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, $\gamma$, is appropriately fixed. This also relates the chemical potential to $\gamma$. 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.

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 $4989$ molecules from the QM9 dataset and a small in-house dataset of $516$ 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 $3$ 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

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