2,584 research outputs found
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.
Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace
Statistical analysis of entropy correction from topological defects in Loop Black Holes
In this paper we discuss the entropy of quantum black holes in the LQG
formalism when the number of punctures on the horizon is treated as a quantum
hair, that is we compute the black hole entropy in the grand canonical (area)
ensemble. The entropy is a function of both the average area and the average
number of punctures and bears little resemblance to the Bekenstein-Hawking
entropy. In the thermodynamic limit, both the "temperature" and the chemical
potential can be shown to be functions only of the average area per puncture.
At a fixed temperature, the average number of punctures becomes proportional to
the average area and we recover the Bekenstein-Hawking area-entropy law to
leading order provided that the Barbero-Immirzi parameter, , is
appropriately fixed. This also relates the chemical potential to . We
obtain a sub-leading correction, which differs in signature from that obtained
in the microcanonical and canonical ensembles in its sign but agrees with
earlier results in the grand canonical ensemble.Comment: 12 pages, no figures. Version to appear in Phys. Rev.
Walking Toward the Demonumentalization of Qualitative Research: A Collaborative Autoethnography Account While Producing an Educational Podcast
This article examines how two teacher educators, as researchers and as research teachers, engaged in a collaborative interpretation of their autoethnographies about questioning an instrumentalist and positivist research culture in the field of English Language Teaching (ELT). The autoethnographies simultaneously emerged from the research activities related to the production of a bilingual podcast named “Conversing about Investigación Cualitativa.” Specifically, the authors conducted a qualitative study of autoethnographic and collaborative nature while working on their podcast. The data were individual written retrospective accounts, which were shared, discussed, and interpreted in online live meetings. The outcomes of the study were encapsulated in a major theme called Qualitative research: The path traveled from dogma to critical awareness, and three subsidiary themes named Questioning the culture of scientificity from our research experiences; Adopting a critical perspective (but still teaching by the book); and Empowering ourselves as teachers and as research teachers. Overall, this study emphasized a questioning attitude toward building a critical perspective from which examine alternatives to demonumentalize qualitative research without falling into extremes. Thus, it contributes to finding a balance between dogma and skepticism through a dialogue between local and global research agendas
Application of quantum-inspired generative models to small molecular datasets
Quantum and quantum-inspired machine learning has emerged as a promising and
challenging research field due to the increased popularity of quantum
computing, especially with near-term devices. Theoretical contributions point
toward generative modeling as a promising direction to realize the first
examples of real-world quantum advantages from these technologies. A few
empirical studies also demonstrate such potential, especially when considering
quantum-inspired models based on tensor networks. In this work, we apply
tensor-network-based generative models to the problem of molecular discovery.
In our approach, we utilize two small molecular datasets: a subset of
molecules from the QM9 dataset and a small in-house dataset of validated
antioxidants from TotalEnergies. We compare several tensor network models
against a generative adversarial network using different sample-based metrics,
which reflect their learning performances on each task, and multiobjective
performances using relevant molecular metrics per task. We also combined
the output of the models and demonstrate empirically that such a combination
can be beneficial, advocating for the unification of classical and
quantum(-inspired) generative learning.Comment: First versio
The song of the dunes as a self-synchronized instrument
Since Marco Polo (1) it has been known that some sand dunes have the peculiar
ability of emitting a loud sound with a well defined frequency, sometimes for
several minutes. The origin of this sustained sound has remained mysterious,
partly because of its rarity in nature (2). It has been recognized that the
sound is not due to the air flow around the dunes but to the motion of an
avalanche (3), and not to an acoustic excitation of the grains but to their
relative motion (4-7). By comparing several singing dunes and two controlled
experiments, one in the laboratory and one in the field, we here demonstrate
that the frequency of the sound is the frequency of the relative motion of the
sand grains. The sound is produced because some moving grains synchronize their
motions. The existence of a velocity threshold in both experiments further
shows that this synchronization comes from an acoustic resonance within the
flowing layer: if the layer is large enough it creates a resonance cavity in
which grains self-synchronize.Comment: minor changes, essentially more references
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Marco Polo: A near Earth object sample return mission
From Introduction:
MARCO POLO is a joint European-Japanese sample return mission to a Near-Earth Object. In late 2007 this mission was selected by ESA, in the framework of COSMIC VISION 2015-2025, for an assessment scheduled to last until mid 2009.
This Euro-Asian mission will go to a primitive Near-Earth Object (NEO), such as a C or D type asteroid. The spacecraft will rendezvous with the object, and over an extended period scientifically characterize it at multiple scales and bring samples back to Earth for detailed scientific investigation
Ubiquitin ligases and beyond
First paragraph (this article has no abstract): In a review published in 2004 [1] and that still repays reading today, Cecile Pickart traced the evolution of research on ubiquitination from its origins in the proteasomal degradation of proteins through the revelation that it has a central role in cell cycle regulation and the recognition of regulatory roles for ubiquitin in intracellular membrane transport, cell signalling, transcription, translation, and DNA repair
Ab Initio Molecular Dynamics on the Electronic Boltzmann Equilibrium Distribution
We prove that for a combined system of classical and quantum particles, it is
possible to write a dynamics for the classical particles that incorporates in a
natural way the Boltzmann equilibrium population for the quantum subsystem. In
addition, these molecular dynamics do not need to assume that the electrons
immediately follow the nuclear motion (in contrast to any adiabatic approach),
and do not present problems in the presence of crossing points between
different potential energy surfaces (conical intersections or spin-crossings).
A practical application of this molecular dynamics to study the effect of
temperature in molecular systems presenting (nearly) degenerate states - such
as the avoided crossing in the ring-closure process of ozone - is presented.Comment: published in New J. Phy
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