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DeepChopper model improves RNA sequencing research by mitigating chimera artifacts

Scientists in the laboratory of Rendong Yang, Ph.D., associate professor of Urology, have developed a new large language model that can interpret transcriptomic data in cancer cell lines more accurately than conventional approaches, as detailed in a recent study published in Nature Communications.

Long-read RNA sequencing technologies have transformed transcriptomics research by detecting complex RNA splicing and gene fusion events that have often been missed by conventional short-read RNA-sequencing methods.

Among these technologies includes nanopore direct RNA sequencing (dRNA-seq), which can sequence full-length RNA molecules directly and produce more accurate analyses of RNA biology. However, previous work suggests this approach may generate chimera artifacts—in which multiple RNA sequences incorrectly join to form a single RNA sequence—and limit the reliability and utility of the data.

Microfluidic method boosts control and separation of tiny particles—a promising tool for medical research

In nanoscale particle research, precise control and separation have long been a bottleneck in biotechnology. Researchers at the University of Oulu have now developed a new method that improves particle separation and purification. The promising technique could be applied, for example, in cancer research.

Separating nanosized particles remains a persistent challenge in biotechnology. Once particle size drops below a few hundred nanometers, their behavior becomes dominated by diffusion—the random walk of particles. This weakens the forces used to guide them, causing separation accuracy to collapse.

A microfluidics research group led by Professor Caglar Elbuken at the University of Oulu has developed a new solution to the problem. The method significantly improves the separation and purification of both small synthetic particles and nanoscale vesicles secreted by living cells.

3D ‘polar chiral bobbers’ identified in ferroelectric thin films

A novel type of three-dimensional (3D) polar topological structure, termed the “polar chiral bobber,” has been discovered in ferroelectric oxide thin films, demonstrating promising potential for high-density multistate non-volatile memory and logic devices. The result was achieved by a collaborative research team from the Institute of Metal Research (IMR) of the Chinese Academy of Sciences, the Songshan Lake Materials Laboratory, and other institutions. The findings were published in Advanced Materials on January 30.

Topological polar textures in ferroelectrics, such as flux-closures, vortices, skyrmions, merons, Bloch points, and high-order radial vortices discovered in recent years, have attracted wide interest for future electronic applications. However, most known polar states possess limited configurational degrees of freedom, constraining their potential for multilevel data storage.

In this study, the researchers used phase-field simulations and aberration-corrected transmission electron microscopy to predict and experimentally confirm the existence of polar chiral bobbers in (111)-oriented ultrathin PbTiO₃ ferroelectric films. This 3D topological structure is characterized by a nanoscale domain with out-of-plane polarization opposite to its surroundings, which starts from the film surface and terminates at a Bloch point inside the film.

Muon Knight shift reveals the behavior of superconducting electron pairs

Quantum materials and superconductors are difficult enough to understand on their own. Unconventional superconductors, which cannot be explained within the framework of standard theory, take the enigma to an entirely new level. A typical example of unconventional superconductivity is strontium ruthenate, SRO214, the superconductive properties of which were discovered by a research team that included Yoshiteru Maeno, who is currently at the Toyota Riken—Kyoto University Research Center.

The findings are published in the journal Physical Review Letters.

Debate over SRO214’s superconducting nature.

Could electronic beams in the ionosphere remove space junk?

A possible alternative to active debris removal (ADR) by laser is ablative propulsion by a remotely transmitted electron beam (e-beam). The e-beam ablation has been widely used in industries, and it might provide higher overall energy efficiency of an ADR system and a higher momentum-coupling coefficient than laser ablation. However, transmitting an e-beam efficiently through the ionosphere plasma over a long distance (10 m–100 km) and focusing it to enhance its intensity above the ablation threshold of debris materials are new technical challenges that require novel methods of external actions to support the beam transmission.

Therefore, Osaka Metropolitan University researchers conducted a preliminary study of the relevant challenges, divergence, and instabilities of an e-beam in an ionospheric atmosphere, and identified them quantitatively through numerical simulations. Particle-in-cell simulations were performed systematically to clarify the divergence and the instability of an e-beam in an ionospheric plasma.

The major phenomena, divergence and instability, depended on the densities of the e-beam and the atmosphere. The e-beam density was set slightly different from the density of ionospheric plasma in the range from 1010 to 1012 m−3. The e-beam velocity was changed from 106 to 108 m/s, in a nonrelativistic range.

Seeing the whole from a part: Revealing hidden turbulent structures from limited observations and equations

The irregular, swirling motion of fluids we call turbulence can be found everywhere, from stirring in a teacup to currents in the planetary atmosphere. This phenomenon is governed by the Navier-Stokes equations—a set of mathematical equations that describe how fluids move.

Despite being known for nearly two centuries, these equations still pose major challenges when it comes to making predictions. Turbulent flows are inherently chaotic, and tiny uncertainties can grow quickly over time.

In real-world situations, scientists can only observe part of a turbulent flow, usually its largest and slowest moving features. Thus, a long-standing question in fluid physics has been whether these partial observations are enough to reconstruct the full motion of the fluid.

Physicists clarify key mechanism behind energy release in molybdenum-93

A team of physicists from the Institute of Modern Physics (IMP) of the Chinese Academy of Sciences, together with collaborators, has identified the dominant physical mechanism responsible for energy release in the nuclear isomer molybdenum-93m (Mo-93m). Using high-precision experiments, the researchers showed that inelastic nuclear scattering—rather than the long-hypothesized nuclear excitation by electron capture (NEEC)—is the primary driver of isomer depletion under their experimental conditions.

The findings, published in Physical Review Letters on February 6, provide crucial experimental evidence concerning a long-debated process and shed new light on the controlled release of nuclear energy.

Quantum dots reveal entropy production, a key measure of nanoscale energy dissipation

In order to build the computers and devices of tomorrow, we have to understand how they use energy today. That’s harder than it sounds. Memory storage, information processing, and energy use in these technologies involve constant energy flow—systems never settle into thermodynamic balance. To complicate things further, one of the most precise ways to study these processes starts at the smallest scale: the quantum domain.

New Stanford research published in Nature Physics combines theory, experimentation, and machine learning to quantify energy costs during a non-equilibrium process with ultrahigh sensitivity. Researchers used extremely small nanocrystals called quantum dots, which have unique light-emitting properties that arise from quantum effects at the nanoscale.

They measured the entropy production of quantum dots—a quantity that describes how reversible a microscopic process is, and encodes information about memory, information loss, and energy costs. Such measurements can determine the ultimate speed limits for a device or how efficient it can be.

How fast can a microlaser switch ‘modes?’ A simple rule reveals a power-law time scaling

Modern technologies increasingly rely on light sources that can be reconfigured on demand. Think of microlasers that can quickly switch between different operating states—much like a car shifting gears—so that an optical chip can route signals, perform computations, or adapt to changing conditions in real time. The microlaser switching is not a smooth, leisurely process, but can be sudden and fast. Generally, nearly identical “candidate” lasing states compete with each other in a microcavity, and the laser may abruptly jump from one state to another when external conditions are tuned.

This raises a practical question: How fast can such a switch be, in principle? For physicists, it raises a deeper one: Does the switching follow a universal rule, like other phase transitions in nature?

A team at Peking University has now provided a clear picture of an ultrahigh-quality microcavity laser—the time the laser needs to complete a state switch follows a remarkably simple power-law rule. When the control knob is swept faster, the switch becomes faster—but not arbitrarily so. Instead, the switching time decreases with the square root of the sweep speed, corresponding to a robust exponent close to half. This result effectively sets a speed limit for how quickly such microlasers can “change gears.” The findings are published in Physical Review Letters.

Stable high-energy pulses achieved with low-stress electro-optic switch

A research team led by Prof. Zhang Tianshu from the Hefei Institutes of Physical Science of the Chinese Academy of Sciences has developed a low-stress electro-optic switch based on large-aperture β-barium borate (BBO) slab crystals and integrated it into an Nd:YAG hybrid-cavity Innoslab laser system. Their study, published in Optics Express on January 13, addresses long-standing challenges in high-energy laser systems, particularly those related to switching modulation consistency and operational stability.

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