Since the Hadean era of Earth's history, peptides/proteins and RNA have undergone a complex evolutionary trajectory. Originating from simple monomeric units, these molecules evolved abiotically under various biochemical and biophysical constraints into functional biomolecules that contributed to the emergence of the first living cells. Within these cells, their interactions could then evolve through Darwinian selection. In this review, we examine current understanding of how protein$-$RNA interactions emerged under prebiotic conditions and developed into today's iconic biomolecular machines such as the ribosome. Particular emphasis is placed on the types of physicochemical interactions accessible to early protein$-$RNA complexes and their roles in driving spatial organization and compartmentalization in protocellular environments.

Two-dimensional (2D) layered magnetic materials (LMMs) are a newly emerging class of van der Waals materials, opening new opportunities to study magneto-excitonic coupling. The air-stable, structurally and optically anisotropic A-type antiferromagnetic chromium sulfur bromide (CrSBr) is one of the most prominent examples of such LMMs. We investigate photoluminescence (PL) and PL excitation of mono- to tri-layers CrSBr and find that it exhibits a unique duplexity, supporting both Frenkel- and Wannier-Mott-like excitons. Our magneto-optical experiments reveal a similar excitonic response from the mono- and trilayer systems and a completely different signature in the bilayer flake. This shows a different origin of the low-lying excitonic species (A, A', and B) in the band structure. We confirm the robustness of the magneto-excitonic coupling in few-layer CrSBr. Our work enables a more comprehensive exploration of the dual excitonic behavior in 2D materials.

The emergence of intelligent matter has sparked significant interest in next generation technologies. We report on the discovery of a reconfigurable magnetic multilayer domain structure in the van der Waals magnet CrSBr, exhibiting a unique combination of magnetic and optical properties. Applying an external magnetic field along the easy axis drives the hysteretic antiferromagnetic-to-ferromagnetic transition that is not universally binary, but instead develops through a cascade of intermediate magnetic configurations whose multiplicity and stability scale systematically with thickness. This material can be considered as a prototypical intelligent matter, capable of encoding, processing, and storing information through its tunable magnetic structure. The directly linked optical properties of CrSBr, modulated by the magnetic structure, provide a readout mechanism for the stored information compatible with modern information distribution using light. With its adaptive properties, CrSBr is an attractive candidate for neuromorphic circuitries, enabling the design of brain-inspired computing architectures that can learn and evolve in response to changing environments.

The \emph{Wiener index} is a widely studied topological index of graphs. One of the main problems in the area is to determine which graphs of given properties attain the extremal values of Wiener index. In this paper we resolve an open problem posed by Du in 2012. To this end we determine the unicyclic bipartite graphs with given size of parts having the maximum Wiener index. This completes the previous research in which the minimum case was solved.

All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and recycling. In fact, peptide bonds are formed only during the elongation phase, which comprises periodic association of transfer RNAs and multiple auxiliary proteins with the ribosome and the addition of an amino acid to the nascent polypeptide one at a time. The protein spends a considerable amount of time attached to the ribosome. Here, we conceptually divide this portion of the protein lifetime into three stages. We define each stage on the basis of the position of the N-terminus of the nascent polypeptide within the ribosome exit tunnel and the context of the catalytic center. We argue that nascent polypeptides experience a variety of forces that determine how they translocate through the tunnel and interact with the tunnel walls. We review current knowledge about nascent polypeptide translocation and identify several white spots in our understanding of the birth of proteins.

Simulating the coupled electronic and nuclear response of a molecule to light excitation requires the application of nonadiabatic molecular dynamics. However, when faced with a specific photophysical or photochemical problem, selecting the most suitable theoretical approach from the wide array of available techniques is not a trivial task. The challenge is further complicated by the lack of systematic method comparisons and rigorous testing on realistic molecular systems. This absence of comprehensive molecular benchmarks remains a major obstacle to advances within the field of nonadiabatic molecular dynamics. A CECAM workshop, Standardizing Nonadiabatic Dynamics: Towards Common Benchmarks, was held in May 2024 to address this issue. This Perspective highlights the key challenges identified during the workshop in defining molecular benchmarks for nonadiabatic dynamics. Specifically, this work outlines some preliminary observations on essential components needed for simulations and proposes a roadmap aiming to establish, as an ultimate goal, a community-driven, standardized molecular benchmark set.

Latent fingerprints, if present, are crucial in identifying the suspect who was at the crime scene. If there are many latent fingerprints or the suspect is from the same household, crime investigators may have difficulty identifying whose latent fingerprints are time-related to the crime. Here, we report changes in the nanoscale topography of latent fingerprints, which may serve as a timeline and could help estimate when the latent fingerprint was imprinted. On the latent fingerprint of an adolescent, we observed a change in nano-topography over time, specifically the formation of nano-chain structures in space between the imprinted papillary ridges. We consequently compared this observation with the decomposition of the latent fingerprints of a child and adult. We observed a significant difference in the time change in nano-topography of latent fingerprints of a child, adolescent, and young adult. The nano-topographical changes of latent fingerprints were studied by atomic force microscopy over 70 days. In the case of child's and adolescent's latent fingerprints, the first nano-chains were observed already 24 hours after imprinting of the latent fingerprint, and the number of nano-chains increased steadily up to 21 days, then we observed that another organic material covered the nano-chains, and they started slowly deteriorating; nevertheless, the nano-chains were still present on the 70th day.

Diamond nanoparticles (nanodiamonds) can transport active drugs in cultured cells as well as in vivo. However, in the latter case, methods allowing to determine their bioavailability accurately are still lacking. Nanodiamond can be made fluorescent with a perfectly stable emission and a lifetime ten times longer than the one of tissue autofluorescence. Taking advantage of these properties, we present an automated quantification method of fluorescent nanodiamonds (FND) in histological sections of mouse organs and tumor, after systemic injection. We use a home-made time-delayed fluorescence microscope comprising a custom pulsed laser source synchronized on the master clock of a gated intensified array detector. This setup allows to obtain ultra-high-resolution images 120 Mpixels of whole mouse organs sections, with subcellular resolution and single-particle sensitivity. As a proof-of-principle experiment, we quantified the biodistribution and aggregation state of new cationic FNDs able to transport small interfering RNA inhibiting the oncogene responsible for Ewing sarcoma. Image analysis showed a low yield of nanodiamonds in the tumor after intravenous injection. Thus, for the in vivo efficacy assay we injected the nanomedicine into the tumor. We achieved a 28-fold inhibition of the oncogene. This method can readily be applied to other nanoemitters with $\approx$100 ns lifetime.

Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains challenging at atomic level, several studies have reported all-atom molecular dynamics simulations of the entire ribosome. However, for certain applications, atomistic simulations are impractical due to the limited simulation timescales achievable. In this study, we investigate the applicability of the coarse-grained MARTINI model for simulations of the bacterial ribosome. After testing several simulation setups, we found that the structure of the ribosome and its components are generally well represented compared to the reference experimental structure. Compared with all-atom simulations of the entire ribosome, coarse-grained simulations result in a less flexible and smaller ribosome. We demonstrate how modifications of some parameters of the model can enhance the dynamics of the ribosome to better align with the atomistic model. Our work provides a detailed protocol for coarse-grained simulations of the ribosome and highlights aspects of the model that need improvements.

Controlling the spatial arrangement of optically active elements is crucial for the advancement of engineered photonic systems. Color centers in nanodiamond offer unique advantages for quantum sensing and information processing; however, their integration into complex optical architectures is limited by challenges in precise and reproducible positioning, as well as efficient coupling. DNA origami provides an elegant solution, as demonstrated by recent studies showcasing nanoscale positioning of fluorescent nanodiamonds and plasmonic gold nanoparticles. Here, we present a scalable and robust method for covalently functionalizing nanodiamonds with DNA, enabling high-yield, spatially controlled assembly of diamond and gold nanoparticles onto DNA origami. By precisely controlling the interparticle spacing, we reveal distance-dependent modulation of NV center photoluminescence with a 10-fold increase in the fastest decay pathway at short interparticle distances. Our findings indicate selective plasmon-driven effects and interplay between radiative and non-radiative processes. This work overcomes key limitations in current nanodiamond assembly strategies and provides insights into engineering NV photoluminescence by plasmonic coupling that advance toward quantum photonic and sensing applications.

We synthesized the astrochemically relevant molecule 3-hydroxypropanal (HOCH$_2$CH$_2$CHO) and subsequently measured and analyzed its rotational spectrum in several frequency regions ranging from 130 to 485 GHz. We analyzed the ground vibrational state as well as the two perturbed lowest-lying vibrationally excited states. With the resulting rotational parameters, we searched for this molecule in the Sagittarius B2(N) and NGC 6334I hot cores, the IRAS 16293-2422B hot corino, and the G+0.693-0.027 and TMC-1 molecular clouds. Rotational emission of 3-hydroxypropanal was tentatively detected toward G+0.693-0.027 and a column density of (8.6$\pm$1.4)$\times$10$^{12}$ cm$^{-2}$ was determined. However, this molecule was not detected in the other sources that were investigated. The chemical implications of this tentative discovery are analyzed and several potential chemical formation pathways of this species are discussed.

Context. Radical chemical reactions on cosmic dust grains play a crucial role in forming various chemical species. Among different radicals, the hydroxyl (OH) is one of the most important ones, with a rather specific chemistry. Aims. The goal of this work is to simulate the recombination dynamics of hydroxyl radicals and the subsequent formation of hydrogen peroxide (H$_{2}$O$_{2}$). Mthods. We employed neural network potentials trained on ONIOM(QM/QM) data, combining multi-reference (CASPT2) and density functional theory (DFT) calculations. This approach allows us to model the recombination of hydroxyl radicals on ice surfaces with high computational efficiency and accuracy. Results. Our simulations reveal that the initial position of the radicals plays a decisive role in determining recombination probability. We found that the formation of hydrogen-bond between radicals, competes with the formation of hydrogen peroxide, reducing the recombination efficiency, contrary to expectancy. This competition reduces the recombination probability for radicals that are initially formed approximately 3 \AA{} apart. Recombination probabilities also depend on the kinetic energy of the added radicals, with values around 0.33 for thermal radicals and a wide range of values between 0.33 and 1.00 for suprathermal OH radicals. Conclusions. Based on our calculations we provide recommendations for introducing OH radical recombination into kinetic astrochemical models, differentiating between thermal and suprathermal radicals. The recombination behavior varies significantly between these two cases: while thermal radicals are sometimes trapped in hydrogen-bonded minima, the case of suprathermal radicals varies with the added energy. Our most important conclusion is that OH radical recombination probability cannot be assumed 1.0 for a wide variety of cases.

The mechanochemistry of ring-opening reactions of cyclopropane derivatives turns out to be unexpectedly rich and puzzling. After showing that a rare so-called uphill bifurcation in the case of trans-gem-difluorocyclopropane turns into a downhill bifurcation upon substitution of fluorine by chlorine, bromine and iodine in the thermal activation limit, the dichloro derivative is studied systematically in the realm of mechanochemical activation. Detailed exploration of the force-transformed potential energy surface of trans-gem-dichlorocyclopropane in terms of Dijkstra path analysis unveils a hitherto unknown topological catastrophe where the global shape of the energy landscape is fundamentally changed. From thermal activation up to moderately large forces, it is an uphill bifurcation that decides about dis-versus conrotatory ring-opening followed by separate transition states along both pathways. Above a critical force, the two distinct transition states merge to yield a single transition state such that the decision about the dis-versus conrotatory ring-opening process is taken at a newly established downhill bifurcation. The discovery of a force-induced qualitative change of the topology of a reaction network vastly transcends the previous understanding of the ring-opening reaction of this species. It would be astonishing to not discover a wealth of such catastrophes for mechanochemically activated reactions which will greatly extend the known opportunities to manipulate chemical reaction networks.

Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems unveil microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C$_8$H$_7$N), tryptophan's chromophore, in water: a strong localized $\text{N-H}\cdots\text{OH}_2$ hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of indole's electronic structure in aqueous solution. We have recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through \emph{ab initio} modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the non-equilibrium polarizable-continuum model. A two-hole electron-population analysis quantitatively describes the Auger spectra. Core-electron binding energies for nitrogen and carbon highlight the specific interaction with a hydrogen-bonded water molecule at the N-H group and otherwise nonspecific solvent interactions.

In this study, novel flexible micro-scale humidity sensors were directly fabricated in graphene oxide (GO) and polyimide (PI) using ion beam writing without any further modifications, and then successfully tested in an atmospheric chamber. Two low fluences of carbon ions with an energy of 5 MeV were used, and structural changes in the irradiated materials were expected. The shape and structure of prepared micro-sensors were studied using scanning electron microscopy (SEM). The structural and compositional changes in the irradiated area were characterized using micro-Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), Rutherford back-scattering spectroscopy (RBS), energy-dispersive X-ray spectroscopy (EDS), and elastic recoil detection analysis (ERDA) spectroscopy. The sensing performance was tested at a relative humidity (RH) ranging from 5 % to 60 %, where the electrical conductivity of PI varied by three orders of magnitude, and the electrical capacitance of GO varied in the order of pico-farads. In addition, the PI sensor has proven long-term sensing stability in air. We demonstrated a novel method of ion micro-beam writing to prepare flexible micro-sensors that function over a wide range of humidity and have good sensitivity and great potential for widespread applications.

This work aims to spectroscopically characterize and provide for the first time direct experimental frequencies of the ground vibrational state and two excited states of the simplest alkynyl thiocyanate (HCCSCN) for astrophysical use. Both microwave (8-16~GHz) and millimeter wave regions (50-120~GHz) of the spectrum have been measured and analyzed in terms of Watson's semirigid rotor Hamiltonian. A total of 314 transitions were assigned to the ground state of HCCSCN and a first set of spectroscopic constants have been accurately determined. Spectral features of the molecule were then searched for in Sgr B2(N), NGC 6334I, G+0.693-0.027 and TMC-1 molecular clouds. Upper limits to the column density are provided.