388 research outputs found
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
The low-density/high-density liquid phase transition for model globular proteins
The effect of molecule size (excluded volume) and the range of interaction on
the surface tension, phase diagram and nucleation properties of a model
globular protein is investigated using a combinations of Monte Carlo
simulations and finite temperature classical Density Functional Theory
calculations. We use a parametrized potential that can vary smoothly from the
standard Lennard-Jones interaction characteristic of simple fluids, to the ten
Wolde-Frenkel model for the effective interaction of globular proteins in
solution. We find that the large excluded volume characteristic of large
macromolecules such as proteins is the dominant effect in determining the
liquid-vapor surface tension and nucleation properties. The variation of the
range of the potential only appears important in the case of small excluded
volumes such as for simple fluids. The DFT calculations are then used to study
homogeneous nucleation of the high-density phase from the low-density phase
including the nucleation barriers, nucleation pathways and the rate. It is
found that the nucleation barriers are typically only a few and that
the nucleation rates substantially higher than would be predicted by Classical
Nucleation Theory.Comment: To appear in Langmui
A possible mechanism for cold denaturation of proteins at high pressure
We study cold denaturation of proteins at high pressures. Using
multicanonical Monte Carlo simulations of a model protein in a water bath, we
investigate the effect of water density fluctuations on protein stability. We
find that above the pressure where water freezes to the dense ice phase
( kbar), the mechanism for cold denaturation with decreasing
temperature is the loss of local low-density water structure. We find our
results in agreement with data of bovine pancreatic ribonuclease A.Comment: 4 pages for double column and single space. 3 figures Added
references Changed conten
Forward Flux Sampling for rare event simulations
Rare events are ubiquitous in many different fields, yet they are notoriously
difficult to simulate because few, if any, events are observed in a conventiona
l simulation run. Over the past several decades, specialised simulation methods
have been developed to overcome this problem. We review one recently-developed
class of such methods, known as Forward Flux Sampling. Forward Flux Sampling
uses a series of interfaces between the initial and final states to calculate
rate constants and generate transition paths, for rare events in equilibrium or
nonequilibrium systems with stochastic dynamics. This review draws together a
number of recent advances, summarizes several applications of the method and
highlights challenges that remain to be overcome.Comment: minor typos in the manuscript. J.Phys.:Condensed Matter (accepted for
publication
Homogeneous Bubble Nucleation driven by local hot spots: a Molecular Dynamics Study
We report a Molecular Dynamics study of homogenous bubble nucleation in a
Lennard-Jones fluid. The rate of bubble nucleation is estimated using
forward-flux sampling (FFS). We find that cavitation starts with compact
bubbles rather than with ramified structures as had been suggested by Shen and
Debenedetti (J. Chem. Phys. 111:3581, 1999). Our estimate of the
bubble-nucleation rate is higher than predicted on the basis of Classical
Nucleation Theory (CNT). Our simulations show that local temperature
fluctuations correlate strongly with subsequent bubble formation - this
mechanism is not taken into account in CNT
Computing stationary distributions in equilibrium and non-equilibrium systems with Forward Flux Sampling
We present a method for computing stationary distributions for activated
processes in equilibrium and non-equilibrium systems using Forward Flux
Sampling (FFS). In this method, the stationary distributions are obtained
directly from the rate constant calculations for the forward and backward
reactions; there is no need to perform separate calculations for the stationary
distribution and the rate constant. We apply the method to the non-equilibrium
rare event problem proposed by Maier and Stein, to nucleation in a
2-dimensional Ising system, and to the flipping of a genetic switch
Long-Term Evolution and Revival Structure of Rydberg Wave Packets for Hydrogen and Alkali-Metal Atoms
This paper begins with an examination of the revival structure and long-term
evolution of Rydberg wave packets for hydrogen. We show that after the initial
cycle of collapse and fractional/full revivals, which occurs on the time scale
, a new sequence of revivals begins. We find that the structure of
the new revivals is different from that of the fractional revivals. The new
revivals are characterized by periodicities in the motion of the wave packet
with periods that are fractions of the revival time scale . These
long-term periodicities result in the autocorrelation function at times greater
than having a self-similar resemblance to its structure for times
less than . The new sequence of revivals culminates with the
formation of a single wave packet that more closely resembles the initial wave
packet than does the full revival at time , i.e., a superrevival
forms. Explicit examples of the superrevival structure for both circular and
radial wave packets are given. We then study wave packets in alkali-metal
atoms, which are typically used in experiments. The behavior of these packets
is affected by the presence of quantum defects that modify the hydrogenic
revival time scales and periodicities. Their behavior can be treated
analytically using supersymmetry-based quantum-defect theory. We illustrate our
results for alkali-metal atoms with explicit examples of the revival structure
for radial wave packets in rubidium.Comment: To appear in Physical Review A, vol. 51, June 199
Metastable liquid-liquid phase transition in a single-component system with only one crystal phase and no density anomaly
We investigate the phase behavior of a single-component system in 3
dimensions with spherically-symmetric, pairwise-additive, soft-core
interactions with an attractive well at a long distance, a repulsive soft-core
shoulder at an intermediate distance, and a hard-core repulsion at a short
distance, similar to potentials used to describe liquid systems such as
colloids, protein solutions, or liquid metals. We showed [Nature {\bf 409}, 692
(2001)] that, even with no evidences of the density anomaly, the phase diagram
has two first-order fluid-fluid phase transitions, one ending in a
gas--low-density liquid (LDL) critical point, and the other in a
gas--high-density liquid (HDL) critical point, with a LDL-HDL phase transition
at low temperatures. Here we use integral equation calculations to explore the
3-parameter space of the soft-core potential and we perform molecular dynamics
simulations in the interesting region of parameters. For the equilibrium phase
diagram we analyze the structure of the crystal phase and find that, within the
considered range of densities, the structure is independent of the density.
Then, we analyze in detail the fluid metastable phases and, by explicit
thermodynamic calculation in the supercooled phase, we show the absence of the
density anomaly. We suggest that this absence is related to the presence of
only one stable crystal structure.Comment: 15 pages, 21 figure
Hard-Sphere Fluids in Contact with Curved Substrates
The properties of a hard-sphere fluid in contact with hard spherical and
cylindrical walls are studied. Rosenfeld's density functional theory (DFT) is
applied to determine the density profile and surface tension for wide
ranges of radii of the curved walls and densities of the hard-sphere fluid.
Particular attention is paid to investigate the curvature dependence and the
possible existence of a contribution to that is proportional to the
logarithm of the radius of curvature. Moreover, by treating the curved wall as
a second component at infinite dilution we provide an analytical expression for
the surface tension of a hard-sphere fluid close to arbitrary hard convex
walls. The agreement between the analytical expression and DFT is good. Our
results show no signs for the existence of a logarithmic term in the curvature
dependence of .Comment: 15 pages, 6 figure
Nonergodicity transitions in colloidal suspensions with attractive interactions
The colloidal gel and glass transitions are investigated using the idealized
mode coupling theory (MCT) for model systems characterized by short-range
attractive interactions. Results are presented for the adhesive hard sphere and
hard core attractive Yukawa systems. According to MCT, the former system shows
a critical glass transition concentration that increases significantly with
introduction of a weak attraction. For the latter attractive Yukawa system, MCT
predicts low temperature nonergodic states that extend to the critical and
subcritical region. Several features of the MCT nonergodicity transition in
this system agree qualitatively with experimental observations on the colloidal
gel transition, suggesting that the gel transition is caused by a low
temperature extension of the glass transition. The range of the attraction is
shown to govern the way the glass transition line traverses the phase diagram
relative to the critical point, analogous to findings for the fluid-solid
freezing transition.Comment: 11 pages, 7 figures; to be published in Phys. Rev. E (1 May 1999
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