Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance.

Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent.

A Focal Traumatic Injury to the Neonatal Rodent Spinal Cord Causes an Immediate and Massive Spreading Depolarization Sustained by Chloride Ions, with Transient Network Dysfunction.

In clinics, physical injuries to the spinal cord cause a temporary motor areflexia below lesion, known as spinal shock. This topic is still underexplored due to the lack of preclinical spinal cord injury (SCI) models that do not use anesthesia, which would affect spinal excitability. Our innovative design considered a custom-made micro impactor that provides localized and calibrated strikes to the ventral surface of the thoracic spinal cord of the entire CNS isolated from neonatal rats.

The neural link between stimulus duration and spatial location in the human visual hierarchy.

Integrating spatial and temporal information is essential for our sensory experience. While psychophysical evidence suggests spatial dependencies in duration perception, few studies have directly tested the neural link between temporal and spatial processing. Using ultra-high-field functional MRI and neuronal-based modeling, we investigated how and where the processing and the representation of a visual stimulus duration is linked to that of its spatial location.

Molecular dynamics studies of knotted polymers.

Molecular dynamics calculations have been used to explore the influence of knots on the strength of a polymer strand. In particular, the mechanism of breaking 31, 41, 51, and 52 prime knots has been studied using two very different models to represent the polymer: (1) the generic coarse-grained (CG) bead model of polymer physics and (2) a state-of-the-art machine learned atomistic neural network (NN) potential for polyethylene derived from electronic structure calculations. While there is a broad overall agreement between the results on the influence of the pulling rate on chain rupture based on the CG and atomistic NN models, for the simple 31 and 41 knots, significant differences are found for the more complex 51 and 52 knots.

Interlaminar and varicose-projection astrocytes: toward a new understanding of the primate brain.

In the last years, science started to move toward a more view, in which astrocytes are hypothesized to be directly involved in cognitive functions. Indeed, astrocytes show a variety of shapes with species-specific characteristics, suggesting a specialization of roles during evolution. Interlaminar (ILA) and varicose-projection (VP-As) astrocytes show an anatomical organization that is different compared to the classical horizontal net typically formed by protoplasmic and fibrous astrocytes.

Identification of anticipatory brain activity in a time discrimination task.

The purpose of this study was to investigate anticipatory functions in temporal cognition, identifying the presence of proactive brain processing specifically preceding a time discrimination task. To this aim, two discriminative response tasks (DRTs) were employed: a feature DRT and a temporal (T-DRT). While the F-DRT required discrimination among different geometrical shapes, the T-DRT required discrimination among different stimulus durations.

The Evolution of Nanoscale Third Body Layer Revealed by Graphite Structural Superlubric Contact.

Revealing the evolution of nanoscale third bodies confined between sliding surfaces is essential to understanding the friction and electrical properties for solid contacts. Here, with graphite/graphite contacts in structural superlubricity, a state of no wear and ultralow friction, we reveal the morphological evolution of a third body layer introduced by air through measuring friction and conductance during cyclic hold-slide tests. The directional transport of confined molecules causes apparent elastic deformation of the third body layer, leading to local graphite/graphite direct contact.

Assessing the Mechanism of Rac1b: An All-Atom Simulation Study of the Alternative Spliced Variant of Rac1 Small Rho GTPase.

The Rho GTPase family plays a key role in cell migration, cytoskeletal dynamics, and intracellular signaling. Rac1 and its splice variant Rac1b, characterized by the insertion of an Extraloop, are frequently associated with cancer. These small GTPases switch between an active GTP-bound state and an inactive GDP-bound state, a process that is regulated by specific protein modulators.

Universal moiré buckling of freestanding 2D bilayers.

The physics of membranes, a classic subject, acquires new momentum from two-dimensional (2D) materials multilayers. This work reports the surprising results emerged during a theoretical study of equilibrium geometry of bilayers as freestanding membranes. While ordinary membranes are prone to buckle around compressive impurities, we predict that all 2D material freestanding bilayers universally undergo, even if impurity-free, a spontaneous out-of-plane buckling.

The Effect of Chalcogen-Chalcogen Bond Formation in the New Delhi Metallo-β-Lactamase 1 Enzyme to Counteract Antibiotic Resistance.

New Delhi metallo-β-lactamase 1 (NDM-1) is an enzyme involved in the drug resistance of many bacteria against most of the widely adopted antibiotics, such as penicillins, cephalosporins, and carbapenems. Consequently, inhibiting NDM-1 swiftly has gained significant interest as a strategy to counteract this bacterial defense mechanism, thereby restoring the effectiveness of antibiotics. Among the inhibitors tested against the enzyme, ebselen () showed particularly promising results.

From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs.

Transposable elements (TEs) are mobile genomic elements constituting a big fraction of eukaryotic genomes. They ignite an evolutionary arms race with host genomes, which in turn evolve strategies to restrict their activity. Despite being tightly repressed, TEs display precisely regulated expression patterns during specific stages of mammalian development, suggesting potential benefits for the host.

Emerging Chirality and Moiré Dynamics in Twisted Layered Material Heterostructures.

Moiré superstructures arising at twisted 2D interfaces have recently attracted the attention of the scientific community due to exotic quantum states and unique mechanical and tribological behaviors that they exhibit. Here, we predict the emergence of chiral distortions in twisted layered interfaces of finite dimensions. This phenomenon originates in intricate interplay between interfacial interactions and contact boundary constraints.

Hybrid Stabilizer Matrix Product Operator.

We introduce a novel hybrid approach combining tensor network methods with the stabilizer formalism to address the challenges of simulating many-body quantum systems. By integrating these techniques, we enhance our ability to accurately model unitary dynamics while mitigating the exponential growth of entanglement encountered in classical simulations. We demonstrate the effectiveness of our method through applications to random Clifford T-doped circuits and random Clifford Floquet dynamics.

The Mechanisms and Neural Signature of Time-averaged Numerosity Perception.

The animal brain is endowed with an innate sense of number allowing to intuitively perceive the approximate quantity of items in a scene, or "numerosity." This ability is not limited to items distributed in space, but also to events unfolding in time and to the average numerosity of dynamic scenes. How the brain computes and represents the average numerosity over time, however, remains unclear.

Nonmonotonic Velocity Dependence of Atomic Friction Induced by Multiple Slips.

The transition from single to multiple atomic slips, theoretically expected and important in atomic-scale friction, has never been demonstrated experimentally as a function of velocity. Here we show by high-resolution friction force microscopy on monolayer MoS_{2}/Au(111) that multiple slips leave a unique footprint-a frictional velocity weakening. Specifically, in a wide velocity interval from 10 to 100  nm/s, friction surprisingly decreases.

A Critical Analysis of the CFD-DEM Simulation of Pharmaceutical Aerosols Deposition in Upper Intra-Thoracic Airways: Considerations on Aerosol Transport and Deposition.

The reliability and accuracy of numerical models and computer simulations to study aerosol deposition in the human respiratory system is investigated for a patient-specific tracheobronchial tree geometry. A computational fluid dynamics (CFD) model coupled with discrete elements methods (DEM) is used to predict the transport and deposition of the aerosol. The results are compared to experimental and numerical data available in the literature to study and quantify the impact of the modeling parameters and numerical assumptions.

The role of personality in social interaction perception: an ERP and source imaging study.

Agreeableness, one of the five personality traits, is associated with socio-cognitive abilities. This study investigates how agreeableness impacts the perception of social interactions, while considering sex that might moderate this effect. Sixty-two young adults, preselected to ensure a wide range of agreeableness scores, underwent EEG recording while viewing images depicting real-world scenes of two people either engaged in a social interaction or acting independently.

Universality in the 2d Quasi-periodic Ising Model and Harris-Luck Irrelevance.

We prove that in the 2D Ising model with a weak bidimensional quasi-periodic disorder in the interaction, the critical behavior is the same as in the non-disordered case; that is, the critical exponents for the specific heat and energy-energy correlations are identical, and no logarithmic corrections are present. The disorder produces a quasi-periodic modulation of the amplitude of the correlations and a renormalization of the velocities, that is, the coefficients of the rescaling of positions, and of the critical temperature. The result establishes the validity of the prediction based on the Harris-Luck criterion, and it provides the first rigorous proof of universality in the Ising model in the presence of quasi-periodic disorder in both directions and for any angle.

Coarse-Grained Molecular Dynamics with Normalizing Flows.

We propose a sampling algorithm relying on a collective variable (CV) of midsize dimension modeled by a normalizing flow and using nonequilibrium dynamics to propose full configurational moves from the proposition of a refreshed value of the CV made by the flow. The algorithm takes the form of a Markov chain with nonlocal updates, allowing jumps through energy barriers across metastable states. The flow is trained throughout the algorithm to reproduce the free energy landscape of the CV.

Structural and biochemical characterization of the C-terminal region of the human RTEL1 helicase.

RTEL1 is an essential DNA helicase which plays an important role in various aspects of genome stability, from telomere metabolism to DNA replication, repair and recombination. RTEL1 has been implicated in a number of genetic diseases and cancer development, including glioma, breast, lung and gastrointestinal tumors. RTEL1 is a FeS helicase but, in addition to the helicase core, it comprises a long C-terminal region which includes a number of folded domains connected by intrinsically disordered loops and mediates RTEL1 interaction with factors involved in pivotal cellular pathways.

Policy-guided Monte Carlo on general state spaces: Application to glass-forming mixtures.

Policy-guided Monte Carlo is an adaptive method to simulate classical interacting systems. It adjusts the proposal distribution of the Metropolis-Hastings algorithm to maximize the sampling efficiency, using a formalism inspired by reinforcement learning. In this work, we first extend the policy-guided method to deal with a general state space, comprising, for instance, both discrete and continuous degrees of freedom, and then apply it to a few paradigmatic models of glass-forming mixtures.

Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins.

Introduction: Molecular Dynamics (MD) simulations can support mechanism-based drug design. Indeed, MD simulations by capturing biomolecule motions at finite temperatures can reveal hidden binding sites, accurately predict drug-binding poses, and estimate the thermodynamics and kinetics, crucial information for drug discovery campaigns. Small-Guanosine Triphosphate Phosphohydrolases (GTPases) regulate a cascade of signaling events, that affect most cellular processes.

Shape and size tunability of sheets of interlocked ring copolymers.

Mechanically bonded membranes of interlocked ring polymers are a significant generalization of conventional elastic sheets, where connectivity is provided by covalent bonding, and represent a promising class of topological meta-materials. In this context, two open questions regard the large-scale reverberations of the heterogeneous composition of the rings and the inequivalent modes of interlocking neighboring rings. We address these questions with Langevin dynamics simulations of chainmails with honeycomb-lattice connectivity, where the rings are block copolymers with two segments of different rigidity.