Conformational Properties Of Polymers Research Articles

Conformational Properties of Polymers at Droplet Interfaces as Model Systems for Disordered Proteins.

Polymer models serve as useful tools for studying the formation and physical properties of biomolecular condensates. In recent years, the interface dividing the dense and dilute phases of condensates has been discovered to be closely related to their functionality, but the conformational preferences of the constituent proteins remain unclear. To elucidate this, we perform molecular simulations of a droplet formed by phase separation of homopolymers as a surrogate model for the prion-like low-complexity domains. By systematically analyzing the polymer conformations at different locations in the droplet, we find that the chains become compact at the droplet interface compared with the droplet interior. Further, segmental analysis revealed that the end sections of the chains are enriched at the interface to maximize conformational entropy and are more expanded than the middle sections of the chains. We find that the majority of chain segments lie tangential to the droplet surface, and only the chain ends tend to align perpendicular to the interface. These trends also hold for the natural proteins FUS LC and LAF-1 RGG, which exhibit more compact chain conformations at the interface compared to the droplet interior. Our findings provide important insights into the interfacial properties of biomolecular condensates and highlight the value of using simple polymer physics models to understand the underlying mechanisms.

Conformational and Dynamic Properties of Poly(ethylene oxide) in an Ionic Liquid: Development and Implementation of a First-Principles Force Field.

The conformational properties of polymers in ionic liquids are of fundamental interest but not well understood. Atomistic and coarse-grained molecular models predict qualitatively different results for the scaling of chain size with molecular weight, and experiments on dilute solutions are not available. In this work, we develop a first-principles force field for poly(ethylene oxide) (PEO) in the ionic liquid 1-butyl 3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) using symmetry adapted perturbation theory (SAPT). At temperatures above 400 K, simulations employing both the SAPT and OPLS-AA force fields predict that PEO displays ideal chain behavior, in contrast to previous simulations at lower temperature. We therefore argue that the system shows a transition from extended to more compact configurations as the temperature is increased from room temperature to the experimental lower critical solution temperature. Although polarization is shown to be important, its implicit inclusion in the OPLS-AA force is sufficient to describe the structure and energetics of the mixture. The simulations emphasize the difference between ionic liquids from typical solvents for polymers.

Conformational Properties of a Polymer in an Ionic Liquid: Computer Simulations and Integral Equation Theory of a Coarse-Grained Model.

We study the conformational properties of polymers in room temperature ionic liquids using theory and simulations of a coarse-grained model. Atomistic simulations have shown that single poly(ethylene oxide) (PEO) molecules in the ionic liquid 1-butyl 3-methyl imidazolium tetrafluoroborate ([BMIM][BF4]) are expanded at room temperature (i.e., the radius of gyration, Rg), scales with molecular weight, Mw, as Rg ∼ Mw(0.9), instead of the expected self-avoiding walk behavior. The simulations were restricted to fairly short chains, however, which might not be in the true scaling regime. In this work, we investigate a coarse-grained model for the behavior of PEO in [BMIM][BF4]. We use existing force fields for PEO and [BMIM][BF4] and Lorentz–Berthelot mixing rules for the cross interactions. The coarse-grained model predicts that PEO collapses in the ionic liquid. We also present an integral equation theory for the structure of the ionic liquid and the conformation properties of the polymer. The theory is in excellent agreement with the simulation results. We conclude that the properties of polymers in ionic liquids are unusually sensitive to the details of the intermolecular interactions. The integral equation theory is sufficiently accurate to be a useful guide to computational work.

Conformational Properties of Polymers Near a Fractal Surface

Abstract The conformational properties of flexible polymer macromolecules grafted to an attractive partially penetrable surface with fractal dimension d pc s =91/49 are studied. Employing computer simulations based on the prunedenriched Rosenbluth chain-growth method, estimates for the surface crossover exponent and adsorption transition temperature are found. Our results quantitatively reveal the slowing down of the adsorption process caused by the fractal self-similar structure of the underlying substrate.

Conformational properties of compact polymers

Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact conformations on a cubic L x L x L lattice with different occupancy fractions by modifying a recently proposed algorithm. The system sizes studied extend up to N=256,000 monomers, going well beyond the limits of older publications on compact polymers. We analyze several conformational properties of these polymers, including segment correlations and screening of excluded volume. Most importantly we propose a scaling law for the end-to-end distance distribution and analyze the moments of this distribution. It shows universality with respect to different occupancy fractions, i.e., system densities. We further analyze the distance distribution between intrachain segments, which turns out to be of great importance for biological experiments. We apply these new findings to the problem of chromatin folding inside interphase nuclei and show that--although chromatin is in a compacted state--the classical theory of compact polymers does not explain recent experimental results.

Multiscale Modeling of Poly(ethylene oxide)-Poly(propylene oxide)-Poly(ethylene oxide) Triblock Copolymer Micelles in Aqueous Solution.

We present a multiscale modeling approach for simulation of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymer micelles in aqueous solution. We rely on systematic elimination of computationally expensive degrees of freedom yet retain implicitly their influence on the remaining degrees freedom in a coarser-grained model. Quantum chemistry (QC) calculations, atomistic explicit solvent (AES) molecular dynamics (MD) simulations, and coarse-grained implicit solvent (CGIS) simulations have been applied to investigate physical properties of these important self-assembling triblock copolymers. High-level QC calculations have been used to parametrize classical atomistic force fields that implicitly take into account and reproduce the important energetic and structural features due to correlations of electronic degrees of freedom. AES MD simulations utilizing the QC-based force fields have been used to provide structural and conformational properties of polymers in aqueous solution which were subsequently used for parametrization of the CGIS model using the Inverted Boltzmann method. The CGIS simulations were then employed to investigate structural properties of two PEO-PPO-PEO micelles (EO13-PO30-EO13 and EO99-PO65-EO99 also known as Pluronic L64 and F127, respectively) in aqueous solution.

Designing generalized statistical ensembles for numerical simulations of biopolymers

Conformational properties of polymers, such as average dihedral angles or molecular alpha-helicity, display a rather weak dependence on the detailed arrangement of the elementary constituents (atoms). We propose a computer simulation method to explore the polymer phase space using a variant of the standard multicanonical method, in which the density of states associated to suitably chosen configurational variables is considered in place of the standard energy density of states. This configurational density of states is used in the Metropolis acceptance/rejection test when configurations are generated with the help of a hybrid Monte Carlo algorithm. The resulting configurational probability distribution is then modulated by exponential factors derived from the general principle of the maximal constrained entropy by requiring that certain average configurational quantities take preassigned (possibly temperature dependent) values. Thermal averages of other configurational quantities can be computed by using the probability distributions obtained in this way. Moments of the energy distribution require an extra canonical sampling of the system phase space at the desired temperature, in order to locally thermalize the configurational degrees of freedom. As an application of these ideas we present the study of the structural properties of two simple models: a bead-and-spring model of polyethylene with independent hindered torsions and an all-atom model of alanine and glycine oligomers with 12 amino acids in vacuum.

Nanofiltration of NaCl solutions using a SPPO membrane (BQ01) Part 1. Membrane characterization and separation mechanisms

Results from an experimental investigation of BQ01 nanofiltration (NF) are reported in this paper aiming at delineating the role of process parameters on BQ01 performances. The data highlight the specific behavior of BQ01 membranes in response to solute type and to variations in solution concentration. Variations in permeability and separation factors due to the presence of electrolytes are recorded. It is demonstrated that the concentration polarization cannot explain the observed variations. To elucidate the mechanisms related to this particular membrane, another approach based on conformational properties of polymer coating (sulfonated polyphenylene oxide, SPPO) is proposed and discussed in relation with characterization results. The hypothesis about mechanisms that are developed in this part will be confronted to a series of NF experiments under the same operating conditions but under electric field (ENF) in part 2 of this study.