Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data.

Single same cell RNAseq/ATACseq multiome data provide unparalleled potential to develop high resolution maps of the cell-type specific transcriptional regulatory circuitry underlying gene expression. We present CREMA, a framework that recovers the full cis-regulatory circuitry by modeling gene expression and chromatin activity in individual cells without peak-calling or cell type labeling constraints. We demonstrate that CREMA overcomes the limitations of existing methods that fail to identify about half of functional regulatory elements which are outside the called chromatin 'peaks'.

Mapping Light-Dressed Floquet Bands by Highly Nonlinear Optical Excitations and Valley Polarization.

Ultrafast nonlinear optical phenomena in solids have been attracting a great deal of interest as novel methodologies for the femtosecond spectroscopy of electron dynamics and control of the properties of materials. Here, we theoretically investigate strong-field nonlinear optical transitions in a prototypical two-dimensional material, hBN, and show that the -resolved conduction band charge occupation patterns induced by an elliptically polarized laser can be understood in a multiphoton resonant picture, but, remarkably, only if using the Floquet light-dressed states instead of the undressed matter states. Our work demonstrates that Floquet dressing affects ultrafast charge dynamics and photoexcitation even from a single pump pulse and establishes a direct measurable signature for band dressing in nonlinear optical processes in solids, opening new paths for ultrafast spectroscopy and valley manipulation.

Tunable Tesla-Scale Magnetic Attosecond Pulses through Ring-Current Gating.

Coherent control over electron dynamics in atoms and molecules using high-intensity circularly polarized laser pulses gives rise to current loops, resulting in the emission of magnetic fields. We propose, and demonstrate with ab initio calculations, "current-gating" schemes to generate direct or alternating-current magnetic pulses in the infrared spectral region, with highly tunable waveform and frequency, and showing femtosecond-to-attosecond pulse duration. In optimal conditions, the magnetic pulse can be highly isolated from the driving laser and exhibits a high flux density (∼1 T at a few hundred nanometers from the source, with a pulse duration of 787 attoseconds) for application in forefront experiments of ultrafast spectroscopy.

Nishimori's Cat: Stable Long-Range Entanglement from Finite-Depth Unitaries and Weak Measurements.

In the field of monitored quantum circuits, it has remained an open question whether finite-time protocols for preparing long-range entangled states lead to phases of matter that are stable to gate imperfections, that can convert projective into weak measurements. Here, we show that in certain cases, long-range entanglement persists in the presence of weak measurements, and gives rise to novel forms of quantum criticality. We demonstrate this explicitly for preparing the two-dimensional Greenberger-Horne-Zeilinger cat state and the three-dimensional toric code as minimal instances.

Protein-Engineered Fibers For Drug Encapsulation Traceable via F Magnetic Resonance.

Theranostic materials research is experiencing rapid growth driven by the interest in integrating both therapeutic and diagnostic modalities. These materials offer the unique capability to not only provide treatment but also track the progression of a disease. However, to create an ideal theranostic biomaterial without compromising drug encapsulation, diagnostic imaging must be optimized for improved sensitivity and spatial localization.

Targeted V1 comodulation supports task-adaptive sensory decisions.

Sensory-guided behavior requires reliable encoding of stimulus information in neural populations, and flexible, task-specific readout. The former has been studied extensively, but the latter remains poorly understood. We introduce a theory for adaptive sensory processing based on functionally-targeted stochastic modulation.

A dynamical model of growth and maturation in .

The decision to stop growing and mature into an adult is a critical point in development that determines adult body size, impacting multiple aspects of an adult's biology. In many animals, growth cessation is a consequence of hormone release that appears to be tied to the attainment of a particular body size or condition. Nevertheless, the size-sensing mechanism animals use to initiate hormone synthesis is poorly understood.

Phonon-enhanced nonlinearities in hexagonal boron nitride.

Polar crystals can be driven into collective oscillations by optical fields tuned to precise resonance frequencies. As the amplitude of the excited phonon modes increases, novel processes scaling non-linearly with the applied fields begin to contribute to the dynamics of the atomic system. Here we show two such optical nonlinearities that are induced and enhanced by the strong phonon resonance in the van der Waals crystal hexagonal boron nitride (hBN).

Weakened Topological Protection of the Quantum Hall Effect in a Cavity.

We study the quantum Hall effect in a two-dimensional homogeneous electron gas coupled to a quantum cavity field. As initially pointed out by Kohn, Galilean invariance for a homogeneous quantum Hall system implies that the electronic center of mass (c.m.

Microscopic theory, analysis, and interpretation of conductance histograms in molecular junctions.

Molecular electronics break-junction experiments are widely used to investigate fundamental physics and chemistry at the nanoscale. Reproducibility in these experiments relies on measuring conductance on thousands of freshly formed molecular junctions, yielding a broad histogram of conductance events. Experiments typically focus on the most probable conductance, while the information content of the conductance histogram has remained unclear.

Morphogens enable interacting supracellular phases that generate organ architecture.

During vertebrate organogenesis, increases in morphological complexity are tightly coupled to morphogen expression. In this work, we studied how morphogens influence self-organizing processes at the collective or "supra"-cellular scale in avian skin. We made physical measurements across length scales, which revealed morphogen-enabled material property differences that were amplified at supracellular scales in comparison to cellular scales.

Cavity Click Chemistry: Cavity-Catalyzed Azide-Alkyne Cycloaddition.

Click chemistry, which refers to chemical reactions that are fast and selective with high product yields, has become a powerful approach in organic synthesis and chemical biology. Due to the cytotoxicity of the transition metals employed in click chemistry reactions, a search for novel metal-free alternatives continues. Herein, we demonstrate that an optical cavity can be utilized as a metal-free alternative in the click chemistry cycloaddition reaction between cyanoacetylene and formylazide using the quantum electrodynamics coupled cluster method.

Mott insulators with boundary zeros.

The topological classification of electronic band structures is based on symmetry properties of Bloch eigenstates of single-particle Hamiltonians. In parallel, topological field theory has opened the doors to the formulation and characterization of non-trivial phases of matter driven by strong electron-electron interaction. Even though important examples of topological Mott insulators have been constructed, the relevance of the underlying non-interacting band topology to the physics of the Mott phase has remained unexplored.

Digital quantum simulation of NMR experiments.

Simulations of nuclear magnetic resonance (NMR) experiments can be an important tool for extracting information about molecular structure and optimizing experimental protocols but are often intractable on classical computers for large molecules such as proteins and for protocols such as zero-field NMR. We demonstrate the first quantum simulation of an NMR spectrum, computing the zero-field spectrum of the methyl group of acetonitrile using four qubits of a trapped-ion quantum computer. We reduce the sampling cost of the quantum simulation by an order of magnitude using compressed sensing techniques.

Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.

Resolving chromatin-remodeling-linked gene expression changes at cell-type resolution is important for understanding disease states. Here we describe MAGICAL (Multiome Accessibility Gene Integration Calling and Looping), a hierarchical Bayesian approach that leverages paired single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing from different conditions to map disease-associated transcription factors, chromatin sites, and genes as regulatory circuits. By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference.

Numerically Exact Solution for a Real Polaritonic System under Vibrational Strong Coupling in Thermodynamic Equilibrium: Loss of Light-Matter Entanglement and Enhanced Fluctuations.

The first numerically exact simulation of a full ab initio molecular quantum system (HD) under strong ro-vibrational coupling to a quantized optical cavity mode in thermal equilibrium is presented. Theoretical challenges in describing strongly coupled systems of mixed quantum statistics (bosons and Fermions) are discussed and circumvented by the specific choice of our molecular system. Our numerically exact simulations highlight the absence of zero temperature for the strongly coupled matter and light subsystems, due to cavity-induced noncanonical conditions.

Chromokinesin Klp-19 regulates microtubule overlap and dynamics during anaphase in .

Recent studies have highlighted the significance of the spindle midzone, the region between the segregating chromosomes, in ensuring proper chromosome segregation. By combining 3D electron tomography, cutting-edge light microscopy and a novel single cell essay allowing single molecule tracking, we have discovered a previously unknown role of the regulation of microtubule dynamics within the spindle midzone of by the chromokinesin KLP-19, and its relevance for proper spindle function. Using Fluorescence recovery after photobleaching and a combination of second harmonic generation and two-photon fluorescence microscopy, we found that the length of the antiparallel microtubule overlap zone in the spindle midzone is constant throughout anaphase, and independent of cortical pulling forces as well as the presence of the microtubule bundling protein SPD-1.

Automated single-cell omics end-to-end framework with data-driven batch inference.

To facilitate single-cell multi-omics analysis and improve reproducibility, we present SPEEDI (Single-cell Pipeline for End to End Data Integration), a fully automated end-to-end framework for batch inference, data integration, and cell type labeling. SPEEDI introduces data-driven batch inference and transforms the often heterogeneous data matrices obtained from different samples into a uniformly annotated and integrated dataset. Without requiring user input, it automatically selects parameters and executes pre-processing, sample integration, and cell type mapping.

Bayesian spatial modelling of localised SARS-CoV-2 transmission through mobility networks across England.

In the early phases of growth, resurgent epidemic waves of SARS-CoV-2 incidence have been characterised by localised outbreaks. Therefore, understanding the geographic dispersion of emerging variants at the start of an outbreak is key for situational public health awareness. Using telecoms data, we derived mobility networks describing the movement patterns between local authorities in England, which we have used to inform the spatial structure of a Bayesian BYM2 model.

A Milky Way-like barred spiral galaxy at a redshift of 3.

The majority of massive disk galaxies in the local Universe show a stellar barred structure in their central regions, including our Milky Way. Bars are supposed to develop in dynamically cold stellar disks at low redshift, as the strong gas turbulence typical of disk galaxies at high redshift suppresses or delays bar formation. Moreover, simulations predict bars to be almost absent beyond z = 1.

Distinct spin and orbital dynamics in SrRuO.

The unconventional superconductor SrRuO has long served as a benchmark for theories of correlated-electron materials. The determination of the superconducting pairing mechanism requires detailed experimental information on collective bosonic excitations as potential mediators of Cooper pairing. We have used Ru L-edge resonant inelastic x-ray scattering to obtain comprehensive maps of the electronic excitations of SrRuO over the entire Brillouin zone.