90 research outputs found
Do theoretical physicists care about the protein-folding problem?
The prediction of the biologically active native conformation of a protein is
one of the fundamental challenges of structural biology. This problem remains
yet unsolved mainly due to three factors: the partial knowledge of the
effective free energy function that governs the folding process, the enormous
size of the conformational space of a protein and, finally, the relatively
small differences of energy between conformations, in particular, between the
native one and the ones that make up the unfolded state.
Herein, we recall the importance of taking into account, in a detailed
manner, the many interactions involved in the protein folding problem (such as
steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar
interactions, coulombic energy or hydrophobic attraction) and we propose a
strategy to effectively construct a free energy function that, including the
effects of the solvent, could be numerically tractable. It must be pointed out
that, since the internal free energy function that is mainly described does not
include the constraints of the native conformation, it could only help to reach
the 'molten globule' state. We also discuss about the limits and the lacks from
which suffer the simple models that we, physicists, love so much.Comment: 27 pages, 4 figures, LaTeX file, aipproc package. To be published in
the book: "Meeting on Fundamental Physics 'Alberto Galindo'", Alvarez-Estrada
R. F. et al. (Ed.), Madrid: Aula Documental, 200
Atomic and vibrational origins of mechanical toughness in bioactive cement during setting
Bioactive glass ionomer cements (GICs) have been in widespread use for ~40 years in dentistry and medicine. However, these composites fall short of the toughness needed for permanent implants. Significant impediment to improvement has been the requisite use of conventional destructive mechanical testing, which is necessarily retrospective. Here we show quantitatively, through the novel use of calorimetry, terahertz (THz) spectroscopy and neutron scattering, how GIC’s developing fracture toughness during setting is related to interfacial THz dynamics, changing atomic cohesion and fluctuating interfacial configurations. Contrary to convention, we find setting is non-monotonic, characterized by abrupt features not previously detected, including a glass–polymer coupling point, an early setting point, where decreasing toughness unexpectedly recovers, followed by stress-induced weakening of interfaces. Subsequently, toughness declines asymptotically to long-term fracture test values. We expect the insight afforded by these in situ non-destructive techniques will assist in raising understanding of the setting mechanisms and associated dynamics of cementitious materials
First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data
Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of
continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a
fully coherent search, based on matched filtering, which uses the position and rotational parameters
obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto-
noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch
between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have
been developed, allowing a fully coherent search for gravitational waves from known pulsars over a
fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of
11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial
outliers, further studies show no significant evidence for the presence of a gravitational wave signal.
Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of
the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for
the first time. For an additional 3 targets, the median upper limit across the search bands is below the
spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried
out so far
Spectroscopic Evidence for an Oxazolone Structure in Anionic b-Type Peptide Fragments
Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b2 fragments of deprotonated AlaAlaAla and AlaTyrAla have been recorded over the 800–1800 cm–1 spectral range by multiple-photon dissociation (MPD) spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Structural characterization of the b-type fragments is accomplished by comparison with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. Although diketopiperazine structures represent the energetically lowest isomers, the IR spectra suggest an oxazolone structure for the b2 fragments of both peptides. Deprotonation is shown to occur on the oxazolone α-carbon, which leads to a conjugated structure in which the negative charge is practically delocalized over the entire oxazolone ring, providing enhanced gas-phase stability
Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry
Searches for gravitational waves from known pulsars at two harmonics in 2015-2017 LIGO data
International audienceWe present a search for gravitational waves from 222 pulsars with rotation frequencies ≳10 Hz. We use advanced LIGO data from its first and second observing runs spanning 2015–2017, which provides the highest-sensitivity gravitational-wave data so far obtained. In this search we target emission from both the l = m = 2 mass quadrupole mode, with a frequency at twice that of the pulsar’s rotation, and the l = 2, m = 1 mode, with a frequency at the pulsar rotation frequency. The search finds no evidence for gravitational-wave emission from any pulsar at either frequency. For the l = m = 2 mode search, we provide updated upper limits on the gravitational-wave amplitude, mass quadrupole moment, and fiducial ellipticity for 167 pulsars, and the first such limits for a further 55. For 20 young pulsars these results give limits that are below those inferred from the pulsars’ spin-down. For the Crab and Vela pulsars our results constrain gravitational-wave emission to account for less than 0.017% and 0.18% of the spin-down luminosity, respectively. For the recycled millisecond pulsar J0711−6830 our limits are only a factor of 1.3 above the spin-down limit, assuming the canonical value of 1038 kg m2 for the star’s moment of inertia, and imply a gravitational-wave-derived upper limit on the star’s ellipticity of 1.2 × 10−8. We also place new limits on the emission amplitude at the rotation frequency of the pulsars
All-sky search for long-duration gravitational-wave bursts in the third Advanced LIGO and Advanced Virgo run
After the detection of gravitational waves from compact binary coalescences, the search for transient gravitational-wave signals with less well-defined waveforms for which matched filtering is not well suited is one of the frontiers for gravitational-wave astronomy. Broadly classified into “short” ≲1 s and “long” ≳1 s duration signals, these signals are expected from a variety of astrophysical processes, including non-axisymmetric deformations in magnetars or eccentric binary black hole coalescences. In this work, we present a search for long-duration gravitational-wave transients from Advanced LIGO and Advanced Virgo’s third observing run from April 2019 to March 2020. For this search, we use minimal assumptions for the sky location, event time, waveform morphology, and duration of the source. The search covers the range of 2–500 s in duration and a frequency band of 24–2048 Hz. We find no significant triggers within this parameter space; we report sensitivity limits on the signal strength of gravitational waves characterized by the root-sum-square amplitude hrss as a function of waveform morphology. These hrss limits improve upon the results from the second observing run by an average factor of 1.8
Search for anisotropic gravitational-wave backgrounds using data from Advanced LIGO and Advanced Virgo's first three observing runs
We report results from searches for anisotropic stochastic gravitational-wave
backgrounds using data from the first three observing runs of the Advanced LIGO
and Advanced Virgo detectors. For the first time, we include Virgo data in our
analysis and run our search with a new efficient pipeline called {\tt PyStoch}
on data folded over one sidereal day. We use gravitational-wave radiometry
(broadband and narrow band) to produce sky maps of stochastic
gravitational-wave backgrounds and to search for gravitational waves from point
sources. A spherical harmonic decomposition method is employed to look for
gravitational-wave emission from spatially-extended sources. Neither technique
found evidence of gravitational-wave signals. Hence we derive 95\%
confidence-level upper limit sky maps on the gravitational-wave energy flux
from broadband point sources, ranging from and on the
(normalized) gravitational-wave energy density spectrum from extended sources,
ranging from , depending on direction () and spectral index
(). These limits improve upon previous limits by factors of . We also set 95\% confidence level upper limits on the frequency-dependent
strain amplitudes of quasimonochromatic gravitational waves coming from three
interesting targets, Scorpius X-1, SN 1987A and the Galactic Center, with best
upper limits range from a factor of
improvement compared to previous stochastic radiometer searches.Comment: 23 Pages, 9 Figure
Diving below the spin-down limit:constraints on gravitational waves from the energetic young pulsar PSR J0537-6910
We present a search for continuous gravitational-wave signals from the young, energetic X-ray pulsar PSR J0537-6910 using data from the second and third observing runs of LIGO and Virgo. The search is enabled by a contemporaneous timing ephemeris obtained using NICER data. The NICER ephemeris has also been extended through 2020 October and includes three new glitches. PSR J0537-6910 has the largest spin-down luminosity of any pulsar and is highly active with regards to glitches. Analyses of its long-term and inter-glitch braking indices provided intriguing evidence that its spin-down energy budget may include gravitational-wave emission from a time-varying mass quadrupole moment. Its 62 Hz rotation frequency also puts its possible gravitational-wave emission in the most sensitive band of LIGO/Virgo detectors. Motivated by these considerations, we search for gravitational-wave emission at both once and twice the rotation frequency. We find no signal, however, and report our upper limits. Assuming a rigidly rotating triaxial star, our constraints reach below the gravitational-wave spin-down limit for this star for the first time by more than a factor of two and limit gravitational waves from the l = m = 2 mode to account for less than 14% of the spin-down energy budget. The fiducial equatorial ellipticity is limited to less than about 3 x 10⁻⁵, which is the third best constraint for any young pulsar
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