Search results for "Biomolecules"
showing 10 items of 549 documents
Statics and dynamics of dense polymer systems studied by monte carlo simulation
1995
Monte Carlo simulations of coarse–grained models of macromolecules offer a unique tool to study the interplay between coil conformations, thermodynamic properties, and chain configurational relaxation and diffusion. Two examples are discussed where the chain conformation strongly differs from a gaussian coil: (i) collapsed chains in a bad solvent, where anomalous diffusion occurs in the Rouse limit and the relaxation time increases at least with the third power of chain length. (ii) Expulsion of a chain from a semidilute polymer brush. The initially stretched chain contracts to a gaussian coil and the center of mass moves outward with constant velocity until it reaches the region of the “la…
Advances in contrast variation for macromolecular structure determination by polarized neutron scattering and anomalous dispersion of synchrotron X-r…
1988
Contrast variation for macromolecular structure determination is usually achieved by isomorphous replacement of 1-H by 2-H (D) using small-angle neutron scattering (SANS). This is particularly easy in aqueous solvents. By adding heavy water the contrast of dissolved proteins, nucleic acids and membranes changes drastically. It is the region inaccesible to solvent molecules, which acts as a label. Measurements of the scattering intensity at three different scattering densities of a solvent yields the three basic scattering functions. The contrast dependence of the radius of gyration receives particular interest. More recently smaller labels have been used. Their dimensions are smaller than t…
Monte Carlo simulation of block copolymers
2000
Monte Carlo simulations deal with crudely simplified but well-defined models and have the advantage that they treat the statistical thermodynamics of the considered model exactly (apart from statistical errors and problems due to finite size effects). Therefore, these simulations are well suited to test various approximate theories of block copolymer ordering, e.g. the self-consistent field theory. Recent examples of this approach include the study of block copolymer ordering at melt surfaces and confinement effects in thin films, adsorption of block copolymers at interfaces of unmixed homopolymer blends, the phase behavior of ternary mixtures of two homopolymers and their block copolymer, …
The phase diagram of a single polymer chain: New insights from a new simulation method
2006
We present simulation results for the phase behavior of a single chain for a flexible lattice polymer model using the Wang-Landau sampling idea. Applying this new algorithm to the problem of the homopolymer collapse allows us to investigate not only the high temperature coil–globule transition but also an ensuing crystallization at lower temperature. Performing a finite size scaling analysis on the two transitions, we show that they coincide for our model in the thermodynamic limit corresponding to a direct collapse of the random coil into the crystal without intermediate coil–globule transition. As a consequence, also the many chain phase diagram of this model can be predicted to consist o…
Local Viscosity in the Vicinity of a Wall Coated by Polymer Brush from Green-Kubo Relations
2008
When fluids are confined in slit pores between parallel walls, their static structures and their dynamical properties exhibit inhomogeneity in the z-direction perpendicular to the wall. Of particular interest are local bulk viscosity η b (z) and shear viscosity η s (z). Here, we discuss an algorithm to estimate these quantities from Green-Kubo relations using equilibrium molecular dynamics. As an application example, a polymer brush (macromolecules end-grafted to a substrate at z= 0) interacting with a solvent formed from point-like particles is given.
Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute
1999
AbstractMolecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the syst…
ChemInform Abstract: The Ins and Outs of Proton Complexation
2009
Proton complexation differs from simple protonation by the fact that the coordinated hydrogen atom is bound intramolecularly to more than one donor atom. This is usually achieved by covalent bonding supplemented by hydrogen bonding. In a few cases, however, the complexed proton is hydrogen-bound to all donor atoms, which gives rise to single well (SWHB) and low barrier (LBHB) hydrogen bonds. This tutorial review highlights a full range of proton complexes formed with chelating and “proton-sponge”-type ligands, cryptand-like macropolycycles, and molecules of topological relevance, such as rotaxanes and catenanes. The concept of proton complexation can explain how the smallest cation possible…
Spectral hole burning study of protoporphyrin IX substituted myoglobin.
1992
Protoporphyrin IX substituted myoglobin reveals excellent hole burning properties. We investigated the frequency shift of persistent spectral holes under isotropic pressure conditions in a range from 0 to 2.4 MPa. In this range, the protein behaves like an elastic solid. The shift of the holes under pressure shows a remarkable frequency dependence from which the compressibility of the protein can be determined. The compressibility, in turn, allows for an estimation of the equilibrium volume fluctuations. Within the frame of the model used to interpret the pressure data, it is possible to determine the absorption frequency of the isolated chromophore and the associated solvent shift in the p…
Estimation of individual Gibbs energies of cation transfer employing the insertion electrochemistry of solid Prussian blue
2011
Abstract A novel method to determine the Gibbs energy of cation transfer between two miscible solvents is described. This method uses electrochemical data for the reversible cation-assisted solid-state reduction of Prussian blue using ferrocene as internal potential standard. Voltammetric data can be used for a direct measurement of the Gibbs energy of ion transfer from one solvent to another using midpeak potentials in solutions of suitable salts in each one of the solvents separately or mixtures of the solvents. Excess Gibbs energies of solvation in solvent mixtures can also be directly estimated. Gibbs energies of cation transfer of Li+, Na+ and K+ ions from water to MeOH, MeCN and DMSO …
Unified model for the ultrafast decay of pyrimidine nucleobases.
2006
Ultrafast decay processes detected after absorption of UV radiation in gas-phase pyrimidine nucleobases uracil, thymine, and cytosine are ascribed to the barrierless character of the pathway along the low-lying 1(pipi*) hypersurface connecting the Franck-Condon region with an out-of-plane distorted ethene-like conical intersection with the ground state. Longer lifetime decays and low quantum yield emission are on the other hand related to the presence of a 1(pipi*) state planar minimum on the S1 surface and the barriers to access other conical intersections. A unified model for the three systems is established on the basis of accurate multiconfigurational CASPT2 calculations, whereas the ef…