6,836 research outputs found
Transient hydrophobic exposure in the molecular dynamics of Abeta peptide at low water concentration
Abeta is a disordered peptide central to Alzheimer's Disease. Aggregation of
Abeta has been widely explored, but its molecular crowding less so. The
synaptic cleft where Abeta locates only holds 60-70 water molecules along its
width. We subjected Abeta40 to 100 different simulations with variable water
cell size. We show that even for this disordered aggregation-prone peptide,
many properties are not cell-size dependent, i.e. a small cell is easily
justified. The radius of gyration, intra-peptide, and peptide-water hydrogen
bonds are well-sampled by short (50 ns) time scales at any cell size. Abeta is
mainly disordered with 0-30% alpha helix but undergoes consistent alpha-beta
transitions up to 14% strand in 5-10% of the simulations regardless of cell
size. The similar prevalence in long and short simulations indicate small
diffusion barriers for structural transitions in contrast to folded globular
proteins, which we suggest is a defining hallmark of intrinsically disordered
proteins. Importantly, the hydrophobic surface increases significantly in small
cells (confidence level 95%, two-tailed t-test), as does the variation in
exposure and backbone conformations (>40% and >27% increased standard
deviations). Whereas hydrophilic exposure dominates hydrophobic exposure in
large cells, this tendency breaks down at low water concentration. We interpret
these findings as a concentration-dependent hydrophobic effect, with the small
water layer unable to keep the protein unexposed, an effect mainly caused by
the layered water-water interactions, not by the peptide dynamics. The exposure
correlates with radius of gyration (R2 0.35-0.50) and could be important in
crowded environments, e.g. the synaptic cleft
A study of purely astrometric selection of extragalactic point sources with Gaia
Selection of extragalactic point sources, e.g. QSOs, is often hampered by
significant selection effects causing existing samples to have rather complex
selection functions. We explore whether a purely astrometric selection of
extragalactic point sources, e.g. QSOs, is feasible with the ongoing Gaia
mission. Such a selection would be interesting as it would be unbiased in terms
of colours of the targets and hence would allow selection also with colours in
the stellar sequence. We have analyzed a total of 18 representative regions of
the sky by using GUMS, the simulator prepared for ESAs Gaia mission, both in
the range of mag and mag. For each region we
determine the density of apparently stationary stellar sources, i.e. sources
for which Gaia cannot measure a significant proper motion. The density is
contrasted with the density of extragalactic point sources, e.g. QSOs, in order
to establish in which celestial directions a pure astrometric selection is
feasible. When targeting regions at galactic latitude
the ratio of QSOs to apparently stationary stars is above 50\% and when
observing towards the poles the fraction of QSOs goes up to about \%.
We show that the proper motions from the proposed Gaia successor mission in
about 20 years would dramatically improve these results at all latitudes.
Detection of QSOs solely from zero proper motion, unbiased by any assumptions
on spectra, might lead to the discovery of new types of QSOs or new classes of
extragalactic point sources.Comment: 4 pages, 4 figures, sent in and accepted for publishing to A&
Local Decoders for the 2D and 4D Toric Code
We analyze the performance of decoders for the 2D and 4D toric code which are
local by construction. The 2D decoder is a cellular automaton decoder
formulated by Harrington which explicitly has a finite speed of communication
and computation. For a model of independent and errors and faulty
syndrome measurements with identical probability we report a threshold of
for this Harrington decoder. We implement a decoder for the 4D toric
code which is based on a decoder by Hastings arXiv:1312.2546 . Incorporating a
method for handling faulty syndromes we estimate a threshold of for
the same noise model as in the 2D case. We compare the performance of this
decoder with a decoder based on a 4D version of Toom's cellular automaton rule
as well as the decoding method suggested by Dennis et al.
arXiv:quant-ph/0110143 .Comment: 22 pages, 21 figures; fixed typos, updated Figures 6,7,8,
Survival of the cheapest: How proteome cost minimization drives evolution
Darwin's theory of evolution emphasized that positive selection of functional
proficiency provides the fitness that ultimately determines the structure of
life, a view that has dominated biochemical thinking of enzymes as perfectly
optimized for their specific functions. The 20th-century modern synthesis,
structural biology, and the central dogma explained the machinery of evolution,
and nearly neutral theory explained how selection competes with random fixation
dynamics that produce molecular clocks essential e.g. for dating evolutionary
histories. However, the quantitative proteomics revealed that fitness effects
not related to functional proficiency play much larger roles on long
evolutionary time scales than previously thought, with particular evidence that
some universal biophysical selection pressures act via protein expression
levels. This paper first summarizes recent progress in the 21st century towards
recovering this universal selection pressure. Then, the paper argues that
proteome cost minimization is the dominant, underlying "non-function" selection
pressure controlling most of the evolution of already functionally adapted
living systems. A theory of proteome cost minimization is described and argued
to have consequences for understanding evolutionary trade-offs, aging, cancer,
and neurodegenerative protein-misfolding diseases
Experimental and theoretical investigation of fatigue life in reusable rocket thrust chambers
During a test program to investigate low-cycle thermal fatigue, 13 rocket combustion chambers were fabricated and cyclically test fired to failure. Six oxygen-free, high-conductivity (OFHC) copper and seven Amzirc chambers were tested. The failures in the OFHC copper chambers were not typical fatigue failures but are described as creep rupture enhanced by ratcheting. The coolant channels bulged toward the chamber centerline, resulting in progressive thinning of the wall during each cycle. The failures in the Amzirc alloy chambers were caused by low-cycle thermal fatigue. The zirconium in this alloy was not evenly distributed in the chamber materials. The life that was achieved was nominally the same as would have been predicted from OFHC copper isothermal test data
Crossing the Logarithmic Barrier for Dynamic Boolean Data Structure Lower Bounds
This paper proves the first super-logarithmic lower bounds on the cell probe
complexity of dynamic boolean (a.k.a. decision) data structure problems, a
long-standing milestone in data structure lower bounds.
We introduce a new method for proving dynamic cell probe lower bounds and use
it to prove a lower bound on the operational
time of a wide range of boolean data structure problems, most notably, on the
query time of dynamic range counting over ([Pat07]). Proving an
lower bound for this problem was explicitly posed as one of
five important open problems in the late Mihai P\v{a}tra\c{s}cu's obituary
[Tho13]. This result also implies the first lower bound for the
classical 2D range counting problem, one of the most fundamental data structure
problems in computational geometry and spatial databases. We derive similar
lower bounds for boolean versions of dynamic polynomial evaluation and 2D
rectangle stabbing, and for the (non-boolean) problems of range selection and
range median.
Our technical centerpiece is a new way of "weakly" simulating dynamic data
structures using efficient one-way communication protocols with small advantage
over random guessing. This simulation involves a surprising excursion to
low-degree (Chebychev) polynomials which may be of independent interest, and
offers an entirely new algorithmic angle on the "cell sampling" method of
Panigrahy et al. [PTW10]
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