– We discuss the stretching of tethered chains subject to a shear flow. Fluorescence microscopy measurements of the extension of sheared tethered DNA, “model polymers”, of various lengths are presented. The tethered chains approach full extension as the flow rate is increased, but very slowly. We show that a general theory to understand the large deformation of any sheared tethered chain must i...

Single-molecule experiments in which force is applied to DNA or RNAmolecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer force-extension behavior to calibrate the experiments; typically the experiments use the worm-like chain (WLC) theory for double-stranded DNA and RNA. This theory agrees w...

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quanti...

Secretory immunoglobulin (Ig) A is a decameric Ig composed of four alpha-heavy chains, four light chains, a joining (J) chain, and a secretory component (SC). The heavy and light chains form two tetrameric Ig molecules that are joined by the J chain and associate with the SC. Expression of a secretory monoclonal antibody in tobacco (Nicotiana tabacum) has been described: this molecule (secretor...

We used an automated Langmuir-Pockels surface balance to characterize the air-water interfacial properties of cholesterol (CH) and its derivatives with hydrophilic OH and F substitutions at isologous sites on the sterol body or side chain. We studied 6-fluorocholesterol, 25-fluorocholesterol, 25,26,26,26,27,27,27-heptafluorocholesterol, 7alpha-hydroxycholesterol, 7beta-hydroxycholesterol, 25-hy...

The derivation of kinetic equations for the oxidation processes by free-radical nonbranched-chain mechanism is shown. This based on proposed reaction scheme initiated addition free radicals to multiple bond molecular oxygen includes peroxyl radical molecule form tetraoxyl radical. competes with chain propagation reactions through a reactive evolution stage in this involves few radicals, one whi...

results our study showed that there were no statistically significant differences in the allele and genotype frequencies of -1661 a/g snp between patients with sle and healthy controls (p > 0.05). conclusions in conclusion, we found no association between snp-1661 a/g of the ctla-4 promoter region and susceptibility to sle in our population. objectives to evaluate the potential influences of co...

in this study, polyaniline molecule (emeraldine base) is modeled as a molecular wire and the effects of the metal/molecule coupling strength and the molecule length on the current-voltage (i-v) characteristics are numerically investigated. using a tight-binding hamiltonian model, the methods based on non-equilibrium green’s function theory, landauer formalism and newns-anderson model, our calcu...

Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which in turn leads to more facile chain rupture under tensile loading. Using firstprinciples molecular dynamics calculations we describe the dynamical evolution of the radicals that form after chain rupture of a single knotted alkane molecule in their very early stages of life. They are able to...

The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in many different conditions have been investigated. Here, we characterize the shape and orientational properties of a polymer chain under tension, a physical con...