Search results for "Thermodynamics"
showing 10 items of 2774 documents
Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase.
2011
O-Glycoprotein 2-acetamino-2-deoxy-β-d-glucopyranosidase (O-GlcNAcase) hydrolyzes O-linked 2-acetamido-2-deoxy-β-d-glucopyranoside (O-GlcNAc) residues from post-translationally modified serine/threonine residues of nucleocytoplasmic protein. The chemical process involves substrate-assisted catalysis, where two aspartate residues have been identified as the two key catalytic residues of O-GlcNAcase. In this report, the first step of the catalytic mechanism used by O-GlcNAcase involving substrate-assisted catalysis has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) Molecular Dynamics (MD) calculations. The free energy profile shows that the formation of the oxazol…
Anomalous diffusion in polymer melts
2002
Abstract We present a study of the anomalous diffusion regimes in polymer melt dynamics performing a Monte Carlo (MC) simulation of the bond-fluctuation lattice model. Special emphasis is laid on the crossover from a Rouse-like motion to the behavior predicted by reptation theory. For the longest chains of N=400 the high statistical accuracy of the data allows for clear identification of the subdiffusive regimes in the center of mass motion and the monomer displacement. They are well compatible with those predicted by reptation theory. Furthermore a detailed analysis of the different short time anomalous diffusion regimes in the melt dynamics of polymer chains is presented and it is shown t…
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…
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.
Translocation dynamics of a short polymer driven by an oscillating force
2013
Under the terms of the Creative Commons Attribution 3.0 Unported License.
A coarse-graining procedure for polymer melts applied to 1,4-polybutadiene
2009
We present a coarse-graining procedure for homopolymer melts mapping intra- as well as inter-molecular interactions from a chemically realistic united atom description to a bead-spring type molecular model. On the coarse-grained level the repeat units interact through bond-length and bond angle potentials and a non-bonded Lennard-Jones type interaction. The latter one is of the 7,4 form and softer than the typically employed 12,6 interactions. The coarse-graining of the intramolecular interactions follows well developed procedures, however, we point out in which way the non-bonded intramolecular interactions in the chemically realistic model should be treated. The parameters of the non-bond…
Selfdiffusion of polymer chains in solutions and melts
2005
Anomalous diffusion of monomers of polymer chains, as well as motion of these chains as a whole, is discussed with an emphasis on Monte Carlo simulations and simple scaling concepts. While the behavior of isolated chains in good solvents or Theta-solvents without excluded volume interactions is fully accounted for by the Rouse model, the behavior is less clear both for isolated chains in bad solvents and for chains in dense melts. Collapsed chains are shown to diffuse as g3(t) = <([rCM (t) -rCM(0)]2〉 ∝ tξ3 where the (effective?) exponent ξ3 simply seems to be linearly temperature-dependent for temperatures T lower than the Σ-temperature, ξ3 T/Θ. A relaxation time τ oc N3 is found, and scali…
Microscopic verification of dynamic scaling in dilute polymer solutions: A molecular-dynamics simulation
1991
The dynamics of a single polymer chain immersed in a large number of solvent particles is studied by molecular dynamics. This is the first simulation where chain length (30, 40, and 60 monomers) and statistical accuracy are sufficient to test the predictions of the Zimm model as a result of the particle-particle interactions: The short-time diffusion constant is in good agreement with the Kirkwood prediction, and the monomer motions exhibit the expected dynamic scaling. The long-range hydrodynamic interaction requires a data analysis that explicitly includes the periodic images via Ewald sums.
Counterion-mediated attraction and kinks on loops of semiflexible polyelectrolyte bundles.
2006
The formation of kinks in a loop of bundled polyelectrolyte filaments is analyzed in terms of the thermal fluctuations of charge density due to polyvalent counterions adsorbed on the polyelectrolyte filaments. It is found that the counterion-mediated attraction energy of filaments depends on their bending. By consideration of curvature elasticity energy and counterion-mediated attraction between polyelectrolyte filaments, the characteristic width of the kink and the number of kinks per loop is found to be in reasonable agreement with existing experimental data for rings of bundled actin filaments.