Probability Distribution of the Radius of Gyration of a Flexible Polymer

1967 ◽  
Vol 8 (6) ◽  
pp. 1276-1284 ◽  
Author(s):  
S. R. Coriell ◽  
J. L. Jackson
Keyword(s):  
Probability Distribution ◽  
Radius Of Gyration ◽  
Flexible Polymer

Macromolecular crowding effects in flexible polymer solutions

2018 ◽  
Vol 17 (03) ◽  
pp. 1840006 ◽  
Author(s):  
Bibhab Bandhu Majumdar ◽  
Simon Ebbinghaus ◽  
Matthias Heyden
Keyword(s):  
Monte Carlo ◽  
Intermolecular Interactions ◽  
Finite Size ◽  
Macromolecular Crowding ◽  
Conformational Space ◽  
Intermolecular Potential ◽  
Radius Of Gyration ◽  
Excluded Volume Effects ◽  
Flexible Polymer ◽  
Mcmc Approach

Biological environments are often “crowded” due to high concentrations (300–400[Formula: see text]g/L) of macromolecules. Computational modeling approaches like Molecular Dynamics (MD), rigid-body Brownian Dynamics and Monte Carlo simulations have recently emerged, which allow to study the effects macromolecular crowding at a microscopic level and to provide complementary information to experiments. Here, we use a recently introduced multiple-conformation Monte Carlo (mcMC) approach in order to study the influence of intermolecular interactions on the structural equilibrium of flexible polyethylene glycol (PEG) polymers under self-crowding conditions. The large conformational space accessible to PEG polymers allows us to evaluate the general applicability of the mcMC approach, which describes the intramolecular degrees of freedom by a finite-size ensemble of discrete conformations. Despite the simplicity of the approach, we show that influences of intermolecular interactions on the intramolecular free energy surface can be described qualitatively using mcMC. By varying the magnitude of distinct terms in the intermolecular potential, we can further study the compensating effects of repulsive and nonspecific attractive intermolecular interactions, which favor compact and extended polymer states, respectively. We use our simulation results to derive an analytical model that describes the effects of intermolecular interactions on the stability of PEG polymer conformations as a function of the radius of gyration and the corresponding solvent accessible surface. We use this model to confirm the role of molecular surfaces for attractive interactions that can counteract excluded volume effects. Extrapolation of the model further allows for the analysis of scenarios that are not easily accessible to direct simulations as described here.

Near-Interface Structure and Mobility of Polymeric Chains in Polymer-Based Nanocomposites

2001 ◽  
Vol 710 ◽  
Author(s):  
Catalin R. Picu ◽  
Murat S. Ozmusul
Keyword(s):  
Solid Wall ◽  
Polymer System ◽  
Thick Layer ◽  
Polymer Chains ◽  
Segment Length ◽  
Radius Of Gyration ◽  
Atom Number ◽  
Chain Mobility ◽  
Flexible Polymer ◽  
Increased Strength

ABSTRACTThe effect of a curved solid wall on the conformations of long, flexible polymer chains is studied in a dense polymer system and in the athermal limit by means of lattice Monte Carlo simulations. It is found that the wall does not perturb the atom number density, which is constant throughout the volume of the polymer, however the chain end density is higher at the wall compared to the bulk. The segregation effect decreases with increasing wall curvature. The bonds are preferentially oriented in the direction tangential to the wall over a two-bond thick layer next to the wall. When probing the preferential orientation on the chain segment length scale, the perturbed region has a thickness on the order of the probing metric considered. The chain mobility is evaluated by computing the bead diffusion coefficient in the direction perpendicular and tangential to the curved wall, and as a function of the distance from the interface. The bead mobility is reduced in a two-bond-thick layer in the vicinity of the wall in both the normal and tangential directions, the reduction being more pronounced in the normal direction. The mobility is seen to decrease with increasing wall curvature. The reduction is most pronounced when the particle size becomes smaller than the chain radius of gyration in the bulk, situation in which the average chain surrounds the particle, which hence becomes an effective entanglement site for the chains. This explains in part the increased strength of polymer-based nanocomposites with small fillers.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

The Reactive Formation of Diblock Copolymer at a Polymer/Polymer Interface and its Effect on Interfacial Structure

2000 ◽  
Vol 629 ◽  
Author(s):  
Jonathan S. Schulze ◽  
Timothy P. Lodge ◽  
Christopher W. Macosko
Keyword(s):  
Molecular Weight ◽  
Interfacial Structure ◽  
Root Mean Square Roughness ◽  
Radius Of Gyration ◽  
Interfacial Region ◽  
Force Microscopy ◽  
Amino Terminal ◽  
Polymer Interface ◽  
Atomic Force ◽  
Time Required

ABSTRACTThe reaction of perdeuterated amino-terminal polystyrene (dPS-NH2) with anhydrideterminal poly(methyl methacrylate) (PMMA-anh) at a PS/PMMA interface has been observed with forward recoil spectrometry (FRES). Bilayer samples were constructed by placing thin films of PS containing ∼8.5 wt % dPS-NH2 on a PMMA-anh layer. Significant reaction was observed only after annealing the samples at 174°C for several hours, a time scale at least two orders of magnitude greater than the time required for the dPS-NH2 chains to diffuse through the bulk PS layer. The topography of the interfacial region as copolymer formed was measured using atomic force microscopy (AFM). Roughening of the PS/PMMA interface was observed to varying degrees in all annealed samples. Furthermore, the extent of this roughening was found to depend on the PS matrix molecular weight. Reaction in the samples with a high molecular weight PS matrix resulted in a root mean square roughness approximately equal to the radius of gyration Rg of the copolymer. However, approximately twice as much roughening was observed in the low molecular weight PS matrix. This study reveals how the molecular weight of one of the phases can affect the rate of reaction at a polymer/polymer interface.

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