Search results for "Biomolecule"
showing 10 items of 666 documents
Conformations and orientational ordering of semiflexible polymers in spherical confinement.
2017
Semiflexible polymers in lyotropic solution confined inside spherical nanoscopic “containers” with repulsive walls are studied by molecular dynamics simulations and density functional theory, as a first step to model confinement effects on stiff polymers inside of miniemulsions, vesicles, and cells. It is shown that the depletion effects caused by the monomer-wall repulsion depend distinctly on the radius R of the sphere. Further, nontrivial orientational effects occur when R, the persistence length ℓp, and the contour length L of the polymers are of similar magnitude. At intermediate densities, a “shell” of wall-attached chains is forming, such that the monomers belonging to those chains a…
Monte Carlo Simulations of Semi-Flexible Polymers
2005
We present Monte Carlo simulations on the phase behavior of semiflexible macromolecules. For a single chain this question is of biophysical interest given the fact that long and stiff DNA chains are typically folded up into very tight compartments. So one can ask the question how the state diagram of a semiflexible chain differs from the coilglobule behavior of a flexible macromolecule. Another effect connected with rigidity of the chains is their tendency to aggregate and form nematically ordered structures. As a consequence one has two competing phase transitions: a gas-liquid and an isotropic-nematic transition potentially giving rise to a complicated phase diagram.
Persistence Length of Cylindrical Brush Molecules Measured by Atomic Force Microscopy
2006
Mechanical properties of single cylindrical polymer brushes with polyisopropylacrylamide (PNIPAM) side chains deposited on mica were probed by atomic force microscopy. Visualization and stretching of individual molecules in aqueous solution clearly reveal the semiflexible nature of the cylindrical macromolecules. Imaging of the brushes on mica and inferring lp from a 〈R2〉 vs L plot results in an average persistence length of lp = 29 ± 3 nm, assuming the chains adopt their equilibrium conformation on the surface. Stretching experiments suggest that an exact determination of the persistence length using force extension curves is impeded by the contribution of the side-chain elasticity. Modeli…
Ejection of a Polymer Chain from a Nanopore: Theory and Computer Experiment
2010
We consider the ejection dynamics of a flexible polymer chain out of confined environment. This situation arises in different physical contexts, including a flexible synthetic polymer partially confined in a nanopore and a viral genome partially ejected from its capsid. We describe the chain release from confinement both analytically and by means of dynamic Monte Carlo simulation. We find two distinct regimes of ejection dynamics depending on whether the chain is fully or partially confined. Partially confined chains are ejected from a pore of length L and diameter D after a typical time τ ∝ L2D5/3, regardless of their contour length N. The process is driven by a constant force f ≈ 5kBT/D a…
A 18F-labeled dibenzocyclooctyne (DBCO) derivative for copper-free click labeling of biomolecules
2016
The new prosthetic group 18F-TEG-DBCO (dibenzocyclooctyne) can be prepared within a total reaction time of 60 min including purification with an overall yield (n.d.c.) of 34 ± 5%. Copper-free click cycloadditions with an azido-cRGD, a folate-azide and two α-MSH analogue azido-peptides resulted in very high RCYs and fast reaction kinetics.
Probing the thermal stability and the decomposition mechanism of a magnesium-fullerene polymer via X-ray Raman spectroscopy, X-ray diffraction and mo…
2016
International audience; We report the microscopic view of the thermal structural stability of the magnesium intercalated fullerene polymer Mg2C60. With the application of X-ray Raman spectroscopy and X-ray diffraction, we study in detail the decomposition pathways of the polymer system upon annealing at temperatures between 300 and 700 degrees C. We show that there are at least two energy scales involved in the decomposition reaction. Intermolecular carbon bonds, which are responsible for the formation of a 2D fullerene polymer, are broken with a relatively modest thermal energy, while the long-range order of the original polymer remains intact. With an increased thermal energy, the crystal…
Sugar-induced stabilization of the monoolein Pn3m bicontinuous cubic phase during dehydration
2001
To explore the molecular mechanism of the protective function of sugars on cubic lipidic systems, the mesomorphic properties of the monoolein-water system, dehydrated in the presence of a series of sugars, have been studied by osmotic stress experiments. Two bicontinuous inverse cubic structures $(Pn3m$ and $\mathrm{Ia}3d)$ and a lamellar ${L}_{\ensuremath{\alpha}}$ phase form under dehydration in pure water. In sugar solutions, the $\mathrm{Pn}3m$ phase shows an extraordinary stability: as a function of sugar concentration, the lattice parameter decreases to very low values, but no phase transitions occur. Instead, the $\mathrm{Pn}3m$ to $\mathrm{Ia}3d$ phase transition is obtained by equi…
Two-state protein-like folding of a homopolymer chain
2010
Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. Here we study an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple flexible homopolymer. Wang-Landau sampling is used to construct the 1D density of states for square-well chains of length 128. Analysis within both the micro-canonical and canonical ensembles shows that, for a chain with sufficiently short-range interactions, the usual polymer collapse transition is preempted by a direct freezing or "folding" transition. A 2D free-energy landscape, built via subsequent multi-canonical sampling, reveals a dominant folding …
Semiflexible Polymers Interacting with Planar Surfaces: Weak versus Strong Adsorption
2020
Semiflexible polymers bound to planar substrates by a short-range surface potential are studied by Molecular Dynamics simulations to clarify the extent to which these chain molecules can be considered as strictly two-dimensional. Applying a coarse-grained bead-spring model, the chain length N and stiffness &kappa
Transitions of tethered chain molecules under tension
2014
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 of experimental data in the intermediate force range, where universal features dominate and finite…