3,648 research outputs found
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
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
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
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
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
Magnetic friction due to vortex fluctuation
We use Monte Carlo and molecular dynamics simulation to study a magnetic
tip-sample interaction. Our interest is to understand the mechanism of heat
dissipation when the forces involved in the system are magnetic in essence. We
consider a magnetic crystalline substrate composed of several layers
interacting magnetically with a tip. The set is put thermally in equilibrium at
temperature T by using a numerical Monte Carlo technique. By using that
configuration we study its dynamical evolution by integrating numerically the
equations of motion. Our results suggests that the heat dissipation in this
system is closed related to the appearing of vortices in the sample.Comment: 6 pages, 41 figure
Cooperative Origin of Low-Density Domains in Liquid Water
We study the size of clusters formed by water molecules possessing large
enough tetrahedrality with respect to their nearest neighbors. Using Monte
Carlo simulation of the SPC/E model of water, together with a geometric
analysis based on Voronoi tessellation, we find that regions of lower density
than the bulk are formed by accretion of molecules into clusters exceeding a
minimum size. Clusters are predominantly linear objects and become less compact
as they grow until they reach a size beyond which further accretion is not
accompanied by a density decrease. The results suggest that the formation of
"ice-like" regions in liquid water is cooperative.Comment: 16 pages, 6 figure
A phase II study of high dose epirubicin in unresectable non small cell lung cancer.
Epirubicin (EPI), a doxorubicin analogue, is reported to have equal antitumour activity with lower cardiac and systemic toxicity. Recently, the maximum tolerated dose of this drug has been revised upwards with reported increased response rates in several malignancies. We initiated a phase II study of high-dose EPI as initial treatment for patients with advanced non-small cell lung cancer (NSCLC) (stage III and IV). Between May 1988 and November 1989, 25 patients were entered. The starting dose of EPI was 135 mg m-2, with dose attenuations and escalations of 15 mg m-2 based on mid-cycle evaluation of toxicity. Treatment was repeated every 3 weeks. Nine partial responses (36%, 95% CI: 18-57.5%) and 11 patients with disease stabilisation (44%) were observed. Median (range) time to progression was 19 (3-70) weeks. Median (range) survival is 32 (9-116+) weeks. There were no treatment related deaths. Major side effects were leukocytopenia WHO grade III/IV (23% of courses) and mucositis WHO grade II/III (15% of courses). In two patients left ventricular ejection fraction decreased greater than 15% compared to baseline values after a cumulative Epirubicin dose of 435 mg m-2, and therefore went off study. In none of the patients clinical signs of congestive heart failure were observed. We conclude from our data that high-dose EPI, contrary to previous negative studies using lower doses of EPI, ranks amongst the most active regimens against advanced NSCLC. Toxicity of high-dose EPI is moderate. Further evaluation of this compound in combination regimens is recommended
Physics of the liquid-liquid critical point
Within the inherent structure (IS) thermodynamic formalism introduced by
Stillinger and Weber [F. H. Stillinger and T. A. Weber, Phys. Rev. A {\bf 25},
978 (1982)] we address the basic question of the physics of the liquid-liquid
transition and of density maxima observed in some complex liquids such as water
by identifying, for the first time, the statistical properties of the potential
energy landscape (PEL) responsible for these anomalies.
We also provide evidence of the connection between density anomalies and the
liquid-liquid critical point. Within the simple (and physically transparent)
model discussed, density anomalies do imply the existence of a liquid-liquid
transition.Comment: Physical Review Letters, in publicatio
High frequency longitudinal and transverse dynamics in water
High-resolution, inelastic x-ray scattering measurements of the dynamic
structure factor S(Q,\omega) of liquid water have been performed for wave
vectors Q between 4 and 30 nm^-1 in distinctly different thermodynamic
conditions (T= 263 - 420 K ; at, or close to, ambient pressure and at P = 2
kbar). In agreement with previous inelastic x-ray and neutron studies, the
presence of two inelastic contributions (one dispersing with Q and the other
almost non-dispersive) is confirmed. The study of their temperature- and
Q-dependence provides strong support for a dynamics of liquid water controlled
by the structural relaxation process. A viscoelastic analysis of the
Q-dispersing mode, associated with the longitudinal dynamics, reveals that the
sound velocity undergoes the complete transition from the adiabatic sound
velocity (c_0) (viscous limit) to the infinite frequency sound velocity
(c_\infinity) (elastic limit). On decreasing Q, as the transition regime is
approached from the elastic side, we observe a decrease of the intensity of the
second, weakly dispersing feature, which completely disappears when the viscous
regime is reached. These findings unambiguously identify the second excitation
to be a signature of the transverse dynamics with a longitudinal symmetry
component, which becomes visible in the S(Q,\omega) as soon as the purely
viscous regime is left.Comment: 28 pages, 12 figure
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