Search results for "Biomolecules"

Simulation of Copolymer Bottle-Brushes

2007

The structure of bottle-brush polymers with a rigid backbone and flexible side chains is studied in three dimensions, varying the grafting density, the side chain length, and the solvent quality. Some preliminary results of theoretical scaling considerations for one-component bottle-brush polymers in a good solvent are compared with Monte Carlo simulations of a simple lattice model. For the simulations a variant of the pruned-enriched Rosenbluth method (PERM) allowing for simultaneous growth of all side chains in the Monte Carlo sampling is employed. For a symmetrical binary (A,B) bottle-brush polymer, where two types (A,B) of flexible side chains are grafted with one chain end to the backb…

Simulations of phase transitions in macromolecular systems

2002

Abstract The study of phase transitions in concentrated solutions and melts of flexible or stiff polymers is a computational challenge for computer simulations, since already a single polymer coil exhibits nontrivial structure from the scale of a chemical bond (1 A) to the coil radius (100 A), and for the simulation of collective phenomena huge simulation boxes containing many polymers are required. A strategy to deal with this problem is the use of highly coarse-grained models on a lattice, such as the bond fluctuation model. Several studies employing such models will be briefly reviewed, e.g.: temperature-driven isotropic-nematic phase transition in concentrated solutions of semiflexible …

1986

Covalently crosslinked liquid crystalline networks with elastic properties were prepared in isotropic solution from linear liquid crystalline polymers. As linear precursors for the networks were used: (i) polymers with the mesogenic groups in the side groups (polyacrylates and polymethacrylates), (ii) polymers with the mesogenic groups in the main chain (polymalonates) and (iii) polymers with the mesogenic groups in main chain and side groups (“combined liquid crystalline polymers”). In all crosslinked polymers the liquid crystalline phases of the linear polymers are retained. For low degrees of crosslinking (≤2 mol-%) the phase transition temperatures remain nearly unchanged. These elastom…

Phase transitions of single polymer chains and of polymer solutions: insights from Monte Carlo simulations

2008

The statistical mechanics of flexible and semiflexible macromolecules is distinct from that of small molecule systems, since the thermodynamic limit can also be approached when the number of (effective) monomers of a single chain (realizable by a polymer solution in the dilute limit) is approaching infinity. One can introduce effective attractive interactions into a simulation model for a single chain such that a swollen coil contracts when the temperature is reduced, until excluded volume interactions are effectively canceled by attractive forces, and the chain conformation becomes almost Gaussian at the theta point. This state corresponds to a tricritical point, as the renormalization gro…

Competition between liquid-crystalline ordering and glassy freezing in melts of semiflexible polymers: A monte carlo simulation

1999

We present results of a Monte Carlo simulation of dense melts of semiflexible polymers using the bond-fluctuation model. The chosen Hamiltonian increases the chain stiffness upon cooling which in turn leads to glass-transition like freezing of the polymer mobility. Employing an efficient simulation algorithm, which is able to equilibrate the simulated systems to lower temperature than the Rouse-type algorithm showing the glassy freezing, we are able to observe an isotropic-nematic phase transition. This transition lies above the glass transition temperature one would extrapolate from the observed freezing behavior.

Monte-Carlo Simulation of 3-Dimensional Glassy Polymer Melts: Reptation Versus Single Monomer Dynamics

1995

A polymer melt is simulated at finite temperature by the Monte-Carlo method. We use a coarse-grained model for the polymer system, the bond-fluctuation model. Static properties of the melt can be obtained by generating configurations not with single-monomer- dynamics which moves individual monomers locally, but reptation-dynamics which allows collec- tive motion of the chains. This algorithm can produce equilibrated configurations much faster. It is demonstrated that static properties do not differ from those obtained by single-monomer- dynamics. Values of the radius of gyration, the mean square bond length and similar quantities for different temperatures and densities are presented.

Biomolecular-solvent stereodynamic coupling probed by deuteration.

1983

Thermodynamic interpretation of experiments with isotopically perturbed solvent supports the view that solvent stereodynamics is directly relevant to thermodynamic stability of biomolecules. According with the current understanding of the structure of the aqueous solvent, in any stereodynamic configuration of the latter, connectivity pathways are identifiable for their topologic and order properties. Perturbing the solvent by isotopic substitution or, e.g., by addition of co-solvents, can therefore be viewed as reinforcing or otherwise perturbing these topologic structures. This microscopic model readily visualizes thermodynamic interpretation. In conclusion, the topologic stereodynamic str…

Conformational Properties of Polymer Mushrooms Under Spherical and Cylindrical Confinement

2010

A coarse grained model of a flexible macromolecule end-grafted on the inside of a sphere or a cylinder under good solvent conditions is studied by Monte Carlo simulations. For cylindrical confinement, two regimes are found: when the cylinder radius R exceeds the gyration radius R 90 of the polymer mushroom grafted to a planar surface, a simple scaling description holds. In the opposite case, a non-monotonic crossover to a cigar-like quasi-one-dimensional structure occurs, and the distribution P e (x) of the free chain end in the x-direction along the cylinder axis becomes bimodal. Spherical confinement, on the other hand, causes a crossover from dilute to semidilute behavior of the structur…

Static and Dynamic Properties of Adsorbed Chains at Surfaces:  Monte Carlo Simulation of a Bead-Spring Model

1996

The adsorption of flexible polymers from dilute solution in good solvents at attractive walls is studied by Monte Carlo simulation of a coarse-grained off-lattice model, varying chain length N and ...

Brownian dynamics simulation of grafted polymer brushes

1995

We present results of computer simulations by the method of Brownian dynamics of polymeric brushes attached to impenetrable planes. For testing both model and method we have used one polymer brush attached to a repulsive plane and compare some results with Monte Carlo results of Lai and Binder on the bond fluctuation model. We have also studied two polymeric brushes attached to two parallel planes at different distances between planes, and investigate the interplay between the interpenetration of the brushes and the configurational properties of the grafted chains.