ForceGen: Using A Diffusion Model To Help Design Novel Proteins

Although proteins are composed out of only a small number of distinct amino acids, this deceptive simplicity quickly vanishes when considering the many possible sequences across a protein, not to mention the many ways in which a single 1D protein sequence can fold into a 3D protein shape with a specific functionality. Although natural evolution has done much of the legwork here already, figuring out new sequences and their functionality is a daunting task where increasingly deep learning algorithms are being applied. As [Bo Ni] and colleagues report in a research article in Science Advances, the hardest challenge is designing a protein sequence based on the desired functionality. They then demonstrate a way to use a generative model to speed up this process.

They set out to design proteins with specific mechanical properties, for which they used the known unfolding characteristics of various protein sequences to train a diffusion model. This approach is thus more akin to the technology behind image generation algorithms like DALL-E than LLMs. Using the trained diffusion model it was then possible to generate likely sequences of which the properties could then be simulated, with favorable results.

As a large data set aid, such a diffusion model could conceivably be very useful in fields even beyond protein synthesis, automating tedious tasks and conceivably speeding up discoveries.

Wolfenstein 3D Clone Makes Arduboy Debut

The 8-bit Arduboy isn’t exactly a powerhouse by modern gaming standards, or even really by old school standards for that matter. But for the talented developers that produce software for the system, that’s just part of the challenge. To date the monochromatic handheld has seen miniaturized takes on many well-known games, with several taxing the hardware beyond what most would have assumed possible.

But the latest entry into this catalog of improbable software, WolfenduinoFX, is easily the most technically impressive. As the name implies, this is a “demake” of 1992’s iconic Wolfenstein 3D. It features 10 levels based on the original game’s shareware release, with the enemies, weapons, and even secret rooms lovingly recreated for the Arduboy’s 128 x 64 OLED display.

Arduboy FX Mod-Chip

Now, those of you who have experience working with the ATMega32u4 microcontroller at the heart of the Arduboy might think this is impossible…and you’d be right. The only way developer [James Howard] was able to pull this feat off was by leveraging the extended flash memory offered by the Arduboy FX.

This upgrade, which was developed in conjunction with the community, allows the handheld to hold hundreds of games by loading them from an SPI flash chip. For WolfenduinoFX, that flash chip is used to hold graphical assets for the game that would otherwise be too large to fit on the MCU alone.

When we looked at the Arduboy FX back in 2021, it was clearly a must-have upgrade, so it’s no wonder that the newest version of the handheld has the capability built-in. Now that games are actually requiring the expanded flash to function, it seems we’ve officially entered into a new era for the quirky little handheld that [Kevin Bates] first sent our way nearly a decade ago. Long live the Arduboy!

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MIT Engineers Pioneer Cost-Effective Protein Purification For Cheaper Drugs

There are a wide variety of protein-based drugs that are used to treat various serious conditions. Insulin is perhaps the most well-known example, which is used for life-saving treatments for diabetes. New antibody treatments also fall into this category, as do various vaccines.

A significant cost element in the production of these treatments is the purification step, wherein the desired protein is separated from the contents of the bioreactor it was produced in. A new nanotech discovery from MIT could revolutionize this area, making these drugs cheaper and easier to produce.

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Wolfenstein 3D, As You Never Imagined It.

When tracing the history of first-person shooting (FPS) games, where do you credit with the genesis of the genre? Anyone who played 3D Monster Maze on the Sinclair ZX81 might dare to raise a hand, but we’re guessing that most of you will return to the early 1990s, and id Software. Their 1992 title Wolfenstein 3D might not have been the first to combine all the elements, but it’s arguably the first modern FPS and the first to gain huge popularity. Back in 1992 it needed at least a VGA card and a 286 to run, but here in 2023 [jhhoward] has taken it back a step further. You can now slay virtual Nazis in 3D on an 8088 PC equipped with a lowly CGA card.

Whether the gameplay survives in the sometimes-bizarre CGA color schemes and whether it becomes too pedestrian on an 8088 remains as an exercise for the reader to discover, but it’s a feat nevertheless. The textures all need converting to CGA mode before they can be used and there are even versions for the shareware and paid-for versions of the game.  It’s possible that an 8088 may never be able to say yes to “Will it run DOOM?”, but at least now it can run the predecessor.

Broken Genes And Scrambled Proteins: How Radiation Causes Biological Damage

If decades of cheesy sci-fi and pop culture have taught us anything, it’s that radiation is a universally bad thing that invariably causes the genetic mutations that gifted us with everything from Godzilla to Blinky the Three-Eyed Fish. There’s a kernel of truth there, of course. One only needs to look at pictures of what happened to Hiroshima survivors or the first responders at Chernobyl to see extreme examples of what radiation can do to living tissues.

But as is usually the case, a closer look at examples a little further away from the extremes can be instructive, and tell us a little more about how radiation, both ionizing and non-ionizing, can cause damage to biochemical structures and processes. Doing so reveals that, while DNA is certainly in the crosshairs for damage by radiation, it’s not the only target — proteins, carbohydrates, and even the lipids that form the membranes within cells are subject to radiation damage, both directly and indirectly. And the mechanisms underlying all of this end up revealing a lot about how life evolved, as well as being interesting in their own right.

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Annotate PDFs On Linux With PDFrankenstein

On Windows and Mac machines, it’s not too troublesome to add text or drawings (such as signatures) to PDF files, but [Mansour Behabadi] found that on Linux machines, there didn’t seem to be a satisfying way or a simple tool. Being an enterprising hacker, [Mansour] set out to fill that gap, and the way it works under the hood is delightfully hacky, indeed.

The main thing standing in the way of creating such a tool is that the PDF format is a complex and twisty thing. Making a general-purpose PDF editing tool capable of inserting hyperlinks, notes, images, or drawings isn’t exactly a weekend project. But [Mansour] didn’t let that stop him; he leveraged the fact that tools already exist on Linux that can read and create PDF files, and tied them all together into what was at one point “a horrific patchwork of tools” which inspired the name pdfrankenstein.

The tool is a GUI that uses Inkscape and qpdf to convert a PDF page to an SVG file, set it as a locked background, then let the user add any annotations they desire, using Inkscape as the editor. After changes are made, the program removes the background, overlays the annotations back onto the originals, and exports a final file. Annotations can therefore be anything that can be done in Inkscape.

Curious about these and other tools for handling PDFs? We’ve shared some programs and tricks when we previously covered dealing with the PDF format in Linux.

Remoticon 2021 // Rob Weinstein Builds An HP-35 From The Patent Up

Fifty years ago, Hewlett-Packard introduced the first handheld scientific calculator, the HP-35. It was quite the engineering feat, since equivalent machines of the day were bulky desktop affairs, if not rack-mounted. [Rob Weinstein] has long been a fan of HP calculators, and used an HP-41C for many years until it wore out. Since then he gradually developed a curiosity about these old calculators and what made them tick. The more he read, the more engrossed he became. [Rob] eventually decided to embark on a three year long reverse-engineer journey that culminated a recreation of the original design on a protoboard that operates exactly like the original from 1972 (although not quite pocket-sized). In this presentation he walks us through the history of the calculator design and his efforts in understanding and eventually replicating it using modern FPGAs.

The HP patent ( US Patent 4,001,569 ) contains an extremely detailed explanation of the calculator in nearly every aspect. There are many novel concepts in the design, and [Rob] delves into two of them in his presentation. Early LED devices were a drain on batteries, and HP engineers came up with a clever solution. In a complex orchestra of multiplexed switches, they steered current through inductors and LED segments, storing energy temporarily and eliminating the need for inefficient dropping resistors. But even more complicated is the serial processor architecture of the calculator. The first microprocessors were not available when HP started this design, so the entire processor was done at the gate level. Everything operates on 56-bit registers which are constantly circulating around in circular shift registers. [Rob] has really done his homework here, carefully studying each section of the design in great depth, drawing upon old documents and books when available, and making his own material when not. For example, in the course of figuring everything out, [Rob] prepared 338 pages of timing charts in addition to those in the patent. Continue reading “Remoticon 2021 // Rob Weinstein Builds An HP-35 From The Patent Up”