Free Energy of Deformation of the Radius of Gyration in Semiflexible Chains

The Effect of Cross-Linking Type on EPDM Elastomer Dynamics and Mechanical Properties: A Molecular Dynamics Simulation Study

The cross-linking structure of the Ethylene-propylene-diene monomer (EPDM) is made up of a number of cross-linking types, including carbon atoms from the main chain or monomer and ether crosslinks formed during degradation. Through molecular dynamic simulations, the contribution of each type of cross-linked structure to the dynamics and mechanical properties of EPDM, the study’s focus, were investigated. Cross-linking between the tertiary carbons of two main chains, cross-linking at the monomer’s unsaturated position, ether cross-linking after oxidation, and other combinations of target cross-linked carbon atoms from different positions, totaling eight types of cross-linked types, were mixed with EPDM free chains in a 1:1 ratio to form eight types of cross-linked EPDMs. These varieties of cross-linked EPDMs were then compared to an uncross-linked EPDM in terms of density, radius of gyration, free volume, mean square displacement, and uniaxial tensile stress-strain curves. It was found that the cross-linking was always proven to have a favorable influence on mechanical characteristics; however, the relaxation inhibition effect varied. The cross-linking between the diene monomer at the C9 position resulted in a more flexible molecular shape and was more than double the free volume of the uncross-linked EPDM, resulting in an improved diffusion ability. The ether cross-linking produced by the oxidation of the side chain cross-linking improved the positive contribution to stiffness and enhanced the inhibitory impact on diffusion properties, whereas the main chain cross-linking had the opposite effect. The research presented in this study leads to a better knowledge of the microscopic aspects underlying EPDM performance.

Compression and Stretching of Single DNA Molecules under Channel Confinement

We study the compression and extension response of single dsDNA (double-stranded DNA) molecules confined in cylindrical channels by means of Monte Carlo simulations. The elastic response of micrometer-sized DNA to the external force acting through the chain ends or through the piston is markedly affected by the size of the channel. The interpretation of the force (f)-displacement (R) functions under quasi-one-dimensional confinement is facilitated by resolving the overall change of displacement ΔR into the confinement contribution ΔR_D and the force contribution ΔR_f. The external stretching of confined DNA results in a characteristic pattern of f-R functions involving their shift to the larger extensions due to the channel-induced pre-stretching ΔR_D. A smooth end-chain compression into loop-like conformations observed in moderately confined DNA can be accounted for by the relationship valid for a Gaussian chain in bulk. In narrow channels, the considerably pre-stretched DNA molecules abruptly buckle on compression by the backfolding into hairpins. On the contrary, the piston compression of DNA is characterized by a gradual reduction of the chain span S and by smooth f-S functions in the whole spatial range from the 3d near to 1d limits. The observed discrepancy between the shape of the f-R and f-S functions from two compression methods can be important for designing nanopiston experiments of compaction and knotting of single DNA in nanochannels.

Force-displacement relations at compression of dsDNA macromolecules

The elasticity of dsDNA molecules is investigated by Monte Carlo simulations based on a coarse-grained model of DNA. The force-displacement (f-r) curves are computed under the constraints of the constant force (Gibbs) or the constant length (Helmholtz) ensemble. Particular attention was paid to the compressional (negative) and weak tensile forces. It was confirmed that simulations using the vector Gibbs ensemble fail to represent the compression behavior of polymers. Simulations using the scalar Gibbs protocol resulted in a qualitatively correct compressional response of DNA provided that the quadratic averages of displacements were employed. Furthermore, a well-known shortcoming of the popular Marko-Siggia relation for DNA elasticity at weak tensile forces is elucidated. Conversely, the function f-r from the simulation at the constant length constraint, as well as the new closed-form expressions, provides a realistic depiction of the DNA elasticity over the wide range of negative and positive forces. Merely a qualitative resemblance of the compression functions f-r predicted by the employed approaches supports the notion that the elastic response of DNA molecules may be greatly affected by the specifics of the experimental setups and the kind of averaging of the measured variable.

Stretching and compression of DNA by external forces under nanochannel confinement

Mechanical deformation of dsDNA molecules inside square nanochannels is investigated using simulations based on a coarse-grained model of DNA. The combined action of confinement and weak external forces is explored in a variety of confinement regimes, including the transition zone relevant to nanofluidic experiments. The computed free energy and force profiles are markedly affected by the channel size. Effective elastic softening of confined DNA molecules relative to the bulk DNA is observed in the channels of intermediate widths. The extension of DNA from its bulk equilibrium length in nanofluidic devices is resolved into contributions from the passive extension due to confinement and from the active stretching induced by force. Potential implications of the very different energy costs computed for the two extension modes (extension by confinement takes much more free energy than stretching by force) for behavior of DNA in nanofluidic chips are indicated.

Density Functional Theory of Polymer Structure and Conformations

We present a density functional approach to quantitatively evaluate the microscopic conformations of polymer chains with consideration of the effects of chain stiffness, polymer concentration, and short chain molecules. For polystyrene (PS), poly(ethylene oxide) (PEO), and poly(methyl methacrylate) (PMMA) melts with low-polymerization degree, as chain length increases, they display different stretching ratios and show non-universal scaling exponents due to their different chain stiffnesses. In good solvent, increase of PS concentration induces the decline of gyration radius. For PS blends containing short (m1=1−100) and long (m=100) chains, the expansion of long chains becomes unobvious once m1 is larger than 40, which is also different to the scaling properties of ideal chain blends.

Photodimerization as an alternative to photocrosslinking of nanoparticles: proof of concept with amphiphilic linear polyoxazoline bearing coumarin unit

The photo-dimerization of the coumarinated inner compartment of the nanoparticles is investigated.