2,226 research outputs found
Solvent-free coarse-grained lipid model for large-scale simulations
A coarse-grained molecular model, which consists of a spherical particle and
an orientation vector, is proposed to simulate lipid membrane on a large length
scale. The solvent is implicitly represented by an effective attractive
interaction between particles. A bilayer structure is formed by
orientation-dependent (tilt and bending) potentials. In this model, the
membrane properties (bending rigidity, line tension of membrane edge, area
compression modulus, lateral diffusion coefficient, and flip-flop rate) can be
varied over broad ranges. The stability of the bilayer membrane is investigated
via droplet-vesicle transition. The rupture of the bilayer and worm-like
micelle formation can be induced by an increase in the spontaneous curvature of
the monolayer membrane.Comment: 13 pages, 19 figure
Effect of hydrophobic solutes on the liquid-liquid critical point
Jagla ramp particles, interacting through a ramp potential with two
characteristic length scales, are known to show in their bulk phase
thermodynamic and dynamic anomalies, similar to what is found in water. Jagla
particles also exhibit a line of phase transitions separating a low density
liquid phase and a high density liquid phase, terminating in a liquid-liquid
critical point in a region of the phase diagram that can be studied by
simulations. Employing molecular dynamics computer simulations, we study the
thermodynamics and the dynamics of solutions of hard spheres (HS) in a solvent
formed by Jagla ramp particles. We consider the cases of HS mole fraction x =
0.10, 0.15 and 0.20, and also the case x = 0.50 (a 1:1 mixture of HS and Jagla
particles). We find a liquid-liquid critical point, up to the highest HS mole
fraction; its position shifts to higher pressures and lower temperatures upon
increasing x. We also find that the diffusion coefficient anomalies appear to
be preserved for all the mole fractions studied.Comment: 8 pages, 7 figures, 1 table. In press (Phys. Rev. E
Solvent-induced micelle formation in a hydrophobic interaction model
We investigate the aggregation of amphiphilic molecules by adapting the
two-state Muller-Lee-Graziano model for water, in which a solvent-induced
hydrophobic interaction is included implicitly. We study the formation of
various types of micelle as a function of the distribution of hydrophobic
regions at the molecular surface. Successive substitution of non-polar surfaces
by polar ones demonstrates the influence of hydrophobicity on the upper and
lower critical solution temperatures. Aggregates of lipid molecules, described
by a refinement of the model in which a hydrophobic tail of variable length
interacts with different numbers of water molecules, are stabilized as the
length of the tail increases. We demonstrate that the essential features of
micelle formation are primarily solvent-induced, and are explained within a
model which focuses only on the alteration of water structure in the vicinity
of the hydrophobic surface regions of amphiphiles in solution.Comment: 11 pages, 10 figures; some rearrangement of introduction and
discussion sections, streamlining of formalism and general compression; to
appear in Phys. Rev.
Induced Crystallization of Polyelectrolyte-Surfactant Complexes at the Gas-Water Interface
Synchrotron-X-ray and surface tension studies of a strong polyelectrolyte
(PE) in the semi-dilute regime (~ 0.1M monomer-charges) with varying surfactant
concentrations show that minute surfactant concentrations induce the formation
of a PE-surfactant complex at the gas/solution interface. X-ray reflectivity
and grazing angle X-ray diffraction (GIXD) provide detailed information of the
top most layer, where it is found that the surfactant forms a two-dimensional
liquid-like monolayer, with a noticeable disruption of the structure of water
at the interface. With the addition of salt (NaCl) columnar-crystals with
distorted-hexagonal symmetry are formed.Comment: 4 pages, 5 eps figure
Origin of Native Driving Force in Protein Folding
We derive an expression with four adjustable parameters that reproduces well
the 20x20 Miyazawa-Jernigan potential matrix extracted from known protein
structures. The numerical values of the parameters can be approximately
computed from the surface tension of water, water-screened dipole interactions
between residues and water and among residues, and average exposures of
residues in folded proteins.Comment: LaTeX file, Postscript file; 4 pages, 1 figure (mij.eps), 2 table
Hydrophobic interactions: an overview
We present an overview of the recent progress that has been made in
understanding the origin of hydrophobic interactions. We discuss the different
character of the solvation behavior of apolar solutes at small and large length
scales. We emphasize that the crossover in the solvation behavior arises from a
collective effect, which means that implicit solvent models should be used with
care. We then discuss a recently developed explicit solvent model, in which the
solvent is not described at the atomic level, but rather at the level of a
density field. The model is based upon a lattice-gas model, which describes
density fluctuations in the solvent at large length scales, and a Gaussian
model, which describes density fluctuations at smaller length scales. By
integrating out the small length scale field, a Hamiltonian is obtained, which
is a function of the binary, large-length scale field only. This makes it
possible to simulate much larger systems than hitherto possible as demonstrated
by the application of the model to the collapse of an ideal hydrophobic
polymer. The results show that the collapse is dominated by the dynamics of the
solvent, in particular the formation of a vapor bubble of critical size.
Implications of these findings to the understanding of pressure denaturation of
proteins are discussed.Comment: 10 pages, 4 figure
Ground States of Two-Dimensional Polyampholytes
We perform an exact enumeration study of polymers formed from a (quenched)
random sequence of charged monomers , restricted to a 2-dimensional
square lattice. Monomers interact via a logarithmic (Coulomb) interaction. We
study the ground state properties of the polymers as a function of their excess
charge for all possible charge sequences up to a polymer length N=18. We
find that the ground state of the neutral ensemble is compact and its energy
extensive and self-averaging. The addition of small excess charge causes an
expansion of the ground state with the monomer density depending only on .
In an annealed ensemble the ground state is fully stretched for any excess
charge .Comment: 6 pages, 6 eps figures, RevTex, Submitted to Phys. Rev.
A Model Ground State of Polyampholytes
The ground state of randomly charged polyampholytes is conjectured to have a
structure similar to a necklace, made of weakly charged parts of the chain,
compacting into globules, connected by highly charged stretched `strings'. We
suggest a specific structure, within the necklace model, where all the neutral
parts of the chain compact into globules: The longest neutral segment compacts
into a globule; in the remaining part of the chain, the longest neutral segment
(the 2nd longest neutral segment) compacts into a globule, then the 3rd, and so
on. We investigate the size distributions of the longest neutral segments in
random charge sequences, using analytical and Monte Carlo methods. We show that
the length of the n-th longest neutral segment in a sequence of N monomers is
proportional to N/(n^2), while the mean number of neutral segments increases as
sqrt(N). The polyampholyte in the ground state within our model is found to
have an average linear size proportional to sqrt(N), and an average surface
area proportional to N^(2/3).Comment: 8 two-column pages. 5 eps figures. RevTex. Submitted to Phys. Rev.
Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins
Water and water-mediated interactions determine thermodynamic and kinetics of
protein folding, protein aggregation and self-assembly in confined spaces. To
obtain insights into the role of water in the context of folding problems, we
describe computer simulations of a few related model systems. The dynamics of
collapse of eicosane shows that upon expulsion of water the linear hydrocarbon
chain adopts an ordered helical hairpin structure with 1.5 turns. The structure
of dimer of eicosane molecules has two well ordered helical hairpins that are
stacked perpendicular to each other. As a prelude to studying folding in
confined spaces we used simulations to understand changes in hydrophobic and
ionic interactions in nano droplets. Solvation of hydrophobic and charged
species change drastically in nano water droplets. Hydrophobic species are
localized at the boundary. The tendency of ions to be at the boundary where
water density is low increases as the charge density decreases. Interaction
between hydrophobic, polar, and charged residue are also profoundly altered in
confined spaces. Using the results of computer simulations and accounting for
loss of chain entropy upon confinement we argue and then demonstrate, using
simulations in explicit water, that ordered states of generic amphiphilic
peptide sequences should be stabilized in cylindrical nanopores
Cold Inactivation of l-Threonine Deaminase from Rhodospirillum rubrum
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66171/1/j.1432-1033.1971.tb01491.x.pd
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