11,217 research outputs found
Is protein folding problem really a NP-complete one ? First investigations
To determine the 3D conformation of proteins is a necessity to understand
their functions or interactions with other molecules. It is commonly admitted
that, when proteins fold from their primary linear structures to their final 3D
conformations, they tend to choose the ones that minimize their free energy. To
find the 3D conformation of a protein knowing its amino acid sequence,
bioinformaticians use various models of different resolutions and artificial
intelligence tools, as the protein folding prediction problem is a NP complete
one. More precisely, to determine the backbone structure of the protein using
the low resolution models (2D HP square and 3D HP cubic), by finding the
conformation that minimize free energy, is intractable exactly. Both the proof
of NP-completeness and the 2D prediction consider that acceptable conformations
have to satisfy a self-avoiding walk (SAW) requirement, as two different amino
acids cannot occupy a same position in the lattice. It is shown in this
document that the SAW requirement considered when proving NP-completeness is
different from the SAW requirement used in various prediction programs, and
that they are different from the real biological requirement. Indeed, the proof
of NP completeness and the predictions in silico consider conformations that
are not possible in practice. Consequences of this fact are investigated in
this research work.Comment: Submitted to Journal of Bioinformatics and Computational Biology,
under revie
Influence of Rough and Smooth Walls on Macroscale Flows in Tumblers
Walls in discrete element method simulations of granular flows are sometimes
modeled as a closely packed monolayer of fixed particles, resulting in a rough
wall rather than a geometrically smooth wall. An implicit assumption is that
the resulting rough wall differs from a smooth wall only locally at the
particle scale. Here we test this assumption by considering the impact of the
wall roughness at the periphery of the flowing layer on the flow of
monodisperse particles in a rotating spherical tumbler. We find that varying
the wall roughness significantly alters average particle trajectories even far
from the wall. Rough walls induce greater poleward axial drift of particles
near the flowing layer surface, but decrease the curvature of the trajectories.
Increasing the volume fill level in the tumbler has little effect on the axial
drift for rough walls, but increases the drift while reducing curvature of the
particle trajectories for smooth walls. The mechanism for these effects is
related to the degree of local slip at the bounding wall, which alters the
flowing layer thickness near the walls, affecting the particle trajectories
even far from the walls near the equator of the tumbler. Thus, the proper
choice of wall conditions is important in the accurate simulation of granular
flows, even far from the bounding wall.Comment: 32 pages, 19 figures, regular article, accepted for publication in
Physical Review E 200
Simulation of the elementary evolution operator with the motional states of an ion in an anharmonic trap
Following a recent proposal of L. Wang and D. Babikov, J. Chem. Phys. 137,
064301 (2012), we theoretically illustrate the possibility of using the
motional states of a ion trapped in a slightly anharmonic potential to
simulate the single-particle time-dependent Schr\"odinger equation. The
simulated wave packet is discretized on a spatial grid and the grid points are
mapped on the ion motional states which define the qubit network. The
localization probability at each grid point is obtained from the population in
the corresponding motional state. The quantum gate is the elementary evolution
operator corresponding to the time-dependent Schr\"odinger equation of the
simulated system. The corresponding matrix can be estimated by any numerical
algorithm. The radio-frequency field able to drive this unitary transformation
among the qubit states of the ion is obtained by multi-target optimal control
theory. The ion is assumed to be cooled in the ground motional state and the
preliminary step consists in initializing the qubits with the amplitudes of the
initial simulated wave packet. The time evolution of the localization
probability at the grids points is then obtained by successive applications of
the gate and reading out the motional state population. The gate field is
always identical for a given simulated potential, only the field preparing the
initial wave packet has to be optimized for different simulations. We check the
stability of the simulation against decoherence due to fluctuating electric
fields in the trap electrodes by applying dissipative Lindblad dynamics.Comment: 31 pages, 8 figures. Revised version. New title, new figure and new
reference
Cooling of the crust in the neutron star low-mass X-ray binary MXB 1659-29
In quasi-persistent neutron star transients, long outbursts cause the neutron
star crust to be heated out of thermal equilibrium with the rest of the star.
During quiescence, the crust then cools back down. Such crustal cooling has
been observed in two quasi-persistent sources: KS 1731-260 and MXB 1659-29.
Here we present an additional Chandra observation of MXB 1659-29 in quiescence,
which extends the baseline of monitoring to 6.6 yr after the end of the
outburst. This new observation strongly suggests that the crust has thermally
relaxed, with the temperature remaining consistent over 1000 days. Fitting the
temperature cooling curve with an exponential plus constant model we determine
an e-folding timescale of 465 +/- 25 days, with the crust cooling to a constant
surface temperature of kT = 54 +/- 2 eV (assuming D=10 kpc). From this, we
infer a core temperature in the range 3.5E7-8.3E7 K (assuming D=10 kpc), with
the uncertainty due to the surface composition. Importantly, we tested two
neutron star atmosphere models as well as a blackbody model, and found that the
thermal relaxation time of the crust is independent of the chosen model and the
assumed distance.Comment: accepted for publication in ApJL, 4 pages, 1 figure
The Quiescent X-ray Spectrum of Accreting Black Holes
The quiescent state is the dominant accretion mode for black holes on all
mass scales. Our knowledge of the X-ray spectrum is limited due to the
characteristic low luminosity in this state. Herein, we present an analysis of
the sample of dynamically-confirmed stellar-mass black holes observed in
quiescence in the \textit{Chandra/XMM-Newton/Suzaku} era resulting in a sample
of 8 black holes with 570 ks of observations. In contrast to the
majority of AGN where observations are limited by contamination from diffuse
gas, the stellar-mass systems allow for a clean study of the X-ray spectrum
resulting from the accretion flow alone. The data are characterized using
simple models. We find a model consisting of a power-law or thermal
bremsstrahlung to both provide excellent descriptions of the data, where we
measure and
respectively in the 0.3 -- 10 keV bandpass, at a median luminosity of . This result in discussed in the context of our
understanding of the accretion flow onto stellar and supermassive black holes
at low luminosities.Comment: 12 pages, 5 figures, 2 tables, MNRAS accepte
The Effects of ITQ Management on Fishermen’s Welfare When the Processing Sector is Imperfectly Competitive
In this paper we use a general model of imperfect competition to predict welfare changes within an open-access fishery transitioning to individual transferable quota (ITQ) management. Although related research has explored the effects of market power in the harvesting sector on ITQ performance, none have considered the implications of an imperfectly competitive processing sector. This study addresses this question specifically in the context of the Atlantic herring fishery, although its implications are relevant to all fisheries with similar industry structure. Our results show that ITQs could have a negative impact on fishermen’s welfare when processors have market power and the cap on aggregate harvest is binding or becomes binding with the implementation of ITQs.ITQ, imperfect competition, welfare analysis, fisheries
Surviving Mathematics
In this essay written in an informal voice, the author shares the ups and downs of her experience in academia. She shares her motivation to study mathematics, her undergraduate experience in Puerto Rico, and her graduate experience in South Texas
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