16,294 research outputs found
Effects of constraints in general branched molecules: A quantitative ab initio study in HCO-L-Ala-NH2
A general approach to the design of accurate classical potentials for protein
folding is described. It includes the introduction of a meaningful statistical
measure of the differences between approximations of the same potential energy,
the definition of a set of Systematic and Approximately Separable and Modular
Internal Coordinates (SASMIC), much convenient for the simulation of general
branched molecules, and the imposition of constraints on the most rapidly
oscillating degrees of freedom. All these tools are used to study the effects
of constraints in the Conformational Equilibrium Distribution (CED) of the
model dipeptide HCO-L-Ala-NH2. We use ab initio Quantum Mechanics calculations
including electron correlation at the MP2 level to describe the system, and we
measure the conformational dependence of the correcting terms to the naive CED
based in the Potential Energy Surface (PES) without any simplifying assumption.
These terms are related to mass-metric tensors determinants and also occur in
the Fixman's compensating potential. We show that some of the corrections are
non-negligible if one is interested in the whole Ramachandran space. On the
other hand, if only the energetically lower region, containing the principal
secondary structure elements, is assumed to be relevant, then, all correcting
terms may be neglected up to peptides of considerable length. This is the first
time, as far as we know, that the analysis of the conformational dependence of
these correcting terms is performed in a relevant biomolecule with a realistic
potential energy function.Comment: 8 pages, 1 figure, LaTeX, aipproc style (included
A Statistical Study of Photospheric Magnetic Field Changes During 75 Solar Flares
Abrupt and permanent changes of photospheric magnetic fields have been
observed during solar flares. The changes seem to be linked to the
reconfiguration of magnetic fields, but their origin is still unclear. We
carried out a statistical analysis of permanent line-of-sight magnetic field
() changes during 18 X-, 37 M-, 19 C- and 1 B-class flares using
data from Solar Dynamics Observatory/Helioseismic and Magnetic Imager. We
investigated the properties of permanent changes, such as frequency, areas, and
locations. We detected changes of in 59/75 flares. We find that
strong flares are more likely to show changes, with all flares M1.6
exhibiting them. For weaker flares, permanent changes are observed in 6/17
C-flares. 34.3\% of the permanent changes occurred in the penumbra and 18.9\%
in the umbra. Parts of the penumbra appeared or disappeared in 23/75 flares.
The area where permanent changes occur is larger for stronger flares. Strong
flares also show a larger change of flux, but there is no dependence of the
magnetic flux change on the heliocentric angle. The mean rate of change of
flare-related magnetic field changes is 20.7 Mx cm min. The
number of permanent changes decays exponentially with distance from the
polarity inversion line. The frequency of the strength of permanent changes
decreases exponentially, and permanent changes up to 750 Mx cm were
observed. We conclude that permanent magnetic field changes are a common
phenomenon during flares, and future studies will clarify their relation to
accelerated electrons, white light emission, and sunquakes to further
investigate their origin.Comment: Piblished in Ap
Flow damping in stellarators close to quasisymmetry
Quasisymmetric stellarators are a type of optimized stellarators for which
flows are undamped to lowest order in an expansion in the normalized Larmor
radius. However, perfect quasisymmetry is impossible. Since large flows may be
desirable as a means to reduce turbulent transport, it is important to know
when a stellarator can be considered to be sufficiently close to quasisymmetry.
The answer to this question depends strongly on the size of the spatial
gradients of the deviation from quasisymmetry and on the collisionality regime.
Recently, formal criteria for closeness to quasisymmetry have been derived in a
variety of situations. In particular, the case of deviations with large
gradients was solved in the regime. Denoting by a parameter
that gives the size of the deviation from quasisymmetry, it was proven that
particle fluxes do not scale with , as typically claimed, but
with . It was also shown that ripple wells are not necessarily the main
cause of transport. This paper reviews those works and presents a new result in
another collisionality regime, in which particles trapped in ripple wells are
collisional and the rest are collisionless.Comment: 14 pages, 2 figures. To appear in Plasma Physics and Controlled
Fusio
Optimizing stellarators for large flows
Plasma flow is damped in stellarators because they are not intrinsically
ambipolar, unlike tokamaks, in which the flux-surface averaged radial electric
current vanishes for any value of the radial electric field. Only
quasisymmetric stellarators are intrinsically ambipolar, but exact
quasisymmetry is impossible to achieve in non-axisymmetric toroidal
configurations. By calculating the violation of intrinsic ambipolarity due to
deviations from quasisymmetry, one can derive criteria to assess when a
stellarator can be considered quasisymmetric in practice, i.e. when the flow
damping is weak enough. Let us denote by a small parameter that
controls the size of a perturbation to an exactly quasisymmetric magnetic
field. Recently, it has been shown that if the gradient of the perturbation is
sufficiently small, the flux-surface averaged radial electric current scales as
for any value of the collisionality. It was also argued that when
the gradient of the perturbation is large, the quadratic scaling is replaced by
a more unfavorable one. In this paper, perturbations with large gradients are
rigorously treated. In particular, it is proven that for low collisionality a
perturbation with large gradient yields, at best, an deviation
from quasisymmetry. Heuristic estimations in the literature incorrectly
predicted an deviation.Comment: 24 pages, 2 figures. To appear in Plasma Physics and Controlled
Fusio
The effect of tangential drifts on neoclassical transport in stellarators close to omnigeneity
In general, the orbit-averaged radial magnetic drift of trapped particles in
stellarators is non-zero due to the three-dimensional nature of the magnetic
field. Stellarators in which the orbit-averaged radial magnetic drift vanishes
are called omnigeneous, and they exhibit neoclassical transport levels
comparable to those of axisymmetric tokamaks. However, the effect of deviations
from omnigeneity cannot be neglected in practice. For sufficiently low
collision frequencies (below the values that define the regime), the
components of the drifts tangential to the flux surface become relevant. This
article focuses on the study of such collisionality regimes in stellarators
close to omnigeneity when the gradient of the non-omnigeneous perturbation is
small. First, it is proven that closeness to omnigeneity is required to
preserve radial locality in the drift-kinetic equation for collisionalities
below the regime. Then, it is shown that neoclassical transport is
determined by two layers in phase space. One of the layers corresponds to the
regime and the other to the superbanana-plateau regime. The
importance of the superbanana-plateau layer for the calculation of the
tangential electric field is emphasized, as well as the relevance of the latter
for neoclassical transport in the collisionality regimes considered in this
paper. In particular, the tangential electric field is essential for the
emergence of a new subregime of superbanana-plateau transport when the radial
electric field is small. A formula for the ion energy flux that includes the
regime and the superbanana-plateau regime is given. The energy
flux scales with the square of the size of the deviation from omnigeneity.
Finally, it is explained why below a certain collisionality value the
formulation presented in this article ceases to be valid.Comment: 36 pages. Version to be published in Plasma Physics and Controlled
Fusio
Phase changes in 38 atom Lennard-Jones clusters. II: A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical
We study the 38-atom Lennard-Jones cluster with parallel tempering Monte
Carlo methods in the microcanonical and molecular dynamics ensembles. A new
Monte Carlo algorithm is presented that samples rigorously the molecular
dynamics ensemble for a system at constant total energy, linear and angular
momenta. By combining the parallel tempering technique with molecular dynamics
methods, we develop a hybrid method to overcome quasi-ergodicity and to extract
both equilibrium and dynamical properties from Monte Carlo and molecular
dynamics simulations. Several thermodynamic, structural and dynamical
properties are investigated for LJ, including the caloric curve, the
diffusion constant and the largest Lyapunov exponent. The importance of
insuring ergodicity in molecular dynamics simulations is illustrated by
comparing the results of ergodic simulations with earlier molecular dynamics
simulations.Comment: Journal of Chemical Physics, accepte
Electrostatic potential variations on stellarator magnetic surfaces in low collisionality regimes
The component of the neoclassical electrostatic potential that is
non-constant on the magnetic surface, that we denote by , can
affect radial transport of highly charged impurities, and this has motivated
its inclusion in some modern neoclassical codes. The number of neoclassical
simulations in which is calculated is still scarce, partly
because they are usually demanding in terms of computational resources,
especially at low collisionality. In this paper the size, the scaling with
collisionality and with aspect ratio, and the structure of on
the magnetic surface are analytically derived in the , and
superbanana-plateau regimes of stellarators close to omnigeneity; i. e.
stellarators that have been optimized for neoclassical transport. It is found
that the largest that the neoclassical equations admit scales
linearly with the inverse aspect ratio and with the size of the deviation from
omnigeneity. Using a model for a perturbed omnigeneous configuration, the
analytical results are verified and illustrated with calculations by the code
KNOSOS. The techniques, results and numerical tools employed in this paper can
be applied to neoclassical transport problems in tokamaks with broken
axisymmetry.Comment: 30 pages, 12 figures, 1 table. Published versio
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