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From Latent Manifolds to Targeted Molecular Probes: An Interpretable, Kinome-Scale Generative Machine Learning Framework for Family-Based Kinase Ligand Design

Newlypublished by gennady verkhivker, et al.

🔍 Key findings: Novel generative framework integrates ChemVAE-based latent space modeling with chemically interpretable structural similarity metric (Kinase Likelihood Score) and Bayesian optimization for SRC kinase ligand design, demonstrating kinase scaffolds spanning 37 protein kinase families spontaneously organize into low-dimensional manifold with chemically distinct carboxyl groups revealing degeneracy in scaffold encoding — local sampling successfully converts scaffolds from other kinase families into novel SRC-like chemotypes accounting for ~40% of high-similarity cutoffs.

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Scaffold-aware artificial intelligence (AI) models enable systematic exploration of chemical space conditioned on protein-interacting ligands, yet the representational principles governing their behavior remain poorly understood. The computational representation of structurally complex kinase small molecules remains a formidable challenge due to the high conservation of ATP active site architecture across the kinome and the topological complexity of structural scaffolds in current generative AI frameworks. In this study, we present a diagnostic, modular and chemistry-first generative framework for design of targeted SRC kinase ligands by integrating ChemVAE-based latent space modeling, a chemically interpretable structural similarity metric (Kinase Likelihood Score), Bayesian optimization, and cluster-guided local neighborhood sampling.

Paragon: Space-Charge-Neutralized Reflective Electron Projection Lithography

This is best exemplified by the RCA Permanent-Magnet Electron Microscope, based on the work of John H. Reisner and collaborators.

“The permanent magnet as an energizing source for magnetic electron lenses is not new. The use of a permanent magnetic yoke for the comparatively coarse focusing of cathode-ray tubes has long been known. The advantages of permanent magnet lens energization are very appealing — excellent stability (beyond the ability of any regulator), no heating losses in energizing coils, no need for extensive current supplies and regulators — advantages which heretofore were limited to electrostatic lenses.”

The Paragon idea is that “die at once” exposure is the key to high-volume manufacturing with electron projection lithography. Anything that would “reduce system throughput and/or require registration of plural exposures” is forbidden.

Ultrafast Movie Reveals Unexpected Plasma Behavior

Using a camera with 2-picosecond time resolution, researchers show that the atoms in a laser-induced plasma are more highly ionized than theory predicts.

With an astonishing 500 billion frames per second, a new movie captures the evolution of a laser-induced plasma, revealing that its atoms have lost more electrons—and thus have stronger interactions within the plasma—than models predict [1]. The movie relies on a ten-year-old technology, called compressed ultrafast photography (CUP), that packs all the information for hundreds of movie frames into a single image. The results suggest that models of plasma formation may need revising, which could have implications for inertial-confinement-fusion experiments, such as those at the National Ignition Facility in California.

Dense plasmas occur in many astrophysical settings and laboratory experiments. Their behavior is difficult to predict, as they often change on picosecond (10−12 s) timescales. A traditional method for probing this behavior is to use a streak camera, which collects a movie on a single image by capturing a small slice of each movie frame. “It’s one picture, but every line occurs at a different time,” explains John Koulakis from UCLA. He and his colleagues have used streak cameras to study anomalous behavior in plasmas [2], but the small region of plasma visible with this technique left doubts about what they were seeing, he says.

Puzzling slow radio pulses are coming from space. A new study could finally explain them

Cosmic radio pulses repeating every few minutes or hours, known as long-period transients, have puzzled astronomers since their discovery in 2022. Our new study, published in Nature Astronomy today, might finally add some clarity.

Radio astronomers are very familiar with pulsars, a type of rapidly rotating neutron star. To us watching the skies from Earth, these objects appear to pulse because powerful radio beams from their poles sweep our telescopes—much like a cosmic lighthouse.

The slowest pulsars rotate in just a few seconds—this is known as their period. But in recent years, long-period transients have been discovered as well. These have periods from 18 minutes to more than six hours.

Why are Tatooine planets rare? General relativity explains why binary star systems rarely host planets

Astronomers have found thousands of exoplanets around single stars, but few around binary stars—even though both types of stars are equally common. Physicists can now explain the dearth.

Of the more than 4,500 stars known to have planets, one puzzling statistic stands out. Even though nearly all stars are expected to have planets and most stars form in pairs, planets that orbit both stars in a pair are rare.

Of the more than 6,000 extrasolar planets, or exoplanets, confirmed to date—most of them found by NASA’s Kepler Space Telescope and the Transiting Exoplanet Survey Satellite (TESS)—only 14 are observed to orbit binary stars. There should be hundreds. Where are all the planets with two suns, like Tatooine in Star Wars?

How a broken DNA repair tool accelerates aging

Although DNA is tightly packed and protected within the cell nucleus, it is constantly threatened by damage from normal metabolic processes or external stressors such as radiation or chemical substances. To counteract this, cells rely on an elaborate network of repair mechanisms. When these systems fail, DNA damage can accumulate, impair cellular function, and contribute to cancer, aging, and degenerative diseases.

One particularly severe form of DNA damage are the so-called DNA–protein crosslinks (DPCs), in which proteins become attached to DNA. DPCs can arise from alcohol consumption, exposure to substances such as formaldehyde or other aldehydes, or from errors made by enzymes involved in DNA replication and repair. Because DPCs can cause serious errors during cell division by stalling DNA replication, DNA–protein crosslinks pose a serious threat to genome integrity.

The enzyme SPRTN removes DPCs by cleaving the DNA-protein crosslinks. SPRTN malfunctions, for example as a result of mutations, may predispose individuals to developing bone deformities and liver cancer in their teenage years. This rare genetic disorder is known as Ruijs-Aalfs syndrome. Its underlying mechanism remains poorly understood, and there are no specific therapies.

Record-breaking photons at telecom wavelengths—on demand

A team of researchers from the University of Stuttgart and the Julius-Maximilians-UniversitĂ€t WĂŒrzburg led by Prof. Stefanie Barz (University of Stuttgart) has demonstrated a source of single photons that combines on-demand operation with record-high photon quality in the telecommunications C-band—a key step toward scalable photonic quantum computation and quantum communication. “The lack of a high-quality on-demand C-band photon source has been a major problem in quantum optics laboratories for over a decade—our new technology now removes this obstacle,” says Prof. Stefanie Barz.

In everyday life, distinguishing features may often be desirable. Few want to be exactly like everyone else. When it comes to quantum technologies, however, complete indistinguishability is the name of the game. Quantum particles such as photons that are identical in all their properties can interfere with each other—much as in noise-canceling headphones, where sound waves that are precisely inverted copies of the incoming noise cancel out the background.

When identical photons are made to act in synchrony, then the probability that certain measurement outcomes occur can be either boosted or decreased. Such quantum effects give rise to powerful new phenomena that lie at the heart of emerging technologies such as quantum computing and quantum networking. For these technologies to become feasible, high-quality interference between photons is essential.

Novel membrane boosts water electrolysis performance in low-alkalinity conditions

As green hydrogen emerges as a key next-generation clean energy source, securing technologies that enable its stable and cost-effective production has become a critical challenge. However, conventional water electrolysis technologies face limitations in large-scale deployment due to high system costs and operational burdens.

In particular, long-term operation often leads to performance degradation and increased maintenance costs, hindering commercialization. As a result, there is growing demand for new electrolysis technologies that can simultaneously improve efficiency, stability, and cost competitiveness.

A research team led by Dr. Dirk Henkensmeier at the Hydrogen and Fuel Cell Research Center of the Korea Institute of Science and Technology (KIST) has developed a novel membrane material for water electrolysis that operates stably and has significantly higher conductivity under low alkalinity conditions than existing systems.

Say what’s on your mind, and AI can tell what kind of person you are

If you say a few words, generative AI will understand who you are—maybe even better than your close family and friends. A new University of Michigan study found that widely available generative AI models (e.g., ChatGPT, Claude, LLaMa) can predict personality, key behaviors and daily emotions as or even more accurately than those closest to you. The findings appear in the journal Nature Human Behavior.

AI as a new personality judge

“What this study shows is AI can also help us understand ourselves better, providing insights into what makes us most human, our personalities,” said the study’s first author Aidan Wright, U-M professor of psychology and psychiatry. “Lots of people may find this of interest and useful. People have long been interested in understanding themselves better. Online personality questionnaires, some valid and many of dubious quality, are enormously popular.”

Study solves key micro-LED challenges, enabling ‘reality-like’ visuals for AR/VR devices

From TVs and smartwatches to rapidly emerging VR and AR devices, micro-LEDs are a next-generation display technology in which each LED—smaller than the thickness of a human hair—emits light on its own. Among the three primary colors required for full-color displays—red, green, and blue—the realization of high-performance red micro-LEDs has long been considered the most difficult.

KAIST researchers have successfully demonstrated a high-efficiency, ultra-high-resolution red micro-LED display, paving the way for displays that can deliver visuals even sharper than reality. The work is published in the journal Nature Electronics.

A research team led by Professor Sanghyeon Kim of the School of Electrical Engineering, in collaboration with Professor Dae-Myeong Geum of Inha University, compound-semiconductor manufacturer QSI, and microdisplay/SoC design company Raontech, has developed a red micro-LED display technology that achieves ultra-high resolution while significantly reducing power consumption.

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