1,423 research outputs found
Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique
The potential energy surface (PES) of Lennard-Jones clusters is investigated
using the activation-relaxation technique (ART). This method defines events in
the configurational energy landscape as a two-step process: (a) a configuration
is first activated from a local minimum to a nearby saddle-point and (b) is
then relaxed to a new minimum. Although ART has been applied with success to a
wide range of materials such as a-Si, a-SiO2 and binary Lennard-Jones glasses,
questions remain regarding the biases of the technique. We address some of
these questions in a detailed study of ART-generated events in Lennard-Jones
(LJ) clusters, a system for which much is already known. In particular, we
study the distribution of saddle-points, the pathways between configurations,
and the reversibility of paths. We find that ART can identify all trajectories
with a first-order saddle point leaving a given minimum, is fully reversible,
and samples events following the Boltzmann weight at the saddle point.Comment: 8 pages, 7 figures in postscrip
Energy landscape of relaxed amorphous silicon
We analyze the structure of the energy landscape of a well-relaxed 1000-atom
model of amorphous silicon using the activation-relaxation technique (ART
nouveau). Generating more than 40,000 events starting from a single minimum, we
find that activated mechanisms are local in nature, that they are distributed
uniformly throughout the model and that the activation energy is limited by the
cost of breaking one bond, independently of the complexity of the mechanism.
The overall shape of the activation-energy-barrier distribution is also
insensitive to the exact details of the configuration, indicating that
well-relaxed configurations see essentially the same environment. These results
underscore the localized nature of relaxation in this material.Comment: 8 pages, 12 figure
Activated sampling in complex materials at finite temperature: the properly-obeying-probability activation-relaxation technique
While the dynamics of many complex systems is dominated by activated events,
there are very few simulation methods that take advantage of this fact. Most of
these procedures are restricted to relatively simple systems or, as with the
activation-relaxation technique (ART), sample the conformation space
efficiently at the cost of a correct thermodynamical description. We present
here an extension of ART, the properly-obeying-probability ART (POP-ART), that
obeys detailed balance and samples correctly the thermodynamic ensemble.
Testing POP-ART on two model systems, a vacancy and an interstitial in
crystalline silicon, we show that this method recovers the proper
thermodynamical weights associated with the various accessible states and is
significantly faster than MD in the diffusion of a vacancy below 700 K.Comment: 10 pages, 3 figure
Gallium self-interstitial relaxation in Gallium Arsenide: an {ab initio} characterization
Ga interstitials in GaAs () are studied using the local-orbital
{ab-initio} code SIESTA in a supercell of {216+1} atoms. Starting from eight
different initial configurations, we find five metastable structures: the two
tetrahedral sites in addition to the 110-split,
111-split, and 100-split. Studying
the competition between various configuration and charges of , we find
that predominant gallium interstitials in GaAs are charged +1, neutral or at
most -1 depending on doping conditions and prefer to occupy the tetrahedral
configuration where it is surrounded by Ga atoms. Our results are in excellent
agreement with recent experimental results concerning the dominant charge of
, underlining the importance of finite size effects in the calculation
of defects.Comment: v1) 18 pages, 5 figures, submitted to PRB (Latex preprint version)
v2) 9 pages, 5 figures, reviewed version resubmitted to PRB (correction to
equation 1, some changes and reformulations, minor grammatical and typo
corrections, added reference
Importance de la photorespiration dans le bilan photosynthétique au cours de la croissance foliaire
Self-vacancies in Gallium Arsenide: an ab initio calculation
We report here a reexamination of the static properties of vacancies in GaAs
by means of first-principles density-functional calculations using localized
basis sets. Our calculated formation energies yields results that are in good
agreement with recent experimental and {\it ab-initio} calculation and provide
a complete description of the relaxation geometry and energetic for various
charge state of vacancies from both sublattices. Gallium vacancies are stable
in the 0, -, -2, -3 charge state, but V_Ga^-3 remains the dominant charge state
for intrinsic and n-type GaAs, confirming results from positron annihilation.
Interestingly, Arsenic vacancies show two successive negative-U transitions
making only +1, -1 and -3 charge states stable, while the intermediate defects
are metastable. The second transition (-/-3) brings a resonant bond relaxation
for V_As^-3 similar to the one identified for silicon and GaAs divacancies.Comment: 14 page
Blimp-1-dependent and -independent natural antibody production by B-1 and B-1-derived plasma cells.
Natural antibodies contribute to tissue homeostasis and protect against infections. They are secreted constitutively without external antigenic stimulation. The differentiation state and regulatory pathways that enable continuous natural antibody production by B-1 cells, the main cellular source in mice, remain incompletely understood. Here we demonstrate that natural IgM-secreting B-1 cells in the spleen and bone marrow are heterogeneous, consisting of (a) terminally differentiated B-1-derived plasma cells expressing the transcriptional regulator of differentiation, Blimp-1, (b) Blimp-1+, and (c) Blimp-1neg phenotypic B-1 cells. Blimp-1neg IgM-secreting B-1 cells are not simply intermediates of cellular differentiation. Instead, they secrete similar amounts of IgM in wild-type and Blimp-1-deficient (PRDM-1ΔEx1A) mice. Blimp-1neg B-1 cells are also a major source of IgG3. Consequently, deletion of Blimp-1 changes neither serum IgG3 levels nor the amount of IgG3 secreted per cell. Thus, the pool of natural antibody-secreting B-1 cells is heterogeneous and contains a distinct subset of cells that do not use Blimp-1 for initiation or maximal antibody secretion
Nucleation and crystallization process of silicon using Stillinger-Weber potential
We study the homogeneous nucleation process in Stillinger-Weber silicon in
the NVT ensemble. A clear first-order transition from the liquid to crystal
phase is observed thermodynamically with kinetic and structural evidence of the
transformation. At 0.75 T_m, the critical cluster size is about 175 atoms. The
lifetime distribution of clusters as a function of the maximum size their reach
follows an inverse gaussian distribution as was predicted recently from the
classical theory of nucleation (CNT). However, while there is a qualitative
agreement with the CNT, the free energy curve obtained from the simulations
differs significantly from the theoretical predictions, suggesting that the
low-density liquid phase found recently could play a role in the nucleation
process.Comment: 21 page
Traveling through potential energy landscapes of disordered materials: the activation-relaxation technique
A detailed description of the activation-relaxation technique (ART) is
presented. This method defines events in the configurational energy landscape
of disordered materials, such as a-Si, glasses and polymers, in a two-step
process: first, a configuration is activated from a local minimum to a nearby
saddle-point; next, the configuration is relaxed to a new minimum; this allows
for jumps over energy barriers much higher than what can be reached with
standard techniques. Such events can serve as basic steps in equilibrium and
kinetic Monte Carlo schemes.Comment: 7 pages, 2 postscript figure
Structural, electronic, and dynamical properties of amorphous gallium arsenide: a comparison between two topological models
We present a detailed study of the effect of local chemical ordering on the
structural, electronic, and dynamical properties of amorphous gallium arsenide.
Using the recently-proposed ``activation-relaxation technique'' and empirical
potentials, we have constructed two 216-atom tetrahedral continuous random
networks with different topological properties, which were further relaxed
using tight-binding molecular dynamics. The first network corresponds to the
traditional, amorphous, Polk-type, network, randomly decorated with Ga and As
atoms. The second is an amorphous structure with a minimum of wrong (homopolar)
bonds, and therefore a minimum of odd-membered atomic rings, and thus
corresponds to the Connell-Temkin model. By comparing the structural,
electronic, and dynamical properties of these two models, we show that the
Connell-Temkin network is energetically favored over Polk, but that most
properties are little affected by the differences in topology. We conclude that
most indirect experimental evidence for the presence (or absence) of wrong
bonds is much weaker than previously believed and that only direct structural
measurements, i.e., of such quantities as partial radial distribution
functions, can provide quantitative information on these defects in a-GaAs.Comment: 10 pages, 7 ps figures with eps
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