Ikerbasque

About: Ikerbasque is a other organization based out in Bilbao, Spain. It is known for research contribution in the topics: Graphene & Population. The organization has 713 authors who have published 7967 publications receiving 231990 citations. The organization is also known as: Basque Foundation for Science.

Circuit quantum electrodynamics in the ultrastrong-coupling regime

Abstract: The Jaynes–Cummings model describes the interaction between a two-level system and a small number of photons. It is now shown that the model breaks down in the regime of ultrastrong coupling between light and matter. The spectroscopic response of a superconducting artificial atom in a waveguide resonator indicates higher-order processes.

Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation

Abstract: Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field.

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

What is the covalency of hydrogen bonding

Abstract: Hydrogen bonding is an important interaction playing a key role in chemical, physical, and biochemical processes. One can mention numerous examples such as the role of hydrogen bonding in enzymatic catalysis, arrangement of molecules in crystals, crystal engineering, proton transfer reactions, and also its important role in life processes. Hence, its nature is often the subject of investigations and polemics. One of the first definitions of hydrogen bonding was formulated by Pauling who stated that “under certain conditions an atom of hydrogen is attracted by rather strong forces to two atoms, instead of only one, so that it may be considered to be acting as a bond between them. This is called the hydrogen bond”. Pauling also pointed out that the hydrogen atom is situated only between the most electronegative atoms and it usually interacts much stronger with one of them. The latter interaction is a typical covalent bond (A-H). The interaction between hydrogen and another electronegative atom is much weaker and mostly electrostatic in nature; it is a nonbonding interaction (H 3 3 3B). This system is often designated as AH 3 3 3B where the B-center (acceptor of proton) should possess at least one lone electron pair; A-H is called the protondonating bond. Pauling stated that sometimes the H 3 3 3B interaction possesses characteristics of the covalent bond. The [FHF] ion is an example where the proton is inserted between two negative fluorine ions, accurately in the middle of the F 3 3 3 F distance. Hence, both H 3 3 3 F interactions are equivalent. This is in line with an early conclusion of Lewis that “an atom of hydrogen may at times be attached to two electron pairs of two different atoms” and with the statement of Latimer and Rodebush that “the hydrogen nucleus held by two octets constitutes a weak bond”. The latter statements correspond to recent studies on proton bound homodimers, that is, systems where the proton is inserted between two closed-shell moieties and where it often interacts equivalently with both of them. Chan and co-workers analyzed recently what factors determine whether the protonbound homodimer has a symmetric or an asymmetric hydrogen bond. In the other study, it is discussed what conditions should be fulfilled for the proton situated accurately in the midpoint of the donor-acceptor distance. The high level calculations up to CCSD(T)/6-311þþ(3df,3pd)//CCSD/6-311þþ(3df,3pd) were performed on the [FHF] ion and systems with O-H 3 3 3O or N-H 3 3 3N hydrogen bonds. The latter study is supported by the experimental X-ray and neutron diffraction data because there are numerous crystal structures with short O-H 3 3 3O hydrogen bonds and the proton situated in the central position or nearly so. Also recently, homogeneous and heterogeneous short and strong hydrogen bonds (SSHBs) as well as the proton bound homodimers were analyzed theoretically at MP2/aug-ccpVDZ þ diffuse(2s,2p) level. Among various topics, the matter was raised if hydrogen bonding is an electrostatic or covalent interaction. The following question arises: what does the covalency of hydrogen bonding mean? The decomposition of the interaction energy is useful to analyze hydrogen bonding and particularly to answer the latter question. One of the first decomposition schemes introduced is one of Morokuma and Kitaura, where the interaction energy is calculated within the Hartree-Fock one-electron approximation and it is decomposed into the following components: the exchange energy, EEX (arising from repulsive forces), and the other components, which might be a result of attractive forces: the polarization energy, EPL, the charge transfer energy, ECT, and the electrostatic energy, EES. If a method is applied where the correlation of electrons is taken into account, then the correlation energy may be included. One of the most important attractive components of the correlation energy is the dispersive energy. Different H-bonded systems were analyzed early by Umeyama and Morokuma who stated that: “The energy components are strongly distance dependent. At a relatively small separation, ES, CT, and PL can all be important attractive components, competing against a large EX repulsion. At larger distances for the same complex the short-range attractions CT and PL are usually unimportant and ES is the only important attraction.” One can see that the “covalency of interaction”may be connected with short H 3 3 3B distances where terms other than the electrostatic attractive one are important.