The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded polymers, we model polymers as penetrable ellipsoids, whose shape fluctuations are governed by the statistics of self-avoiding walks, appropriate for a polymer in a good solvent. Within this coarse-grained model, we perform Monte Carlo simulations of mixtures of polymers and hard-nanosphere crowders, including trial changes in polymer size and shape. Penetration of polymers by crowders is incorporated via a free energy cost predicted by polymer field theory. To analyze the impact of crowding on polymer conformations in different solvents, we compute average polymer shape distributions, radius of gyration, volume, and asphericity over ranges of polymer-to-crowder size ratio and crowder volume fraction. The simulation results are accurately predicted by a free-volume theory of polymer crowding. Comparison of results for polymers in good and theta solvents indicates that excluded-volume interactions between polymer segments significantly affect crowding, especially in the limit of crowders much smaller than polymers. Our approach may help to motivate future experimental studies of polymers in crowded environments, with possible relevance for drug delivery and gene therapy.
Conformations of a single semiflexible polymer chain dissolved in a low molecular weight liquid crystalline solvents (nematogens) are examined by using a mean field theory. We takes into account a stiffness and partial orientational ordering of the polymer. As a result of an anisotropic coupling between the polymer and nematogen, we predict a discontinuous (or continuous) phase transition from a condensed-rodlike conformation to a swollen-one of the polymer chain, depending on the stiffness of the polymer. We also discuss the effects of the nematic interaction between polymer segments.
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the poly…
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the density of crowders. The conformations of the polymer under good solvent conditions are largely independent of crowder density, even when the polymer is strongly confined. However, for poor solvents and attractive walls, the polymer shows a transition between an adsorbed extended state to a globular conformation on the surface as a function of crowder parti…
We analyze the universal size characteristics of flexible ring polymers in solutions in presence of structural obstacles (impurities) in d dimensions. One encounters such situations when considering polymers in gels, colloidal solutions, intra- and extracellular environments. A special case of extended impurities correlated on large distances r according to a power law \sim r^{-a} is considered. Applying the direct polymer renormalization scheme, we evaluate the estimates for averaged gyration radius $\langle R_{g\,{\rm ring}} \rangle$ and spanning radius $\langle R_{1/2\,{\rm ring}} \rangle$ …
We demonstrate in this paper the influence of solvent quality on the structure of the semi-dilute solution of a hydrophobic polyelectrolyte, partially sulfonated Poly-Styrene Sulfonate. Two solvents are used: (i) one mixture of water and an organic solvent: THF, which is also slightly polar; (ii) DMSO, a polar organic solvent. In case (i), it is shown by SAXS study that the structure - namely the scattering from all chains, characterised by a maximum ("polyelectrolyte peak"), of the aqueous hydrophobic polyelectrolyte solutions (PSS) depends on the solvent quality through the added amount of o…
We study conformational properties of diluted dumbbell polymers which consist of two rings that are attached to both ends of a linear spacer segment by using analytical methods of field theory and bead-spring coarse-grained molecular dynamics simulations. We investigate the influence of the relative length of the spacer segment to the length of side rings on the shape and the relative size of dumbbells as compared to linear polymers of equal mass. We find that dumbbells with short spacers are much more compact than linear polymers. Oppositely, we observe that the influence of side rings on the…
Small angle X-ray scattering (SAXS) studies in poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) with varying conjugation, and polyethylene dioxythiophene complexed with polystyrene sulfonate (PEDOT-PSS) in different solvents have shown the important role of pi-electron conjugation and solvent-chain interactions in controlling the chain conformation and assembly. In MEH-PPV, by increasing the extent of conjugation from 30 to 100 %, the persistence length (l_p) increases from 20 to 66 Angstrom. Moreover, a pronounced second peak in the pair distribution function has been ob…
Using molecular dynamics simulations we study the behavior of a dilute solution of strongly charged polyelectrolytes in poor solvents, where we take counterions explicitly into account. We focus on the chain conformational properties under conditions where chain-chain interactions can be neglected, but the counterion concentration remains finite. We investigate the conformations with regard to the parameters chain length, Coulomb interaction strength, and solvent quality, and explore in which regime the competition between short range hydrophobic interactions and long range Coulomb interaction…
We have used neutron scattering to investigate the influence of concentration on the conformation of a star polymer. By varying the contrast between the solvent and isotopically labeled stars, we obtain the distributions of polymer and solvent within a star polymer from analysis of scattering data. A correlation between the local desolvation and the inward folding of star branches is discovered. From the perspective of thermodynamics, we find an analogy between the mechanism of polymer localization driven by solvent depletion and that of the hydrophobic collapse of polymers in solutions.
TiO2 nanoparticles (NPs) are attracting materials for biomedical applications, provided that they are coated with polymers to improve solubility, dispersion and biocompatibility. Conformation, coverage density and solvent effects largely influence their functionality and stability. In this work, we use atomistic molecular dynamics simulations to study polyethylene glycol (PEG) grafting to highly curved TiO2 NPs (2-3 nm) in different solvents. We compare the coating polymer conformations on NPs with those on (101) flat surfaces. In water, the transition from mushroom to brush conformation start…
We study the behavior of a flexible polymer chain in the presence of a low-molecular weight solvent in the vicinity of a liquid-gas critical point within the framework of a self-consistent field theory. The total free energy of the dilute polymer solution is expressed as a function of the radius of gyration of the polymer and the average solvent number density within the gyration volume at the level of the mean-field approximation. Varying the strength of attraction between polymer and solvent we show that two qualitatively different regimes occur at the liquid-gas critical point. In case of w…
An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. To investigate these effects theoretically, we study tethered chains under tension with Wang-Landau simulations of a bond-fluctuation lattice model. Applying our model to pulling experiments on biological molecules we obtain a good description…
Understanding the atomic level interactions and the resulting structural characteristics is required for developing beta-cyclodextrin ($β$CD) derivatives for pharmaceutical and other applications. The effect of four different solvents on the structures of the native $β$CD and its hydrophilic (methylated $β$CD; ME$β$CD and hydroxypropyl $β$CD; HP$β$CD) and hydrophobic derivatives (ethylated $β$CD; ET$β$CD) were explored using molecular dynamics (MD) simulations and solvation free energy calculations. The native $β$CD, 2-ME$β$CD, 6-ME$β$CD, 2,6-DM$β$CD, 2,3,6-TM$β$CD, 6-HP$β$CD, 2,6-HP$β$CD and …
We introduce and study the behavior of a tethered membrane of non-zero thickness embedded in three dimensions subject to an effective self-attraction induced by hydrophobicity arising from the tendency to minimize the area exposed to a solvent. The phase behavior and the nature of the folded conformations are found to be quite distinct in the small and large solvent size regimes. We demonstrate spontaneous symmetry-breaking with the membrane folding along a preferential axis, when the solvent molecules are small compared to the membrane thickness. For large solvent molecule size, a local crink…
The conformational behavior of a polymer in a critical binary solvent confined in a porous medium is studied. The size of the polymer in bulk, which is mainly governed by the correlation length of the solvent density fluctuations, depends on the proximity to the critical point of the binary mixture. We find that in contrast to the bulk behavior, the conformational properties of the polymer in a porous medium depends strongly on the pore size. The latter controls the correlation length of the solvent density fluctuations and thus determines the polymer size.
Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to important insights into these processes. Although techniques such as the indirect umbrella sampling (INDUS) method (Patel et al. J. Stat. Phys. 2011, 145, 265-275) can be used to characterize solvent fluctuations in static observation volumes of various sizes and shapes, characterizing how the solvent mediates inherently dynamic processes, such as self-assembl…
During the last decade, the laser trapping technique has been actively applied to elucidate the property of macromolecules, DNA, RNA, cytoskeleton fibres, etc. Due to the inherent difficulty in the direct trapping of single molecules at approximately 300 K, most of the current studies on laser trapping utilize the experimental technique to grasp microbeads that are attached to a single macromolecule, instead of using direct trapping. A few studies have demonstrated the applicability of laser trapping for highly packed compact DNA under a `poor' solvent condition without any beads. The present …
We present simulations on charged polymers in poor solvent. First we investigate in detail the dilute concentration range with and without imposed extension constraints. The resulting necklace polymer conformations are analyzed in detail. We find strong fluctuations in the number of pearls and their sizes leading only to small signatures in the form factor and the force-extension relation. The scaling of the peak in the structure factor with the monomer density shows a pertinent different behavior from good solvent chains.
The radius of gyration of a polymer chain immersed in a low molecular weight solvent is known to vary monotonically with the solvent quality. Here, we consider the behavior of a chain immersed in a high molecular weight solvent (polymer melt). Unsurprisingly, we find that, as the incompatibility between the chain and the polymer melt is increased, the two limiting conformations of the chain are the ideal random coil (R = aN^1/2) and the dense globule (R = aN^1/3). We show, however, that between these two limits the radius of gyration of the chain presents a hysteretic behavior .
Extensive coarse grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowded densities, the polymer predominantly shows three phases as a function of both intra polymer and polymer-crowder interactions: (1) weak intra polymer and weak polymer-crowder attractive interactions induce extended or coil polymer conformations (phase E) (2) strong intra polymer and relatively weak polymer-crowder attractive interactions induce collapsed or globular conformations (phase CI…
Smart polymers are a modern class of polymeric materials that often exhibit unpredictable behavior in mixtures of solvents. One such phenomenon is co-non-solvency. Co-non-solvency occurs when two (perfectly) miscible and competing good solvents, for a given polymer, are mixed together. As a result, the same polymer collapses into a compact globule within intermediate mixing ratios. More interestingly, polymer collapses when the solvent quality remains good and even gets increasingly better by the addition of the better cosolvent. This is a puzzling phenomenon that is driven by strong local con…
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and exten…
Confinement effects on protein stability in a freezing water environment
University of Pamplona（潘普洛纳大学）；Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP)（液体与生物系统物理研究所 (CONICET-UNLP)）；Universidad Nacional Arturo Jauretche（阿图罗·豪雷切国立大学）；Universidad Nacional de La Plata（拉普拉塔国立大学）；Universidad Tecnológica Nacional, Facultad Regional La Plata（国家技术大学，拉普拉塔地区学院）
As first explained by the classic Asakura-Oosawa (AO) model, effective attractive forces between colloidal particles induced by depletion of nonadsorbing polymers can drive demixing of colloid-polymer mixtures into colloid-rich and colloid-poor phases, with practical relevance for purification of water, stability of foods and pharmaceuticals, and macromolecular crowding in biological cells. By idealizing polymer coils as effective penetrable spheres, the AO model qualitatively captures the influence of polymer depletion on thermodynamic phase behavior of colloidal suspensions. In previous work…
We have studied the conformational and scaling behaviors of a flexible dendrimer immersed in athermal or good solvents. A self-consistent field theory combined with a pre-averaged excluded volume potential representing the two-body short-ranged interaction between the segments, was adopted to calculate the density profile of various generations and branch points thoroughly. Our calculation results support the "dense-core" model. We find the conformation of the dendrimer is strongly stretched in the dense central region, but much weakly stretched in the outer region where the segment density pr…
A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or for a biomembrane with active protein inclusions. Our numerical simulations demonstrate that non-equilibrium conformational activity of particles can strongly affect diffusion and structural relaxation: while a passive colloid behaves as a glass, it gets progressively fluidized when the activity is turned on. Qualitatively, this agrees with experimental resu…
Using molecular dynamics and thermodynamic integration, we report on the solvation process in water and in cyclohexane of seven polypeptides (GLY, ALA, ILE, ASN, LYS, ARG, GLU). The polypeptides are selected to cover the full hydrophobic scale while varying their chain length from tri- to undeca-homopeptides provide indications on possible non-additivity effects as well as the role of the peptide backbone in the overall stability of the polypeptides. The use of different solvents and different polypeptides allows us to investigate the relation between solvent quality -- the capacity of a given…
Understanding the role of self-propulsion on the conformational properties of active filamentous objects has relevance in biology. In this context, we consider a flexible bead-spring model polymer for which along with both attractive and repulsive interactions among the non-bonded monomers, activity for each bead works along its intrinsic direction of self-propulsion. We study its kinetics in the overdamped limit, following a quench from good to poor solvent condition. We observe that with low activities, though the kinetic pathways remain similar, the scaling exponent for the relaxation time …
We present an application of Flory-type self-consistent field theory of the flexible polymer chain dissolved in the binary mixture of solvents to theoretical description of co-nonsolvency. We show that our theoretical predictions are in good quantitative agreement with the recently published MD simulation results for the conformational behavior of a Lennard-Jones flexible chain in a binary mixture of the Lennard-Jones fluids. We show that our theory is able to describe co-nonsolvency suppression through pressure enhancement to extremely high values recently discovered in experiment and reprodu…
Conformational phases of a semiflexible off-lattice homopolymer model near an attractive substrate are investigated by means of multicanonical computer simulations. In our polymer-substrate model, nonbonded pairs of monomers as well as monomers and the substrate interact via attractive van der Waals forces. To characterize conformational phases of this hybrid system, we analyze thermal fluctuations of energetic and structural quantities, as well as adequate docking parameters. Introducing a solvent parameter related to the strength of the surface attraction, we construct and discuss the solubi…
Theoretical considerations based on chain connectivity and conformational variability of polymers have lead to an uncomplicated relation for the dependence of the Flory-Huggins interaction parameter, chi, on the volume fraction of the polymer, phi, and on its number of segments, N. The validity of this expression is being tested extensively by means of vapor pressure measurements and inverse gas chromatography (complemented by osmotic and light scattering data from literature) for solutions of poly(dimethylsiloxane) in the thermodynamically vastly different solvents n-octane (n-C8), toluene (T…
Understanding the hydrodynamic alignment of colloidal rods in polymer solutions is pivotal for manufacturing structurally ordered materials. How polymer crowding influences the flow-induced alignment of suspended colloidal rods remains unclear when rods and polymers share similar length-scales. We tackle this problem by analyzing the alignment of colloidal rods suspended in crowded polymer solutions, and comparing against the case where crowding is provided by additional colloidal rods in a pure solvent. We find that the polymer dynamics govern the onset of shear-induced alignment of colloidal…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three regions: a classical MD region, a continuum domain where the dynamical equations are solved by standard CFD methods, and an overlap domain where transport information from the other two domains is exchanged. The exchange of information in the overlap region ensures that momentum, energy and mass are conserved. The validity of the hybrid code is demonstrated by stu…
In this paper, we show how the method of field theoretical renormalization group may be used to analyze universal shape properties of long polymer chains in porous environment. So far such analytical calculations were primarily focussed on the scaling exponents that govern conformational properties of polymer macromolecules. However, there are other observables that along with the scaling exponents are universal (i.e. independent of the chemical structure of macromolecules and of the solvent) and may be analyzed within the renormalization group approach. Here, we address the question of shape …
Using the language of the Flory chi parameter, we develop a theory that unifies the treatment of the single-chain structure and the solution thermodynamics of polymers in poor solvents. The structure of a globule and its melting thermodynamics is examined using the self-consistent filed theory. Our results show that the chain conformation involves three states prior to the globule-to-coil transition: the fully-collapsed globule, the swollen globule and the molten globule, which are distinguished by the core density and the interfacial thickness. By examining the chain-length dependence of the …
Force induced stretching of polymers is important in a variety of contexts. We have used theory and simulations to describe the response of homopolymers, with $N$ monomers, to force ($f$) in good and poor solvents. In good solvents and for {sufficiently large} $N$ we show, in accord with scaling predictions, that the mean extension along the $f$ axis $<Z>\sim f$ for small $f$, and $<Z>\sim f^{2/3}$ (the Pincus regime) for intermediate values of $f$. The theoretical predictions for $\la Z\ra$ as a function of $f$ are in excellent agreement with simulations for N=100 and 1600. However, even with…
We present an off-lattice statistical model of a single polymer chain in mixed solvent media. Taking into account a polymer conformational entropy, renormalization of solvent composition near the polymer backbone, the universal intermolecular excluded volume and Van-der-Waals interactions within the self-consistent field theory the reentrant coil-to-globule-to-coil transition (co-nonsolvency) has been described in this paper. For convenience we split the system volume in two parts: the volume occupied by the polymer chain and the volume of bulk solution. Considering the equilibrium between two…
In the present work, we study the equilibrium conformations of linear polyelectrolytes tethered onto a spherical, oppositely charged core in equilibrium with an ionic reservoir of fixed concentration. Particular focus is placed on the situation of stretched chains, where the monomer concentration is known to display an inverse square-law decay far away from the spherical surface, which is then further extrapolated all the way down to the grafting core. While the equilibrium distributions of mobile ions are computed in the framework of a classical Density Functional Theory (cDFT) that incorpora…
We use molecular dynamics simulations to study the swelling of randomly end-cross-linked polymer networks in good solvent conditions. We find that the equilibrium degree of swelling saturates at Q_eq = N_e**(3/5) for mean strand lengths N_s exceeding the melt entanglement length N_e. The internal structure of the network strands in the swollen state is characterized by a new exponent nu=0.72. Our findings are in contradiction to de Gennes' c*-theorem, which predicts Q_eq proportional N_s**(4/5) and nu=0.588. We present a simple Flory argument for a self-similar structure of mutually interpenet…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40 effective monomers. By variation of the solvent quality and the grafting density $σ$ with which side chains are grafted onto the flexible backbone, we study for backbone lengths of up to $N_b=100$ the crossover from the brush/coil regime to the dense collapsed state. At lower temperatures, where collapsed chains with a constant monomer density are observed, the…
We present a set of molecular dynamics (MD) simulations of strongly charged, flexible polyelectrolyte chains under poor solvent conditions in a salt free solution. Structural properties of the chains and of the solutions are reported. By varying the polymer density and the electrostatic interaction strength we study the crossover from a dominating electrostatic interaction to the regime of strong screening, where the hydrophobic interactions dominate. During the crossover a multitude of structures is observed. In the limit of low polymer density strongly stretched, necklace like conformations …
The solvent quality determines the collapsed or the expanded state of a polymer. For example, a polymer dissolved in a poor solvent collapses, whereas in a good solvent it opens up. While this standard understanding is generally valid, there are examples when a polymer collapses even in a mixture of two good solvents. This phenomenon, commonly known as co-non-solvency, is usually associated with smart polymers. Moreover, recent experiments have shown that the elastin-like polypeptides (ELPs) show co-non-solvency behavior in aqueous-ethanol mixtures. In this study, we investigate the phase beha…
We investigate the driven polymer translocation through a nanometer-scale pore in the presence and absence of hydrodynamics both in good and bad solvent. We present our results on tension propagating along the polymer segment on the cis-side that is measured for the first time using our method that works also in the presence of hydrodynamics. For simulations we use stochastic rotation dynamics, also called multi-particle collision dynamics. We find that in the good solvent the tension propagates very similarly whether hydrodynamics is included or not. Only the tensed segment is by a constant f…
A fundamental paradigm in polymer physics is that macromolecular conformations in equilibrium can be described by universal scaling laws, being key for structure, dynamics, and function of soft (biological) matter and in the materials sciences. Here, we reveal that during diffusion-influenced, nonequilibrium chain-growth polymerization, scaling laws change qualitatively, in particular, the growing polymers exhibit a surprising self-avoiding walk (SAW) behavior in poor and theta-solvents. Our analysis, based on monomer-resolved reaction-diffusion computer simulations, demonstrates that this phe…
We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two dimensional system. Specifically, we analyse the polymer looping properties versus the SPP activity and investigate how the presence of the active particles alters the chain conformational statistics. We find that SPPs tend to extend flexible polymer chains while they rather compactify stiffer semiflexible polymers, in agreement with previous results. Here we show that larger activities of SPPs yield a higher effective temperature of the bath and thus facilita…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in terms of individual properties of monomers, such as the exposure to the solvent and the steric factor.
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated α-helices. However all simulations to date have obtained a qualitatively opposite result within the experimen- tal pressure range. We show that using a protein force field (Amber03w) parametrized in conjunction with an accurate water model (TIP4P/2005) recovers the correct pressure- dependence and an overall stability diagram for helix formation similar to that from experi- ment; on the other hand, we confirm that using TIP3P water resu…
