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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.

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?

Quantum mechanical effects help overcome a fundamental limitation of optical microscopy

Researchers from Regensburg and Birmingham have overcome a fundamental limitation of optical microscopy. With the help of quantum mechanical effects, they succeeded for the first time in performing optical measurements with atomic resolution. Their work is published in the journal Nano Letters.

From smartphone cameras to space telescopes, the desire to see ever finer detail has driven technological progress. Yet as we probe smaller and smaller length scales, we encounter a fundamental boundary set by light itself. Because light behaves as a wave, it cannot be focused arbitrarily sharply due to an effect called diffraction. As a result, conventional optical microscopes are unable to resolve structures much smaller than the wavelength of light, placing the very building blocks of matter beyond direct optical observation.

Now, researchers at the Regensburg Center for Ultrafast Nanoscopy, together with colleagues at the University of Birmingham, have found a novel way to overcome this limitation. Using standard continuous-wave lasers, they have achieved optical measurements at distances comparable to the spacing between individual atoms.

Beyond the eye of the beholder: Mathematically defining attributes essential to color perception

Research on the perception of color differences is helping resolve a century-old understanding of color developed by Erwin Schrödinger. Los Alamos scientist Roxana Bujack led a team that used geometry to mathematically define the perception of color as it relates to hue, saturation and lightness.

Presented at the 2025 Eurographics Conference on Visualization, their work formalizes Schrödinger’s model of color, decisively establishing the perception of color attributes as an intrinsic property. The paper, “The Geometry of Color in the Light of a Non-Riemannian Space,” was published in the Computer Graphics Forum.

“What we conclude is that these color qualities don’t emerge from additional external constructs such as cultural or learned experiences but reflect the intrinsic properties of the color metric itself,” Bujack said. “This metric geometrically encodes the perceived color distance—that is, how different two colors appear to an observer.”

Exploration of exoplanets: A mathematical solution for investigating their atmospheres

Dr. Leonardos Gkouvelis, researcher at LMU’s University Observatory Munich and member of the ORIGINS Excellence Cluster, has solved a fundamental mathematical problem that had obstructed the interpretation of exoplanet atmospheres for decades. In a paper published in The Astrophysical Journal, Gkouvelis presents the first closed-form analytical theory of transmission spectroscopy that accounts for how atmospheric opacity varies with pressure—an effect that is crucial in the scientific exploration of real atmospheres but had until now been considered mathematically intractable.

For more than 30 years, analytical models were based on a “simplified” atmosphere, as the full mathematical treatment requires solving a complex geometric integral in the presence of altitude-dependent opacity—a problem that could only be tackled using expensive numerical simulations. However, this limitation concealed how the true vertical structure of an atmosphere alters the signals observed by telescopes.

The new model provides key insights into why many exoplanet atmospheres display “muted” spectral features, directly links laboratory molecular-physics data with astronomical observations, and significantly improves agreement with real data—both for Earth’s atmosphere and for high-precision observations of exoplanets.

NASA researchers probe tangled magnetospheres of merging neutron stars

New simulations performed on a NASA supercomputer are providing scientists with the most comprehensive look yet into the maelstrom of interacting magnetic structures around city-sized neutron stars in the moments before they crash. The team identified potential signals emitted during the stars’ final moments that may be detectable by future observatories.

“Just before neutron stars crash, the highly magnetized, plasma-filled regions around them, called magnetospheres, start to interact strongly. We studied the last several orbits before the merger, when the entwined magnetic fields undergo rapid and dramatic changes, and modeled potentially observable high-energy signals,” said lead scientist Dimitrios Skiathas, a graduate student at the University of Patras, Greece, who is conducting research for the Southeastern Universities Research Association in Washington at NASA’s Goddard Space Flight Center in Greenbelt, Maryland.

A paper describing the findings is published in the The Astrophysical Journal.

2D discrete time crystals realized on a quantum computer for the first time

Physical systems become inherently more complicated and difficult to produce in a lab as the number of dimensions they exist in increases—even more so in quantum systems. While discrete time crystals (DTCs) had been previously demonstrated in one dimension, two-dimensional DTCs were known to exist only theoretically. But now, a new study, published in Nature Communications, has demonstrated the existence of a DTC in a two-dimensional system using a 144-qubit quantum processor.

Like regular crystalline materials, DTCs exhibit a kind of periodicity. However, the crystalline materials most people are familiar with have a periodically repeating structure in space, while the particles in DTCs exhibit periodic motion over time. They represent a phase of matter that breaks time-translation symmetry under a periodic driving force and cannot experience an equilibrium state.

“Consequently, local observables exhibit oscillations with a period that is a multiple of the driving frequency, persisting indefinitely in perfectly isolated systems. This subharmonic response represents a spontaneous breaking of discrete time-translation symmetry, analogous to the breaking of continuous spatial symmetry in conventional solid-state crystals,” the authors of the new study explain.

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