Ribonanza: deep learning of RNA structure through dual crowdsourcing.

Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity of experimental data. Here, we present Ribonanza, a dataset of chemical mapping measurements on two million diverse RNA sequences collected through Eterna and other crowdsourced initiatives. Ribonanza measurements enabled solicitation, training, and prospective evaluation of diverse deep neural networks through a Kaggle challenge, followed by distillation into a single, self-contained model called RibonanzaNet. When fine tuned on auxiliary datasets, RibonanzaNet achieves state-of-the-art performance in modeling experimental sequence dropout, RNA hydrolytic degradation, and RNA secondary structure, with implications for modeling RNA tertiary structure.

Kinetics of laser-induced melting of thin gold film: How slow can it get?

Melting is a common and well-studied phenomenon that still reveals new facets when triggered by laser excitation and probed with ultrafast electron diffraction. Recent experimental evidence of anomalously slow nanosecond-scale melting of thin gold films irradiated by femtosecond laser pulses motivates computational efforts aimed at revealing the underlying mechanisms of melting. Atomistic simulations reveal that a combined effect of lattice superheating and relaxation of laser-induced stresses ensures the dominance of the homogeneous melting mechanism at all energies down to the melting threshold and keeps the time scale of melting within ~100 picoseconds. The much longer melting times and the prominent contribution of heterogeneous melting inferred from the experiments cannot be reconciled with the atomistic simulations by any reasonable variation of the electron-phonon coupling strength, thus suggesting the need for further coordinated experimental and theoretical efforts aimed at addressing the mechanisms and kinetics of laser-induced melting in the vicinity of melting threshold.

Correction: The effect of pulse duration on nanoparticle generation in pulsed laser ablation in liquids: insights from large-scale atomistic simulations.

Correction for 'The effect of pulse duration on nanoparticle generation in pulsed laser ablation in liquids: insights from large-scale atomistic simulations' by Cheng-Yu Shih et al., Phys. Chem. Chem. Phys., 2020, 22, 7077-7099, DOI: .

Effect of a liquid environment on single-pulse generation of laser induced periodic surface structures and nanoparticles.

The effect of a liquid environment on the fundamental mechanisms of surface nanostructuring and generation of nanoparticles by single pulse laser ablation is investigated in a closely integrated computational and experimental study. A large-scale molecular dynamics simulation of spatially modulated ablation of Cr in water reveals a complex picture of the dynamic interaction between the ablation plume and water. Ablation plume is found to be rapidly decelerated by the water environment, resulting the formation and prompt disintegration of a hot metal layer at the interface between the ablation and water. A major fraction of the ablation plume is laterally redistributed and redeposited back to the target, forming smooth frozen surface features. Good agreement between the shapes of the surface features predicted in the simulation and the ones generated in single pulse laser ablation experiments performed for Cr in water supports the mechanistic insights revealed in the simulation. The results of this study suggest that the presence of a liquid environment can eliminate the sharp features of the surface morphology, reduce the amount of the material removed from the target by more than an order of magnitude, and narrow down the nanoparticle size distribution as compared to laser ablation under vacuum. Moreover, the computational predictions of the effective incorporation of molecules constituting the liquid environment into the surface region of the irradiated target and the generation of high vacancy concentrations, exceeding the equilibrium levels by more than an order of magnitude, suggest a potential for hyperdoping of laser-generated surfaces by solutes present in the liquid environment.

The effect of pulse duration on nanoparticle generation in pulsed laser ablation in liquids: insights from large-scale atomistic simulations.

The generation of colloidal solutions of chemically clean nanoparticles through pulsed laser ablation in liquids (PLAL) has evolved into a thriving research field that impacts industrial applications. The complexity and multiscale nature of PLAL make it difficult to untangle the various processes involved in the generation of nanoparticles and establish the dependence of nanoparticle yield and size distribution on the irradiation parameters. Large-scale atomistic simulations have yielded important insights into the fundamental mechanisms of ultrashort (femtoseconds to tens of picoseconds) PLAL and provided a plausible explanation of the origin of the experimentally observed bimodal nanoparticle size distributions. In this paper, we extend the atomistic simulations to short (hundreds of picoseconds to nanoseconds) laser pulses and focus our attention on the effect of the pulse duration on the mechanisms responsible for the generation of nanoparticles at the initial dynamic stage of laser ablation. Three distinct nanoparticle generation mechanisms operating at different stages of the ablation process and in different parts of the emerging cavitation bubble are identified in the simulations. These mechanisms are (1) the formation of a thin transient metal layer at the interface between the ablation plume and water environment followed by its decomposition into large molten nanoparticles, (2) the nucleation, growth, and rapid cooling/solidification of small nanoparticles at the very front of the emerging cavitation bubble, above the transient interfacial metal layer, and (3) the spinodal decomposition of a part of the ablation plume located below the transient interfacial layer, leading to the formation of a large population of nanoparticles growing in a high-temperature environment through inter-particle collisions and coalescence. The coexistence of the three distinct mechanisms of the nanoparticle formation at the initial stage of the ablation process can be related to the broad nanoparticle size distributions commonly observed in nanosecond PLAL experiments. The strong dependence of the nanoparticle cooling and solidification rates on the location within the low-density metal-water mixing region has important implications for the long-term evolution of the nanoparticle size distribution, as well as for the ability to quench the nanoparticle growth or dope them by adding surface-active agents or doping elements to the liquid environment.

Laser-Rewriteable Ferromagnetism at Thin-Film Surfaces.

Manipulation of magnetism using laser light is considered as a key to the advancement of data storage technologies. Until now, most approaches seek to optically switch the direction of magnetization rather than to reversibly manipulate the ferromagnetism itself. Here, we use ∼100 fs laser pulses to reversibly switch ferromagnetic ordering on and off by exploiting a chemical order-disorder phase transition in Fe60Al40, from the B2 to the A2 structure and vice versa. A single laser pulse above a threshold fluence causes nonferromagnetic B2 Fe60Al40 to disorder and form the ferromagnetic A2 structure. Subsequent laser pulsing below the threshold reverses the surface to B2 Fe60Al40, erasing the laser-induced ferromagnetism. Simulations reveal that the order-disorder transition is regulated by the extent of surface supercooling; above the threshold for complete melting throughout the film thickness, the liquid phase can be deeply undercooled before solidification. As a result, the vacancy diffusion in the resolidified region is limited and the region is trapped in the metastable chemically disordered state. Laser pulsing below the threshold forms a limited supercooled surface region that solidifies at sufficiently high temperatures, enabling diffusion-assisted reordering. This demonstrates that ultrafast lasers can achieve subtle atomic rearrangements in bimetallic alloys in a reversible and nonvolatile fashion.

Two mechanisms of nanoparticle generation in picosecond laser ablation in liquids: the origin of the bimodal size distribution.

The synthesis of chemically clean and environmentally friendly nanoparticles through pulsed laser ablation in liquids has shown a number of advantages over conventional chemical synthesis methods and has evolved into a thriving research field attracting laboratory and industrial applications. The fundamental understanding of processes leading to the nanoparticle generation, however, still remains elusive. In particular, the origin of bimodal nanoparticle size distributions in femto- and picosecond laser ablation in liquids, where small nanoparticles (several nanometers) with narrow size distribution are commonly observed to coexist with larger (tens to hundreds of nanometers) ones, has not been explained so far. In this paper, joint computational and experimental efforts are applied to understand the mechanisms of nanoparticle formation in picosecond laser ablation in liquids and to explain the bimodal nanoparticle size distributions. The results of a large-scale atomistic simulation reveal the critical role of the dynamic interaction between the ablation plume and the liquid environment, leading to the generation of large nanoparticles through a sequence of hydrodynamic instabilities at the plume-liquid interface and a concurrent nucleation and growth of small nanoparticles in an expanding metal-liquid mixing region. The computational predictions are supported by a series of stroboscopic videography experiments showing the emergence of small satellite bubbles surrounding the main cavitation bubble generated in single pulse experiments. Carefully timed double pulse irradiation triggers expansion of secondary cavitation bubbles indicating, in accord with the simulation results, the presence of localized sites of laser energy deposition (possibly large nanoparticles) injected into the liquid at the early stage of the bubble formation.

Generation of Subsurface Voids, Incubation Effect, and Formation of Nanoparticles in Short Pulse Laser Interactions with Bulk Metal Targets in Liquid: Molecular Dynamics Study.

The ability of short pulse laser ablation in liquids to produce clean colloidal nanoparticles and unusual surface morphology has been employed in a broad range of practical applications. In this paper, we report the results of large-scale molecular dynamics simulations aimed at revealing the key processes that control the surface morphology and nanoparticle size distributions by pulsed laser ablation in liquids. The simulations of bulk Ag targets irradiated in water are performed with an advanced computational model combining a coarse-grained representation of liquid environment and an atomistic description of laser interaction with metal targets. For the irradiation conditions that correspond to the spallation regime in vacuum, the simulations predict that the water environment can prevent the complete separation of the spalled layer from the target, leading to the formation of large subsurface voids stabilized by rapid cooling and solidification. The subsequent irradiation of the laser-modified surface is found to result in a more efficient ablation and nanoparticle generation, thus suggesting the possibility of the incubation effect in multipulse laser ablation in liquids. The simulations performed at higher laser fluences that correspond to the phase explosion regime in vacuum reveal the accumulation of the ablation plume at the interface with the water environment and the formation of a hot metal layer. The water in contact with the metal layer is brought to the supercritical state and provides an environment suitable for nucleation and growth of small metal nanoparticles from metal atoms emitted from the hot metal layer. The metal layer itself has limited stability and can readily disintegrate into large (tens of nanometers) nanoparticles. The layer disintegration is facilitated by the Rayleigh-Taylor instability of the interface between the higher density metal layer decelerated by the pressure from the lighter supercritical water. The nanoparticles emerging from the layer disintegration are rapidly cooled and solidified due to the interaction with water environment, with a cooling rate of ∼2 × 1012 K/s observed in the simulations. The computational prediction of two distinct mechanisms of nanoparticle formation yielding nanoparticles with different characteristic sizes provides a plausible explanation for the experimental observations of bimodal nanoparticle size distributions in laser ablation in liquids. The ultrahigh cooling and solidification rates suggest the possibility for generation of nanoparticles featuring metastable phases and highly nonequilibrium structures.

Atomistic modeling of nanoparticle generation in short pulse laser ablation of thin metal films in water.

Laser ablation in liquids is actively used for generation of clean colloidal nanoparticles with unique shapes and functionalities. The fundamental mechanisms of the laser ablation in liquids and the key processes that control the nanoparticle structure, composition, and size distribution, however, are not yet fully understood. In this paper, we report the results of first atomistic simulations of laser ablation of metal targets in liquid environment. A model combining a coarse-grained representation of the liquid environment (parameterized for water), a fully atomistic description of laser interactions with metal targets, and acoustic impedance matching boundary conditions is developed and applied for simulation of laser ablation of a thin silver film deposited on a silica substrate. The simulations, performed at two laser fluences in the regime of phase explosion, predict a rapid deceleration of the ejected ablation plume and the formation of a dense superheated molten layer at the water-plume interface. The water in contact with the hot metal layer is brought to the supercritical state and transforms into an expanding low density metal-water mixing region that serves as a precursor for the formation of a cavitation bubble. Two distinct mechanisms of the nanoparticle formation are predicted in the simulations: (1) the nucleation and growth of small (mostly ⩽10nm) nanoparticles in the metal-water mixing region and (2) the formation of larger (tens of nm) nanoparticles through the breakup of the superheated molten metal layer triggered by the emergence of complex morphological features attributed to the Rayleigh-Taylor instability of the interface between at the superheated metal layer and the supercritical water. The first mechanism is facilitated by the rapid cooling of the growing nanoparticles in the supercritical water environment, resulting in solidification of the nanoparticles located in the upper part of the mixing region on the timescale of nanoseconds. The computational prediction of the two mechanisms of nanoparticle formation yielding nanoparticles with different characteristic sizes is consistent with experimental observations of two distinct nanoparticle populations appearing at different stages of the ablation process.

Growth Twinning and Generation of High-Frequency Surface Nanostructures in Ultrafast Laser-Induced Transient Melting and Resolidification.

The structural changes generated in surface regions of single crystal Ni targets by femtosecond laser irradiation are investigated experimentally and computationally for laser fluences that, in the multipulse irradiation regime, produce sub-100 nm high spatial frequency surface structures. Detailed experimental characterization of the irradiated targets combining electron back scattered diffraction analysis with high-resolution transmission electron microscopy reveals the presence of multiple nanoscale twinned domains in the irradiated surface regions of single crystal targets with (111) surface orientation. Atomistic- and continuum-level simulations performed for experimental irradiation conditions reproduce the generation of twinned domains and establish the conditions leading to the formation of growth twin boundaries in the course of the fast transient melting and epitaxial regrowth of the surface regions of the irradiated targets. The observation of growth twins in the irradiated Ni(111) targets provides strong evidence of the role of surface melting and resolidification in the formation of high spatial frequency surface structures. This also suggests that the formation of twinned domains can be used as a sensitive measure of the levels of liquid undercooling achieved in short pulse laser processing of metals.