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Iterative SCRaMbLE for engineering synthetic genome modules and chromosomes

SCRaMbLE can optimise traits via gene rearrangement but is limited by screening. Here the authors use FACS and long-read sequencing with iterative SCRaMbLE to map genotype diversity and gene arrangements, identifying solutions for improving genome design.

New physical model aims to boost energy storage research

Engineers rely on computational tools to develop new energy storage technologies, which are critical for capitalizing on sustainable energy sources and powering electric vehicles and other devices. Researchers have now developed a new classical physics model that captures one of the most complex aspects of energy storage research—the dynamic nonequilibrium processes that throw chemical, mechanical and physical aspects of energy storage materials out of balance when they are charging or discharging energy.

The new Chen-Huang Nonequilibrium Phasex Transformation (NExT) Model was developed by Hongjiang Chen, a former Ph.D. student at NC State, in conjunction with his advisor, Hsiao-Ying Shadow Huang, who is an associate professor of mechanical and aerospace engineering at the university. A paper on the work, “Energy Change Pathways in Electrodes during Nonequilibrium Processes,” is published in The Journal of Physical Chemistry C.

But what are “nonequilibrium processes”? Why are they important? And why would you want to translate those processes into mathematical formulae? We talked with Huang to learn more.

Davidkimai/Context-Engineering: “Context engineering is the delicate art and science of filling the context window with just the right information for the next step.” — Andrej Karpathy. A frontier

“Context engineering is the delicate art and science of filling the context window with just the right information for the next step.” — Andrej Karpathy. A frontier, first-principles handbook inspired by Karpathy and 3Blue1Brown for moving beyond prompt engineering to the wider discipline of context design, orchestration, and optimization.

Johns Hopkins scientists grow novel ‘whole-brain’ organoid

Johns Hopkins University researchers have grown a novel whole-brain organoid, complete with neural tissues and rudimentary blood vessels—an advance that could usher in a new era of research into neuropsychiatric disorders such as autism.

“We’ve made the next generation of brain organoids,” said lead author Annie Kathuria, an assistant professor in JHU’s Department of Biomedical Engineering who studies brain development and neuropsychiatric disorders. “Most brain organoids that you see in papers are one brain region, like the cortex or the hindbrain or midbrain. We’ve grown a rudimentary whole-brain organoid; we call it the multi-region brain organoid (MRBO).”

Could Metasurfaces Be The Next Quantum Information Processors?

In the race toward practical quantum computers and networks, photons — fundamental particles of light — hold intriguing possibilities as fast carriers of information at room temperature. Photons are typically controlled and coaxed into quantum states via waveguides on extended microchips, or through bulky devices built from lenses, mirrors, and beam splitters. The photons become entangled – enabling them to encode and process quantum information in parallel – through complex networks of these optical components. But such systems are notoriously difficult to scale up due to the large numbers and imperfections of parts required to do any meaningful computation or networking.

Could all those optical components could be collapsed into a single, flat, ultra-thin array of subwavelength elements that control light in the exact same way, but with far fewer fabricated parts?

Optics researchers in the Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS) did just that. The research team led by Federico Capasso, the Robert L. Wallace Professor of Applied Physics and Vinton Hayes Senior Research Fellow in Electrical Engineering, created specially designed metasurfaces — flat devices etched with nanoscale light-manipulating patterns — to act as ultra-thin upgrades for quantum-optical chips and setups.


Researchers blend theoretical insight and precision experiments to entangle photons on an ultra-thin chip.

Ionic-electronic photodetector brings in-sensor vision closer to reality

In an advance at the intersection of neuromorphic engineering and photonics, researchers have developed an ionic-electronic photodetector that not only detects light but also performs in-sensor image processing, offering the potential to surpass some limitations of human vision—including color vision deficiencies.

Optimized cycle system recovers waste heat from fusion reactor

A research team led by Prof. Guo Bin from the Hefei Institutes of Physical Science of the Chinese Academy of Sciences has designed and optimized an organic Rankine cycle (ORC) system specifically for recovering low-grade waste heat from the steady-state Chinese Fusion Engineering Testing Reactor (CFETR) based on organic fluid R245fa, achieving enhanced thermal efficiency and reduced heat loss.

CFETR, a steady-state magnetic reactor, is a crucial step toward realizing commercial fusion energy. However, managing the large amount of low-grade waste heat produced by components such as the divertor and blanket remains a key challenge.

To solve the thermodynamic and heat integration issues, the researchers developed advanced simulation models using Engineering Equation Solver for cycle analysis and MATLAB-based LAMP modeling for dynamic system configuration. These tools enabled a comprehensive investigation and optimization of the ORC configuration, leading to significantly improved thermal performance.

New Plague Linux malware stealthily maintains SSH access

A newly discovered Linux malware, which has evaded detection for over a year, allows attackers to gain persistent SSH access and bypass authentication on compromised systems.

Nextron Systems security researchers, who identified the malware and dubbed it “Plague,” describe it as a malicious Pluggable Authentication Module (PAM) that uses layered obfuscation techniques and environment tampering to avoid detection by traditional security tools.

This malware features anti-debugging capabilities to thwart analysis and reverse engineering attempts, string obfuscation to make detection more difficult, hardcoded passwords for covert access, as well as the ability to hide session artifacts that would normally reveal the attacker’s activity on infected devices.

Galaxy Scale Megastructures & Kardashev 3 Civilizations

Imagine engineering projects so vast they mold galaxies into new shapes. We’ll explore the staggering feats of Kardashev-3 and beyond civilizations, crafting CARD galaxies, Birch Planets, and even rearranging superclusters.

Watch my exclusive video Dark Biospheres: https://nebula.tv/videos/isaacarthur–
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Credits:
Spaceport Innovations — Designing the Next Generation of Launch Sites.
August 3, 2025; Episode 746
Written, Produced & Narrated by: Isaac Arthur.
Galaxy-Scale Megastructures & Kardashev-3 Civilizations.
Written by: Isaac Arthur.
Editor: Darius Said.
Graphics: Jeremy Jozwik, Ken York, Sergio Botero, Steve Bowers.
Select imagery/video supplied by Getty Images.
Music Courtesy of Epidemic Sound http://epidemicsound.com/creator.
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