Aminoacyl-tRNA synthetases Rubio Gomez, Miguel Angel; Ibba, Michael
RNA (Cambridge),
08/2020, Volume:
26, Issue:
8
Journal Article
Peer reviewed
Open access
The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for ...decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key players in an increasing number of other cellular processes, with far-reaching consequences in health and disease. The biochemical versatility of the synthetases has also proven pivotal in efforts to expand the genetic code, further emphasizing the wide-ranging roles of the aminoacyl-tRNA synthetase family in synthetic and natural biology.
In this work, we provide an overview of how well-established concepts in the fields of quantum chemistry and material sciences have to be adapted when the quantum nature of light becomes important in ...correlated matter–photon problems. We analyze model systems in optical cavities, where the matter–photon interaction is considered from the weak- to the strong-coupling limit and for individual photon modes as well as for the multimode case. We identify fundamental changes in Born–Oppenheimer surfaces, spectroscopic quantities, conical intersections, and efficiency for quantum control. We conclude by applying our recently developed quantum-electrodynamical density-functional theory to spontaneous emission and show how a straightforward approximation accurately describes the correlated electron–photon dynamics. This work paves the way to describe matter–photon interactions from first principles and addresses the emergence of new states of matter in chemistry and material science.
Energy transfer in terms of excitation or charge is one of the most basic processes in nature, and understanding and controlling them is one of the major challenges of modern quantum chemistry. In ...this work, we highlight that these processes as well as other chemical properties can be drastically altered by modifying the vacuum fluctuations of the electromagnetic field in a cavity. By using a real-space formulation from first principles that keeps all of the electronic degrees of freedom in the model explicit and simulates changes in the environment by an effective photon mode, we can easily connect to well-known quantum-chemical results such asDexter charge-transfer and Förster excitation-transfer reactions, taking into account the often-disregarded Coulomb and self-polarization interaction. We find that the photonic degrees of freedom introduce extra electron–electron correlations over large distances and that the coupling to the cavity can drastically alter the characteristic charge-transfer behavior and even selectively improve the efficiency. For excitation transfer, we find that the cavity renders the transfer more efficient, essentially distance-independent, and further different configurations of highest efficiency depending on the coherence times. For strong decoherence (short coherence times), the cavity frequency should be in between the isolated excitations of the donor and acceptor, while for weak decoherence (long coherence times), the cavity should enhance a mode that is close to resonance with either donor or acceptor. Our results highlight that changing the photonic environment can redefine chemical processes, rendering polaritonic chemistry a promising approach toward the control of chemical reactions.
The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron–photon interactions in terms of effective ...Kohn–Sham potentials. In this work, we numerically construct the exact electron–photon Kohn–Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light–matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account.
Two-dimensional materials, obtained by van der Waals stacking of layers, are fascinating objects of contemporary condensed matter research, exhibiting a variety of new physics. Inspired by the ...breakthroughs of twisted bilayer graphene (TBG), we demonstrate that twisted bilayer boron nitride (TBBN) is an even more exciting novel system that turns out to be an excellent platform to realize new correlated phases and phenomena; exploration of its electronic properties shows that in contrast to TBG in TBBN multiple families of 2,4, and 6-fold degenerate flat bands emerge without the need to fine tune close to a “magic angle”, resulting in dramatic and tunable changes in optical properties and exciton physics, and providing an additional platform to study strong correlations. Upon doping, unforeseen new correlated phases of matter (insulating and superconducting) emerge. TBBN could thus provide a promising experimental platform, insensitive to small deviations in the twist angle, to study novel exciton condensate and spatial confinement physics, and correlations in two dimensions.
Experiments at the interface of quantum optics and chemistry have revealed that strong coupling between light and matter can substantially modify the chemical and physical properties of molecules and ...solids. While the theoretical description of such situations is usually based on nonrelativistic quantum electrodynamics, which contains quadratic light–matter coupling terms, it is commonplace to disregard these terms and restrict the treatment to purely bilinear couplings. In this work, we clarify the physical origin and the substantial impact of the most common quadratic terms, the diamagnetic and self-polarization terms, and highlight why neglecting them can lead to rather unphysical results. Specifically, we demonstrate their relevance by showing that neglecting these terms leads to the loss of gauge invariance, basis set dependence, disintegration (loss of bound states) of any system in the basis set limit, unphysical radiation of the ground state, and an artificial dependence on the static dipole. Besides providing important guidance for modeling of strongly coupled light–matter systems, the presented results also indicate conditions under which those effects might become accessible.
The generation of high-order harmonics from atomic and molecular gases enables the production of high-energy photons and ultrashort isolated pulses. Obtaining efficiently similar photon energy from ...solid-state systems could lead, for instance, to more compact extreme ultraviolet and soft x-ray sources. We demonstrate from ab initio simulations that it is possible to generate high-order harmonics from free-standing monolayer materials, with an energy cutoff similar to that of atomic and molecular gases. In the limit in which electrons are driven by the pump laser perpendicularly to the monolayer, they behave qualitatively the same as the electrons responsible for high-harmonic generation (HHG) in atoms, where their trajectories are described by the widely used semiclassical model, and exhibit real-space trajectories similar to those of the atomic case. Despite the similarities, the first and last steps of the well-established three-step model for atomic HHG are remarkably different in the two-dimensional materials from gases. Moreover, we show that the electron-electron interaction plays an important role in harmonic generation from monolayer materials because of strong local-field effects, which modify how the material is ionized. The recombination of the accelerated electron wave packet is also found to be modified because of the infinite extension of the material in the monolayer plane, thus leading to a more favorable wavelength scaling of the harmonic yield than in atomic HHG. Our results establish a novel and efficient way of generating high-order harmonics based on a solid-state device, with an energy cutoff and a more favorable wavelength scaling of the harmonic yield similar to those of atomic and molecular gases. Two-dimensional materials offer a unique platform where both bulk and atomic HHG can be investigated, depending on the angle of incidence. Devices based on two-dimensional materials can extend the limit of existing sources.
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