3,739 research outputs found
Neurophysiology
Contains reports on one research project.Bell Telephone Laboratories, IncorporatedNational Institutes of HealthTeagle Foundation, IncorporatedU. S. Air Force under WADD Contract AF33(616)-778
On the "generalized Generalized Langevin Equation"
In molecular dynamics simulations and single molecule experiments,
observables are usually measured along dynamic trajectories and then averaged
over an ensemble ("bundle") of trajectories. Under stationary conditions, the
time-evolution of such averages is described by the generalized Langevin
equation. In contrast, if the dynamics is not stationary, it is not a priori
clear which form the equation of motion for an averaged observable has. We
employ the formalism of time-dependent projection operator techniques to derive
the equation of motion for a non-equilibrium trajectory-averaged observable as
well as for its non-stationary auto-correlation function. The equation is
similar in structure to the generalized Langevin equation, but exhibits a
time-dependent memory kernel as well as a fluctuating force that implicitly
depends on the initial conditions of the process. We also derive a relation
between this memory kernel and the autocorrelation function of the fluctuating
force that has a structure similar to a fluctuation-dissipation relation. In
addition, we show how the choice of the projection operator allows to relate
the Taylor expansion of the memory kernel to data that is accessible in MD
simulations and experiments, thus allowing to construct the equation of motion.
As a numerical example, the procedure is applied to Brownian motion initialized
in non-equilibrium conditions, and is shown to be consistent with direct
measurements from simulations
Intermittent permeation of cylindrical nanopores by water
Molecular Dynamics simulations of water molecules in nanometre sized
cylindrical channels connecting two reservoirs show that the permeation of
water is very sensitive to the channel radius and to electric polarization of
the embedding material. At threshold, the permeation is {\emph{intermittent}}
on a nanosecond timescale, and strongly enhanced by the presence of an ion
inside the channel, providing a possible mechanism for gating. Confined water
remains surprisingly fluid and bulk-like. Its behaviour differs strikingly from
that of a reference Lennard-Jones fluid, which tends to contract into a highly
layered structure inside the channel.Comment: 4 pages, 4 figure
Protein mechanical unfolding: importance of non-native interactions
Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin
(DDFLN4) was studied by all-atom molecular dynamics simulations, using the
GROMOS96 force field 43a1 and the simple point charge explicit water solvent.
Our study reveals an important role of non-native interactions in the unfolding
process. Namely, the existence of a peak centered at the end-to-end extension
22 nm in the force-extension curve, is associated with breaking of non-native
hydrogen bonds. Such a peak has been observed in experiments but not in Go
models, where non-native interactions are neglected. We predict that an
additional peak occurs at 2 nm using not only GROMOS96 force field 43a1 but
also Amber 94 and OPLS force fields. This result would stimulate further
experimental studies on elastic properties of DDFLN4.Comment: 27 pages, 15 figure
Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended x-ray absorption fine structure spectroscopy:A case study of Sr2+ in methanol solution
Molecular dynamics simulations have been carried out for Sr2+ in methanol using different Sr2+ Lennard-Jones parameters and methanol models. X-ray absorption fine structure. (EXAFS) spectroscopy has been employed to assess the reliability of the ion-ion and ion-methanol potential functions used in the simulations. Radial distribution functions of Sr2+ in methanol have been. calculated for each simulation and compared with the EXAFS experimental data. This procedure has allowed the determinations of reliable Sr2+-methanol models which have been used in longer simulations providing an accurate description of the dynamic and structural properties of this system
Cooling rate, heating rate and aging effects in glassy water
We report a molecular dynamics simulation study of the properties of the
potential energy landscape sampled by a system of water molecules during the
process of generating a glass by cooling, and during the process of
regenerating the equilibrium liquid by heating the glass. We study the
dependence of these processes on the cooling/heating rates as well as on the
role of aging (the time elapsed in the glass state). We compare the properties
of the potential energy landscape sampled during these processes with the
corresponding properties sampled in the liquid equilibrium state to elucidate
under which conditions glass configurations can be associated with equilibrium
liquid configurations.Comment: to be published in Phys. Rev. E (rapid comunication
Wetting and contact-line effects for spherical and cylindrical droplets on graphene layers: A comparative molecular-dynamics investigation
In Molecular Dynamics (MD) simulations, interactions between water molecules
and graphitic surfaces are often modeled as a simple Lennard-Jones potential
between oxygen and carbon atoms. A possible method for tuning this parameter
consists of simulating a water nanodroplet on a flat graphitic surface,
measuring the equilibrium contact angle, extrapolating it to the limit of a
macroscopic droplet and finally matching this quantity to experimental results.
Considering recent evidence demonstrating that the contact angle of water on a
graphitic plane is much higher than what was previously reported, we estimate
the oxygen-carbon interaction for the recent SPC/Fwwater model. Results
indicate a value of about 0.2 kJ/mol, much lower than previous estimations. We
then perform simulations of cylindrical water filaments on graphitic surfaces,
in order to compare and correlate contact angles resulting from these two
different systems. Results suggest that modified Young's equation does not
describe the relation between contact angle and drop size in the case of
extremely small systems and that contributions different from the one deriving
from contact line tension should be taken into account.Comment: To be published on Physical Review E (http://pre.aps.org/
Free energy of hydrophobic hydration:A molecular dynamics study of noble gases in water
The potential utility and limitations of two methods to determine free energy differences from molecular dynamics simulations (MD) are studied. The computation of the free energy of hydration of the inert gases serves as a simple but illustrative example. Good results are obtained for the inert gases from a perturbation treatment, using a reference ensemble obtained from a MD simulation of a cavity in water, if these atoms are comparable in size to the cavity and the calculated free energy differences are small. This limits the applicability of the perturbation treatment of a small number of cases. Larger free energy differences can be obtained with reasonable accuracy from MD simulations with continuously changing interaction parameters. This integration method is more generally applicable, but makes an additional simulation necessary
Proton exchange and molecular orientation of water in hydrated collagen fibers:An NMR study of H2O and D2O
An experimental study of proton and deuteron magnetic resonance of the hydration of collagen as a function of water content, temperature, and the addition of salts has been made. From the temperature dependency of linewidths, correlation times for molecular rotation of water molecules and proton exchange times have been determined. For a water content of 45 g H2O per 100 g collagen the rotational correlation time is 3× 10−8sec at 25 °C, with an activation energy of 4.8 kcal/mole, and the proton exchange time is 1.3 × 10−4sec with an activation energy of 10 kcal/mole. Ammonium ions increase the proton exchange rate. The proton exchange most probably occurs between proton donating and proton accepting groups on the macromolecule, intermediated by hydrogen‐bonded water molecules. It is shown that the exchange theory of Gutowsky, McCall, and Slichter is applicable to dipole coupling in anisotropic systems. From an analysis of the anisotropy of H2O and D2O rotation in terms of Saupe's parameters, is is concluded that a model with two specific water binding sites is consistent with experimental results
Polarization forces in water deduced from single molecule data
Intermolecular polarization interactions in water are determined using a
minimal atomic multipole model constructed with distributed polarizabilities.
Hydrogen bonding and other properties of water-water interactions are
reproduced to fine detail by only three multipoles , , and
and two polarizabilities and , which
characterize a single water molecule and are deduced from single molecule data.Comment: 4 revtex pages, 3 embedded color PS figure
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