Using the Metropolis algorithm to explore the loss surface of a recurrent neural network.

In the limit of small trial moves the Metropolis Monte Carlo algorithm is equivalent to gradient descent on the energy function in the presence of Gaussian white noise. This observation was originally used to demonstrate a correspondence between Metropolis Monte Carlo moves of model molecules and overdamped Langevin dynamics, but it also applies in the context of training a neural network: making small random changes to the weights of a neural network, accepted with the Metropolis probability, with the loss function playing the role of energy, has the same effect as training by explicit gradient descent in the presence of Gaussian white noise. We explore this correspondence in the context of a simple recurrent neural network.

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research.

Introduction: The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped.

Intrinsic-dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing.

Multi-omics data have revolutionized biomedical research by providing a comprehensive understanding of biological systems and the molecular mechanisms of disease development. However, analyzing multi-omics data is challenging due to high dimensionality and limited sample sizes, necessitating proper data-reduction pipelines to ensure reliable analyses. Additionally, its multimodal nature requires effective data-integration pipelines.

Automated Gold Nanorod Spectral Morphology Analysis Pipeline.

The development of a colloidal synthesis procedure to produce nanomaterials with high shape and size purity is often a time-consuming, iterative process. This is often due to quantitative uncertainties in the required reaction conditions and the time, resources, and expertise intensive characterization methods required for quantitative determination of nanomaterial size and shape. Absorption spectroscopy is often the easiest method for colloidal nanomaterial characterization.

A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions.

While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology.

Emergent actin flows explain distinct modes of gliding motility.

During host infection, and related unicellular parasites move using gliding, which differs fundamentally from other known mechanisms of eukaryotic cell motility. Gliding is thought to be powered by a thin layer of flowing filamentous (F)-actin sandwiched between the plasma membrane and a myosin-covered inner membrane complex. How this surface actin layer drives the various gliding modes observed in experiments-helical, circular, twirling and patch, pendulum or rolling-is unclear.

Expression of a mammalian RNA demethylase increases flower number and floral stem branching in .

RNA methylation plays a central regulatory role in plant biology and is a relatively new target for plant improvement efforts. In nearly all cases, perturbation of the RNA methylation machinery results in deleterious phenotypes. However, a recent landmark paper reported that transcriptome-wide use of the human RNA demethylase FTO substantially increased the yield of rice and potatoes.

Electron-Phonon Coupling in Copper-Substituted Lead Phosphate Apatite.

Recent reports of room-temperature, ambient pressure superconductivity in copper-substituted lead phosphate apatite, commonly referred to as LK99, have prompted numerous theoretical and experimental studies into its properties. As the electron-phonon interaction is a common mechanism for superconductivity, the electron-phonon coupling strength is an important quantity to compute for LK99. In this work, we compare the electron-phonon coupling strength among the proposed compositions of LK99.

Stabilized Oxygen Vacancy Chemistry toward High-Performance Layered Oxide Cathodes for Sodium-Ion Batteries.

Anionic redox has emerged as a transformative paradigm for high-energy layered transition-metal (TM) oxide cathodes, but it is usually accompanied by the formation of anionic redox-mediated oxygen vacancies (OVs) due to irreversible oxygen release. Additionally, external factor-induced OVs (defined as intrinsic OVs) also play a pivotal role in the physicochemical properties of layered TM oxides. However, an in-depth understanding of the interplay between intrinsic and anionic redox-mediated OVs and the corresponding regulation mechanism of the dynamic evolution of OVs is still missing.

Green microalga conserves substrate uptake pattern but changes their metabolic uses across trophic transition.

The terrestrial green alga is an emerging model species with potential applications including production of triacylglycerol or astaxanthin. How interacts with the diverse substrates during trophic transitions is unknown. To characterize its substrate utilization and secretion dynamics, we cultivated the alga in a soil-based defined medium in transition between conditions with and without glucose supplementation.

Strong electron-phonon coupling in magic-angle twisted bilayer graphene.

The unusual properties of superconductivity in magic-angle twisted bilayer graphene (MATBG) have sparked considerable research interest. However, despite the dedication of intensive experimental efforts and the proposal of several possible pairing mechanisms, the origin of its superconductivity remains elusive. Here, by utilizing angle-resolved photoemission spectroscopy with micrometre spatial resolution, we reveal flat-band replicas in superconducting MATBG, where MATBG is unaligned with its hexagonal boron nitride substrate.

Photosynthetic responses to temperature across the tropics: a meta-analytic approach.

Background And Aims: Tropical forests exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial biome. Yet, uncertainty in the projected carbon balance over the next century is roughly three-times greater for the tropics than other ecosystems. Our limited knowledge of tropical plant physiological responses, including photosynthetic, to climate change is a substantial source of uncertainty in our ability to forecast the global terrestrial carbon sink.

High-precision chemical quantum sensing in flowing monodisperse microdroplets.

A method is presented for high-precision chemical detection that integrates quantum sensing with droplet microfluidics. Using nanodiamonds (ND) with fluorescent nitrogen-vacancy (NV) centers as quantum sensors, rapidly flowing microdroplets containing analyte molecules are analyzed. A noise-suppressed mode of optically detected magnetic resonance is enabled by pairing controllable flow with microwave control of NV electronic spins, to detect analyte-induced signals of a few hundredths of a percent of the ND fluorescence.

Advances in the photon avalanche luminescence of inorganic lanthanide-doped nanomaterials.

Photon avalanche (PA)-where the absorption of a single photon initiates a 'chain reaction' of additional absorption and energy transfer events within a material-is a highly nonlinear optical process that results in upconverted light emission with an exceptionally steep dependence on the illumination intensity. Over 40 years following the first demonstration of photon avalanche emission in lanthanide-doped bulk crystals, PA emission has been achieved in nanometer-scale colloidal particles. The scaling of PA to nanomaterials has resulted in significant and rapid advances, such as luminescence imaging beyond the diffraction limit of light, optical thermometry and force sensing with (sub)micron spatial resolution, and all-optical data storage and processing.

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015.

Synthetically Reversible, Proton-Mediated Nitrite N-O Bond Cleavage at a Dicopper Site.

A monocationic dicopper(I,I) nitrite complex [Cu(μ-κ:κ-ON)DPFN][NTf] () (DPFN = 2,7-bis(fluoro-di(2-pyridyl)methyl)-1,8-naphthyridine, NTf = N(SOCF)), was synthesized by treatment of a dicopper acetonitrile complex, [Cu(μ-MeCN)DPFN][NTf] (), with tetrabutylammonium nitrite ([BuN][NO]). DFT calculations indicate that is one of three linkage isomers that are close in energy and presumably accessible in solution. Reaction of the μ-κ:κ-ON complex with -TolSH produces nitrous acid (HONO) and the corresponding dicopper thiolate species via an acid-base exchange reaction.

Bridging the Gap between Molecular Simulations and Surface Complexation Modeling for Heterogeneous Surfaces: A Case Study with Uranium and Arsenic Adsorption on Clay Minerals.

Among all natural submicrosized phases, clay minerals are ubiquitous in soils and sedimentary rocks in nature as well as in engineered environments, and while clay minerals' adsorption properties have been studied extensively, their unique level of surface reactivity heterogeneities necessitates further investigation at the molecular level to understand and predict the influence of these heterogeneities on their macroscopic properties. In this study, we investigated the surface structures and desorption-free energies of U(VI) species (UO) and As(V) species (HAsO and HAsO) complexed at different edge surface reactive sites of a cis-vacant montmorillonite layer using first-principles molecular dynamics (FPMD). We show that U(VI) forms bidentate and tridentate complexes on montmorillonite edge surfaces, whereas As(V) monodentate complexes are the most stable.

Voltage Mining for (De)lithiation-Stabilized Cathodes and a Machine Learning Model for Li-Ion Cathode Voltage.

Advances in lithium-metal anodes have inspired interest in discovery of Li-free cathodes, most of which are natively found in their charged state. This is in contrast to today's commercial lithium-ion battery cathodes, which are more stable in their discharged state. In this study, we combine calculated cathode voltage information from both categories of cathode materials, covering 5577 and 2423 total unique structure pairs, respectively.

Ferromagnetic Exchange and Slow Magnetic Relaxation in Cobalt Bis(1,2-dithiolene)-Bridged Dilanthanide Complexes.

The construction of multinuclear lanthanide-based molecules with significant magnetic exchange interactions represents a key challenge in the realization of single-molecule magnets with high operating temperatures. Here, we report the synthesis and magnetic characterization of two series of heterobimetallic compounds, (Cp*Ln)(μ-Co(pdt)) (Ln = Y, Gd, Dy; pdt = 1,2-diphenylethylenedithiolate) and [K(18-crown-6)][(Cp*Ln)(μ-Co(pdt))] (Ln = Y, Gd), featuring two lanthanide centers bridged by a cobalt bis(1,2-dithiolene) complex. Dc magnetic susceptibility data collected for the Gd congeners indicate significant Gd-Co ferromagnetic exchange interactions with fits affording = +11.

Hydrogen ejection from hydrocarbons: Characterization and relevance in soot formation and interstellar chemistry.

Polycyclic aromatic hydrocarbons (PAHs) play a major role in the chemistry of combustion, pyrolysis, and the interstellar medium. Production (or activation) of radical PAHs and propagation of their resulting reactions require efficient dehydrogenation, but the preferred method of hydrogen loss is not well understood. Unimolecular hydrogen ejection (i.