability of the lamellar phase is marginal for small block copolymer volume fraction. For α>1, on the other hand, three-phase coexistence either between the disorder, A-rich and B-rich phases or between the lamellar, A-rich and B-rich phases is observed. [ABSTRACT FROM AUTHOR]

Statistical properties of flexible polymers with controlled molecular weights (length of arms) and branching patterns (topology) has been attracting strong interest. Basically, the lattice enrichment algorithms are suitable for simulating this kind of subject because they allow direct estimation of the total configuration number. However, it is difficult to apply this kind of algorithm for polymers with highly complicated structures, namely the comb-polymers. One of the difficulties is that the efficiency of simulation is severely limited. In this paper, a previously reported improvement technique is revisited, enhanced, and combined with several new ideas for developing a modified algorithm, which can solve such a situation. The validation and performance evaluation of the modified algorithm is presented. The algorithm is then applied to small scale polymer combs. In particular, the value of the critical exponent related to the configuration number is estimated on these combs. The result obtained for an H-shaped polymer is in accordance with previous simulations and a theoretical prediction formula already proposed. Possibilities for the future extension of the algorithm are briefly discussed. [ABSTRACT FROM AUTHOR]

The self-consistent-field (SCF) theory developed in Part I [J. Chem. Phys. 116, 7283 (2002), preceding paper] is employed to compute the interaction between particles coated by end-grafted homopolymers in good solvent, where the particles and the homopolymers have comparable sizes. The result shows that, contrary to the prediction of the conventional theory for colloidal stabilization and previous SCF studies, the interaction is attractive, repulsive, and attractive at large, intermediate, and small distances, respectively, for densely grafted particles, while it is purely attractive for sparsely grafted particles. The attractive interaction is a consequence of two important factors that were ignored in previous studies: (i) the sphere–sphere geometry of the system and (ii) the segment density associated with individual particle being deformed anisotropically, with respect to the particle, under the perturbation of other particles. We argue that the conventional wisdom that end-grafted homopolymers in good solvent always impart stability indeed is correct only in a kinetic sense and that our result will become more observable in systems composed of nanoparticles. Limitations of our prediction and considerations that must be carefully taken into account when generalizing our result to micron-sized particles and star polymers are discussed. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The frequency and molecular mass dependences of nuclear magnetic resonance spin-lattice relaxation and the time dependence of the mean-squared segment displacement of Kuhn segment chains confined in static straight and randomly coiled tubes with "soft" and "hard" walls were studied. "Soft" walls were modeled in the form of a cylindrical distribution of a harmonic radial potential. This scenario is analytically solvable in contrast to the situation of "hard" (reflecting) walls corresponding to an infinitely deep square-well radial potential. In the latter case, we have therefore employed Monte Carlo simulations using a modified Stockmayer chain model. In both situations, qualitatively equivalent results were obtained. Depending on the effective tube diameter (or width of the potential well) a crossover from Rouse to reptation behavior occurs which sets on already far beyond the Flory radius of the polymer. In terms of the spin-lattice relaxation dispersion, reptation reveals itself by T[sub 1] ∝ M[sup 0]ω[sup 3/4] in the chain mode regime, in good agreement with experimental data for polymers in artificial tubes reported in our previous paper by Kimmich et al. [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 (0.7T(c)), 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.

Functionalizing nanoparticles with organic ligands, such as oligomers, polymers, DNA, and proteins, is an attractive way to manipulate the interfacial interactions between the nanoparticles and the medium the particles are placed in, and thus control the nanoparticle assembly. In this paper we have conducted a Monte Carlo simulation study on copolymer grafted spherical nanoparticles to show the tremendous potential of using monomer sequence on the copolymers to tune the grafted chain conformation, and thus the effective interactions between copolymer grafted nanoparticles. We have studied AB copolymers with alternating, multiblock, or diblock sequences, where either A monomers or B monomers have monomer-monomer attractive interactions. Our focus has been to show the nontrivial effect of monomer sequence on the conformations of the grafted copolymers at various particle diameters, grafting densities, copolymer chain lengths, and monomer-monomer interactions in an implicit small molecule solvent. We observe that the monomer sequence, particle diameter, and grafting density dictate whether (a) the grafted chains aggregate to bring attractive monomers from multiple grafted chains together (interchain and intrachain monomer aggregation) if the enthalpy gained by doing so offsets the entropic loss caused by stretching of chains, or (b) each grafted chain folds onto itself to bring its attractive monomers together (only intrachain monomer aggregation) if the entropic loss from interchain aggregation cannot be overcome by the enthalpic gain. For six copolymers of chain length N=24 grafted on a spherical particle of diameter D=4, interchain and intrachain monomer aggregation occurs, and the radius of gyration varies nonmonotonically with increasing blockiness of the monomer sequence. At larger particle diameters the grafted chains transition to purely intrachain monomer aggregation. The radius of gyration varies monotonically with monomer sequence for intrachain monomer aggregation because as the sequence becomes blockier (like monomers are grouped together), the copolymer chain has to fold less compactly to maximize the enthalpically favorable contacts while maintaining high conformational entropy. The radius of gyration of alternating and diblock copolymers scales with chain length N through a power law (1/2) = alphaN(nu) with the prefactor alpha and scaling exponent nu, varying with monomer sequence and monomer-monomer attraction strength.

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.

In a previous paper [Ghysels et al., J. Chem. Phys. 126, 224102 (2007)] the mobile block Hessian (MBH) approach was presented. The method was designed to accurately compute vibrational modes of partially optimized molecular structures. The key concept was the introduction of several blocks of atoms, which can move as rigid bodies with respect to a local, fully optimized subsystem. The choice of the blocks was restricted in the sense that none of them could be connected, and also linear blocks were not taken into consideration. In this paper an extended version of the MBH method is presented that is generally applicable and allows blocks to be adjoined by one or two common atoms. This extension to all possible block partitions of the molecule provides a structural flexibility varying from very rigid to extremely relaxed. The general MBH method is very well suited to study selected normal modes of large macromolecules (such as proteins and polymers) because the number of degrees of freedom can be greatly reduced while still keeping the essential motions of the molecular system. The reduction in the number of degrees of freedom due to the block linkages is imposed here directly using a constraint method, in contrast to restraint methods where stiff harmonic couplings are introduced to restrain the relative motion of the blocks. The computational cost of this constraint method is less than that of an implementation using a restraint method. This is illustrated for the alpha-helix conformation of an alanine-20-polypeptide.

In this paper a Clifford algebra-based method is applied to calculate polymer chain conformations. The approach enables the calculation of the position of an atom in space with the knowledge of the bond length (l), valence angle (theta), and rotation angle (phi) of each of the preceding bonds in the chain. Hence, the set of geometrical parameters {l(i),theta(i),phi(i)} yields all the position coordinates p(i) of the main chain atoms. Moreover, the method allows the calculation of side chain conformations and the computation of rotations of chain segments. With these features it is, in principle, possible to generate conformations of any type of chemical structure. This method is proposed as an alternative for the classical approach by matrix algebra. It is more straightforward and its final symbolic representation considerably simpler than that of matrix algebra. Approaches for realistic modeling by means of incorporation of energetic considerations can be combined with it. This article, however, is entirely focused at showing the suitable mathematical framework on which further developments and applications can be built.

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.

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 n(ij) 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 C(800)H(1602) 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.

The conjugation of an uncharged polymer to DNA fragments makes it possible to separate DNA by free-solution electrophoresis. This end-labeled free-solution electrophoresis method has been shown to successfully separate ssDNA with single monomer resolution up to about 110 bases. It is the aim of this paper to investigate in more detail the coupled hydrodynamic and electrophoretic deformation of the ssDNA-label conjugate at fields below 400 V/cm. Our model is an extension of the theoretical approach originally developed by Stigter and Bustamante [Biophys. J. 75, 1197 (1998)] to investigate the problems of a tethered chain stretching in a hydrodynamic flow and of the electrophoretic stretch of a tethered polyelectrolyte. These two separate models are now used together since the charged DNA is "tethered" to the uncharged polymer (and vice versa), and the resulting self-consistent model is used to predict the deformation and the electrophoretic velocity for the hybrid molecule. Our theoretical and experimental results are in good qualitative agreement.

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.

Although macromolecules such as polymers are in widespread industrial use, pure formulations rarely have precisely the properties new applications demand. Pure polymer is often too brittle and inflexible, necessitating plasticizers to soften or toughen films and bulk polymer materials. In practice, new formulations are developed by extensive trial-and-error methods, as no general molecular explanations exist for the mechanism of plasticization to aid in determining the optimal structure and concentration of plasticizers. Here, through atomistic molecular simulations augmented with advanced sampling techniques, we develop an atomic-level picture of the processes in plasticization by directly calculating free energies that govern the interaction between polymers and small-molecule plasticizers. This work focuses on the influence of two common plasticizer molecules—glycerol and sorbitol—interacting with polyvinyl alcohol (PVA), a frequently used component of polymer films. In particular, we focus on conformational and hydrogen bond structure changes induced in globules of PVA by the plasticizer molecules, with the hypothesis that hydrogen bonding plays a role in the incorporation of these plasticizers into PVA and, thus, in the observed mechanical properties. While we focus on nanoscopic systems, we observe distinct preferences in the conformational free energy that can be connected to the performance of polymer materials at laboratory and industrial scales. This work presents a new molecular perspective from which effective plasticizers can be developed and presents a firm basis from which important analyses of plasticization in complex chemical environments relevant to industry may be developed. [ABSTRACT FROM AUTHOR]