28 research outputs found
Vapour-liquid coexistence in many-body dissipative particle dynamics
Many-body dissipative particle dynamics is constructed to exhibit
vapour-liquid coexistence, with a sharp interface, and a vapour phase of
vanishingly small density. In this form, the model is an unusual example of a
soft-sphere liquid with a potential energy built out of local-density dependent
one-particle self energies. The application to fluid mechanics problems
involving free surfaces is illustrated by simulation of a pendant drop.Comment: 8 pages, 6 figures, revtex
Foundations of Dissipative Particle Dynamics
We derive a mesoscopic modeling and simulation technique that is very close
to the technique known as dissipative particle dynamics. The model is derived
from molecular dynamics by means of a systematic coarse-graining procedure.
Thus the rules governing our new form of dissipative particle dynamics reflect
the underlying molecular dynamics; in particular all the underlying
conservation laws carry over from the microscopic to the mesoscopic
descriptions. Whereas previously the dissipative particles were spheres of
fixed size and mass, now they are defined as cells on a Voronoi lattice with
variable masses and sizes. This Voronoi lattice arises naturally from the
coarse-graining procedure which may be applied iteratively and thus represents
a form of renormalisation-group mapping. It enables us to select any desired
local scale for the mesoscopic description of a given problem. Indeed, the
method may be used to deal with situations in which several different length
scales are simultaneously present. Simulations carried out with the present
scheme show good agreement with theoretical predictions for the equilibrium
behavior.Comment: 18 pages, 7 figure
Three-dimensional lattice-Boltzmann simulations of critical spinodal decomposition in binary immiscible fluids
We use a modified Shan-Chen, noiseless lattice-BGK model for binary
immiscible, incompressible, athermal fluids in three dimensions to simulate the
coarsening of domains following a deep quench below the spinodal point from a
symmetric and homogeneous mixture into a two-phase configuration. We find the
average domain size growing with time as , where increases
in the range , consistent with a crossover between
diffusive and hydrodynamic viscous, , behaviour. We find
good collapse onto a single scaling function, yet the domain growth exponents
differ from others' works' for similar values of the unique characteristic
length and time that can be constructed out of the fluid's parameters. This
rebuts claims of universality for the dynamical scaling hypothesis. At early
times, we also find a crossover from to in the scaled structure
function, which disappears when the dynamical scaling reasonably improves at
later times. This excludes noise as the cause for a behaviour, as
proposed by others. We also observe exponential temporal growth of the
structure function during the initial stages of the dynamics and for
wavenumbers less than a threshold value.Comment: 45 pages, 18 figures. Accepted for publication in Physical Review
A Dissipative-Particle-Dynamics Model for Simulating Dynamics of Charged Colloid
A mesoscopic colloid model is developed in which a spherical colloid is
represented by many interacting sites on its surface. The hydrodynamic
interactions with thermal fluctuations are taken accounts in full using
Dissipative Particle Dynamics, and the electrostatic interactions are simulated
using Particle-Particle-Particle Mesh method. This new model is applied to
investigate the electrophoretic mobility of a charged colloid under an external
electric field, and the influence of salt concentration and colloid charge are
systematically studied. The simulation results show good agreement with
predictions from the electrokinetic theory.Comment: 17 pages, 8 figures, submitted to the proceedings of High Performance
Computing in Science & Engineering '1
Spreading Dynamics of Polymer Nanodroplets
The spreading of polymer droplets is studied using molecular dynamics
simulations. To study the dynamics of both the precursor foot and the bulk
droplet, large drops of ~200,000 monomers are simulated using a bead-spring
model for polymers of chain length 10, 20, and 40 monomers per chain. We
compare spreading on flat and atomistic surfaces, chain length effects, and
different applications of the Langevin and dissipative particle dynamics
thermostats. We find diffusive behavior for the precursor foot and good
agreement with the molecular kinetic model of droplet spreading using both flat
and atomistic surfaces. Despite the large system size and long simulation time
relative to previous simulations, we find no evidence of hydrodynamic behavior
in the spreading droplet.Comment: Physical Review E 11 pages 10 figure
Multipolar Reactive DPD: A Novel Tool for Spatially Resolved Systems Biology
This article reports about a novel extension of dissipative particle dynamics
(DPD) that allows the study of the collective dynamics of complex chemical and
structural systems in a spatially resolved manner with a combinatorially
complex variety of different system constituents. We show that introducing
multipolar interactions between particles leads to extended membrane structures
emerging in a self-organized manner and exhibiting both the necessary
mechanical stability for transport and fluidity so as to provide a
two-dimensional self-organizing dynamic reaction environment for kinetic
studies in the context of cell biology. We further show that the emergent
dynamics of extended membrane bound objects is in accordance with scaling laws
imposed by physics.Comment: submitted to CMSB 0
Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics
We present a novel method for simulating hydrodynamic phenomena. This particle-based method combines features from molecular dynamics and lattice-gas automata. It is shown theoretically as well as in simulations that a quantitative description of isothermal Navier-Stokes flow is obtained with relatively few particles. Computationally, the method is much faster than molecular dynamics, and the at same time it is much more flexible than lattice-gas automata schemes
Outcome of central nervous system relapses in childhood acute lymphoblastic leukaemia--prospective open cohort analyses of the ALLR3 trial
Contains fulltext :
138929.pdf (publisher's version ) (Open Access)The outcomes of Central Nervous System (CNS) relapses in children with acute lymphoblastic leukaemia (ALL) treated in the ALL R3 trial, between January 2003 and March 2011 were analysed. Patients were risk stratified, to receive a matched donor allogeneic transplant or fractionated cranial irradiation with continued treatment for two years. A randomisation of Idarubicin with Mitoxantrone closed in December 2007 in favour of Mitoxantrone. The estimated 3-year progression free survival for combined and isolated CNS disease were 40.6% (25.1, 55.6) and 38.0% (26.2, 49.7) respectively. Univariate analysis showed a significantly better survival for age <10 years, progenitor-B cell disease, good-risk cytogenetics and those receiving Mitoxantrone. Adjusting for these variables (age, time to relapse, cytogenetics, treatment drug and gender) a multivariate analysis, showed a poorer outcome for those with combined CNS relapse (HR 2.64, 95% CI 1.32, 5.31, p = 0.006 for OS). ALL R3 showed an improvement in outcome for CNS relapses treated with Mitoxantrone compared to Idarubicin; a potential benefit for matched donor transplant for those with very early and early isolated-CNS relapses. TRIAL REGISTRATION: Controlled-Trials.com ISRCTN45724312
Identification of new possible targets for leukemia treatment by kinase activity profiling
Item does not contain fulltextTo date, the biology of acute leukemia has been unclear, and defining new therapeutic targets without prior knowledge remains complicated. The use of high-throughput techniques would enable us to learn more about the biology of the disease, and make it possible to directly assess a broader range of therapeutic targets. In this study we have identified comprehensive tyrosine kinase activity profiles in leukemia samples using the PamChip(R) kinase activity profiling system. Strikingly, 31% (44/120) of the detected peptides were active in all three groups of leukemia samples. The recently reported activity of platelet-derived growth factor receptor (PDGFR) and neurotrophic tyrosine kinase receptors (NTRK1 and NTRK2) in leukemia could be appreciated in our array results. In addition, high levels of peptide phosphorylation were demonstrated for peptides related to macrophage stimulating 1 receptor (MST1R). A provisional signal transduction scheme of the common active peptides was constructed and used to specifically select an inhibitor for leukemic blast cell survival assays. As expected, a dose-dependent decrease in leukemic blast cell survival was achieved for all leukemia samples. Our data demonstrate that kinase activity profiling in leukemic samples is feasible and provides novel insights into the pathogenesis of leukemia. This approach can be used for the rapid discovery of potential drug targets