Search results for "Biomolecule"
showing 10 items of 666 documents
On the first-order collapse transition of a three-dimensional, flexible homopolymer chain model
2005
We present simulation results for the phase behavior of flexible lattice polymer chains using the Wang-Landau sampling idea. These chains display a two-stage collapse through a coil-globule transition followed by a crystallization at lower temperatures. Performing a finite-size scaling analysis on the two transitions, we show that they coincide in the thermodynamic limit corresponding to a direct collapse of the random coil into the crystal without intermediate coil-globule transition.
Unified Thermodynamic Modeling of Polymer Solutions: Polyelectrolytes, Proteins, and Chain Molecules
2013
The thermodynamic description of the systems specified in the title requires in general dissimilar theories. This contribution presents an approach that is capable of modeling all of them with a maximum of three adjustable parameters. The Ansatz starts from the Flory–Huggins theory and extends it in a 2-fold manner: The number of segments assigned to the solvent is no longer one but treated as an adjustable parameter to account for the differences in the molecular geometries and in the free volumes of the components. Furthermore, the modeling allows for effects resulting from ternary contacts of the solvent/polymer/polymer type. Examination of the acquired thermodynamic expressions by means…
Structure and dynamics of grafted polymer layers: A Monte Carlo simulation
1991
The bond fluctuation model of polymer chains on lattices is used to study layers of polymers anchored with one end at a hard wall, assuming good solvent conditions and repulsive interactions between the monomers and the wall. Chain lengths from N=10 to N=80 and grafting densities σ from 0.025 to 0.20 are considered, both for the ‘‘quenched’’ case, where the anchor points are kept fixed at randomly chosen surface sites, and the ‘‘annealed’’ case, where lateral diffusion of the anchored ends at the wall is considered. Profiles of monomer density and free end density, chain linear dimensions parallel and perpendicular to the wall, as well as corresponding mean square displacements of inner and…
Monte Carlo simulations of chain dynamics in polymer brushes
1994
The bond-fluctuation model of polymer chains has been used to study layers of end-grafted polymers anchoring at repulsive walls for a broad range of chain length, grafting densities and solvent quality. The dynamics of monomers and associated relaxation times are investigated and interpreted by phenomenological theories and scaling arguments. The case is also considered where a chain is cut off from its anchor point and the chain is subsequently expelled from the brush. Both the velocity with which the chain leaves the brush and the associated conformational changes (chain contraction etc.) are analysed and interpreted in terms of recent theoretical concepts.
A comparison of neutron scattering studies and computer simulations of polymer melts
2000
Abstract Neutron scattering and computer simulations are powerful tools for studying structural and dynamical properties of condensed matter systems in general and of polymer melts in particular. When neutron scattering studies and quantitative atomistic molecular dynamics simulations of the same material are combined, synergy between the methods can result in exciting new insights into polymer melts not obtainable from either method separately. We present here an overview of our recent efforts to combine neutron scattering and atomistic simulations in the study of melt dynamics of polyethylene and polybutadiene. Looking at polymer segmental motion on a picosecond time scale, we show how at…
Fractal calibration in size-exclusion chromatography
2003
Abstract The elution behaviour of different polymer–solvent systems in three types of organic columns for SEC has been compared and interpreted. The experimental data show that the classical universal calibration is not accomplished. Deviations from a unique curve are observed due to the binary and ternary interactions between the components of the system (solvent, polymer and gel) which results on secondary mechanisms accompanying the main pure or “ideal” SEC separation mechanism. Both, enthalpic and entropic effects are interpreted in terms of the swelling and crosslinking degrees of the gel packings, and are also related with the fractal characteristics of their surfaces, such as the fra…
Multivalent ion-exchange model of biopolymer chromatography for mass overload conditions
1991
Abstract The simple model of multivalent ion-exchange biopolymer chromatography is analyzed on the basis of classical quasi-chemical temperature. The rigorous isotherm equation deduced from the stoichiometric displacement model (SDM) was used to stimulate the migration of a solute through the chromatographic column in the isocratic and gradient elution modes. The peak profiles generated for various sample sizes were compared with those obtained on the basis of a Langmuir isotherm. Peak tailing increases with the value of the exponent Z, defined as the ratio of the protein valency to the displacing counter-ion valency. For large Z the asymmetries due to the non-linearity of the isotherm are …
Osmotic pressure of catenanes in solution
1989
We propose a nonuniversal scaling for the osmotic pressure in the case of concatenating ring polymers. The size exponent depends on the molecular weight of the catenans. The effect is more significant the shorter and the stiffer the molecules are.
Energy-stable linear schemes for polymer-solvent phase field models
2017
We present new linear energy-stable numerical schemes for numerical simulation of complex polymer-solvent mixtures. The mathematical model proposed by Zhou, Zhang and E (Physical Review E 73, 2006) consists of the Cahn-Hilliard equation which describes dynamics of the interface that separates polymer and solvent and the Oldroyd-B equations for the hydrodynamics of polymeric mixtures. The model is thermodynamically consistent and dissipates free energy. Our main goal in this paper is to derive numerical schemes for the polymer-solvent mixture model that are energy dissipative and efficient in time. To this end we will propose several problem-suited time discretizations yielding linear scheme…
Anomalous Structure and Scaling of Ring Polymer Brushes
2011
A comparative simulation study of polymer brushes formed by grafting at a planar surface either flexible linear polymers (chain length $N_L$) or (non-catenated) ring polymers (chain length $N_R=2 N_L$) is presented. Two distinct off-lattice models are studied, one by Monte Carlo methods, the other by Molecular Dynamics, using a fast implementation on graphics processing units (GPUs). It is shown that the monomer density profiles $\rho(z)$ in the $z$-direction perpendicular to the surface for rings and linear chains are practically identical, $\rho_R(2 N_L, z)=\rho_L(N_L, z)$. The same applies to the pressure, exerted on a piston at hight z, as well. While the gyration radii components of ri…