Search results for "Biomolecules"
showing 10 items of 549 documents
Unconventional ordering behavior of semi-flexible polymers in dense brushes under compression
2014
Using a coarse-grained bead-spring model for semi-flexible macromolecules which form a polymer brush, the structure and dynamics of the polymers were investigated, varying the chain stiffness and the grafting density. The anchoring conditions for the grafted chains were chosen such that their first bonds were oriented along the normal to the substrate plane. The compression of such a semi-flexible brush by a planar piston was observed to be a two-stage process: for a small compression the chains were shown to contract by "buckling" deformation whereas for a larger compression the chains exhibited a collective (almost uniform) bending deformation. Thus, the stiff polymer brush underwent a 2n…
Effect of the solvent quality on the structural rearrangement of spherical brushes: coarse-grained models
2012
A coarse-grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is studied for various polymer lengths, grafting densities, and nanoparticle sizes by molecular dynamics simulations, considering variable solvent quality in the framework of an implicit solvent treatment. Below the theta point, the tuning of the temperature strongly influences the coverage of the nanoparticle surface by collapsed single chains or clusters of several chains. The shape and size of the aggregates depend on the number of monomers and surface density of the polymers. Specifically we analyzed the effect of the solvent quality on the density profiles and radius of gyration of the single …
Zero-field NMR of urea : spin-topology engineering by chemical exchange
2021
Well-resolved and information-rich J-spectra are the foundation for chemical detection in zero-field NMR. However, even for relatively small molecules, spectra exhibit complexity, hindering the analysis. To address this problem, we investigate an example biomolecule with a complex J-coupling network─urea, a key metabolite in protein catabolism─and demonstrate ways of simplifying its zero-field spectra by modifying spin topology. This goal is achieved by controlling pH-dependent chemical exchange rates of 1H nuclei and varying the composition of the D2O/H2O mixture used as a solvent. Specifically, we demonstrate that by increasing the proton exchange rate in the [13C,15N2]-urea solution, the…
Pattern-recognising Polymer Adsorption on Structured Surfaces: Gaussian Polymers vs. Freely Jointed Chains
2014
Abstract Selective adsorption of homopolymers is exploited as a model for pattern recognition. To this end the strong adsorption regime of Gaussian polymers adsorbed on a regularly structured surface is investigated for square and triangular lattices within a discrete Edwards model. The equilibrium behaviour of the specific heat, the gyration tensor and the (nematic) bond order tensor are analysed and compared to the properties for adsorbed freely jointed polymer chains.
A fast Monte Carlo algorithm for studying bottle-brush polymers
2011
Obtaining reliable estimates of the statistical properties of complex macromolecules by computer simulation is a task that requires high computational effort as well as the development of highly efficient simulation algorithms. We present here an algorithm combining local moves, the pivot algorithm, and an adjustable simulation lattice box for simulating dilute systems of bottle-brush polymers with a flexible backbone and flexible side chains under good solvent conditions. Applying this algorithm to the bond fluctuation model, very precise estimates of the mean square end-to-end distances and gyration radii of the backbone and side chains are obtained, and the conformational properties of s…
Stochastic dynamics of polymer brushes under shear deformation
1998
The dynamical properties of polymer brushes under shear deformation have been studied by computer simulation. Both the local and the global dynamic properties at various shear rates have been calculated. The distribution of orientational and translational mobilities of the different monomers along the chain have been obtained. It was shown that the local mobility of the brushes changes very slowly with increasing of shear rates up to the largest rates. Increase in grafting density leads to an increasingly step like dependence of the correlation times as a function of shear rate.
Polymer-Polymer Interaction: Consistent Modeling in Terms of Chain Connectivity and Conformational Response
2006
An approach developed for the modeling of polymer solutions is extended to polymer blends. It accounts explicitly for the fact that the segments of a given macromolecule cannot spread out over the entire volume of the system (chain connectivity) and that the space a polymer molecule occupies may change after contact formation between the components of a mixture (conformational response ζ). The validity of the equation obtained for the Flory-Huggins interaction parameter between polymers is tested by means of critical data published for the system PVME/PS. The measured phase diagrams can be modeled equally well by two limiting assumptions concerning the temperature dependence of the conforma…
Polymer droplets on substrates with striped surface domains: molecular dynamics simulations of equilibrium structure and liquid bridge rupture
2005
The structure of a polymer nanodroplet adsorbed on a flat lyophobic substrate chemically decorated with a lyophilic stripe of width 2RD is studied by molecular dynamics simulation of a coarse-grained bead–spring model of short macromolecules (containing N = 20 effective monomers). Varying the stripe width, the strength of the monomer–wall attraction and the temperature, the equilibrium morphology of the resulting droplets is studied and discussed in terms of current phenomenological theories. In the second part, the behaviour of a liquid bridge connecting two such lyophilic stripes a distance L apart is analysed. It is shown that for large enough L such free-standing films are unstable and …
On the thermodynamic treatment of poly(vinylidene fluoride)/polystyrene blend under liquid—liquid phase separation conditions
1995
Abstract This paper deals with experimental and theoretical investigations on the compatibility of binary of polymer blends in solution. The experimental phase boundary of a crystalline polymer such as poly(vinylidene fluoride) with polystyrene (an amorphous polymer) in dimethylformamide as solvent has been determined by size-exclusion chromatography at 25°C. The composition of the coexisting phases has been used to calculate interaction parameters by means of the Flory—Huggins-type function for the free energy of mixing, including composition dependence of the polymer-polymer interaction parameter and a first correction term denoted as ternary interaction parameter. The calculation of thes…
A Unified Theory of Liquid-Liquid Demixing and Polymer Formation Kinetics
2009
Sickle hemoglobin is a natural hemoglobin mutation with a hydrophobic replacement of a charged aminoacid on the molecular surface. This leads to aggregation into rigid helical structures (“polymerization”), the underlying cause of sickle cell disease. It has also been shown that polymerization occurs in close correspondence with the phase transition of liquid-liquid demixing , or with the critically diverging fluctuations of local concentration occurring in its proximity. Due to this correspondence, polymerization kinetics remarkably appear to exhibit, with respect to demixing temperature, the same universal scaling features shown by amplitudes and lifetimes of fluctuations occurring in pro…