328 research outputs found
Formation of Chain-Folded Structures from Supercooled Polymer Melts
The formation of chain-folded structures from the melt is observed in
molecular dynamics simulations resembling the lamellae of polymer crystals.
Crystallization and subsequent melting temperatures are related linearly to the
inverse lamellar thickness. Analysis of the single chain conformations in the
crystal shows that most chains reenter the same lamella by tight backfolds.
Simulations are performed with a mesoscopic bead-spring model including a
specific angle bending potential. They demonstrate that chain stiffness alone,
without an attractive inter-particle potential, is a sufficient driving force
for the formation of chain-folded lamellae.Comment: 4 pages, 5 figure
Coarse Graining of Nonbonded Inter-particle Potentials Using Automatic Simplex Optimization to Fit Structural Properties
We implemented a coarse-graining procedure to construct mesoscopic models of
complex molecules. The final aim is to obtain better results on properties
depending on slow modes of the molecules. Therefore the number of particles
considered in molecular dynamics simulations is reduced while conserving as
many properties of the original substance as possible. We address the problem
of finding nonbonded interaction parameters which reproduce structural
properties from experiment or atomistic simulations. The approach consists of
optimizing automatically nonbonded parameters using the simplex algorithm to
fit structural properties like the radial distribution function as target
functions. Moreover, any mix of structural and thermodynamic properties can be
included in the target function. Different spherically symmetric inter-particle
potentials are discussed. Besides demonstrating the method for Lennard--Jones
liquids, it is applied to several more complex molecular liquids such as
diphenyl carbonate, tetrahydrofurane, and monomers of poly(isoprene).Comment: 24 pages, 3 tables, 14 figures submitted to the Journal of Chemical
Physics (JCP
Multilevel coarse graining and nano--pattern discovery in many particle stochastic systems
In this work we propose a hierarchy of Monte Carlo methods for sampling
equilibrium properties of stochastic lattice systems with competing short and
long range interactions. Each Monte Carlo step is composed by two or more sub -
steps efficiently coupling coarse and microscopic state spaces. The method can
be designed to sample the exact or controlled-error approximations of the
target distribution, providing information on levels of different resolutions,
as well as at the microscopic level. In both strategies the method achieves
significant reduction of the computational cost compared to conventional Markov
Chain Monte Carlo methods. Applications in phase transition and pattern
formation problems confirm the efficiency of the proposed methods.Comment: 37 page
IFCC recommendation on sampling, transport and storage for the determination of the concentration of ionized calcium in whole blood, plasma and serum
The substance concentration of ionized calcium (c
Ca2+) in blood, plasma or serum preanalytically may be affected by pH changes of the sample, calcium binding by heparin, and dilution by the anticoagulant solution
International Federation of Clinical Chemistry (IFCC): Scientific Division, Committee on pH, Blood Gases and Electrolytes: Guidelines for Transcutaneouspo2andpco2 Measurement
This document provides guidelines for the terminology, methodology,
and for the interpretation of data obtained from the use of skin
(transcutaneous) po2 and pco2 electrodes. The transcutaneous
technique has found special application in newborn infants. The
causes of analytical bias with respect to arterial blood gas values,
and imprecision obtained with transcutaneous pco2 electrodes, are reviewed. Electrode temperatures above 44°C should not be used
routinely, and, at a measuring temperature of 44°C, the measuring
site should be changed at least every 4 h to avoid skin burns
Coupled coarse graining and Markov Chain Monte Carlo for lattice systems
We propose an efficient Markov Chain Monte Carlo method for sampling
equilibrium distributions for stochastic lattice models, capable of handling
correctly long and short-range particle interactions. The proposed method is a
Metropolis-type algorithm with the proposal probability transition matrix based
on the coarse-grained approximating measures introduced in a series of works of
M. Katsoulakis, A. Majda, D. Vlachos and P. Plechac, L. Rey-Bellet and
D.Tsagkarogiannis,. We prove that the proposed algorithm reduces the
computational cost due to energy differences and has comparable mixing
properties with the classical microscopic Metropolis algorithm, controlled by
the level of coarsening and reconstruction procedure. The properties and
effectiveness of the algorithm are demonstrated with an exactly solvable
example of a one dimensional Ising-type model, comparing efficiency of the
single spin-flip Metropolis dynamics and the proposed coupled Metropolis
algorithm.Comment: 20 pages, 4 figure
Molecular Dynamics Simulations
A tutorial introduction to the technique of Molecular Dynamics (MD) is given,
and some characteristic examples of applications are described. The purpose and
scope of these simulations and the relation to other simulation methods is
discussed, and the basic MD algorithms are described. The sampling of intensive
variables (temperature T, pressure p) in runs carried out in the microcanonical
(NVE) ensemble (N= particle number, V = volume, E = energy) is discussed, as
well as the realization of other ensembles (e.g. the NVT ensemble). For a
typical application example, molten SiO2, the estimation of various transport
coefficients (self-diffusion constants, viscosity, thermal conductivity) is
discussed. As an example of Non-Equilibrium Molecular Dynamics (NEMD), a study
of a glass-forming polymer melt under shear is mentioned.Comment: 38 pages, 11 figures, to appear in J. Phys.: Condens. Matte
Simulation of dimensionality effects in thermal transport
The discovery of nanostructures and the development of growth and fabrication
techniques of one- and two-dimensional materials provide the possibility to
probe experimentally heat transport in low-dimensional systems. Nevertheless
measuring the thermal conductivity of these systems is extremely challenging
and subject to large uncertainties, thus hindering the chance for a direct
comparison between experiments and statistical physics models. Atomistic
simulations of realistic nanostructures provide the ideal bridge between
abstract models and experiments. After briefly introducing the state of the art
of heat transport measurement in nanostructures, and numerical techniques to
simulate realistic systems at atomistic level, we review the contribution of
lattice dynamics and molecular dynamics simulation to understanding nanoscale
thermal transport in systems with reduced dimensionality. We focus on the
effect of dimensionality in determining the phononic properties of carbon and
semiconducting nanostructures, specifically considering the cases of carbon
nanotubes, graphene and of silicon nanowires and ultra-thin membranes,
underlying analogies and differences with abstract lattice models.Comment: 30 pages, 21 figures. Review paper, to appear in the Springer Lecture
Notes in Physics volume "Thermal transport in low dimensions: from
statistical physics to nanoscale heat transfer" (S. Lepri ed.
Conformational and Structural Relaxations of Poly(ethylene oxide) and Poly(propylene oxide) Melts: Molecular Dynamics Study of Spatial Heterogeneity, Cooperativity, and Correlated Forward-Backward Motion
Performing molecular dynamics simulations for all-atom models, we
characterize the conformational and structural relaxations of poly(ethylene
oxide) and poly(propylene oxide) melts. The temperature dependence of these
relaxation processes deviates from an Arrhenius law for both polymers. We
demonstrate that mode-coupling theory captures some aspects of the glassy
slowdown, but it does not enable a complete explanation of the dynamical
behavior. When the temperature is decreased, spatially heterogeneous and
cooperative translational dynamics are found to become more important for the
structural relaxation. Moreover, the transitions between the conformational
states cease to obey Poisson statistics. In particular, we show that, at
sufficiently low temperatures, correlated forward-backward motion is an
important aspect of the conformational relaxation, leading to strongly
nonexponential distributions for the waiting times of the dihedrals in the
various conformational statesComment: 13 pages, 13 figure
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