From forming muscle fibers to protecting us from disease,proteins play an essential role in almost all biological processes in humans and other life forms alike. There has been extraordinary progress in recent years toward better understanding protein structures using deep learning, enabling the accurate prediction of protein structuresfrom their amino acid sequences. However, predicting a single protein structure from its amino acid sequence is like looking at a single frame of a movieit offers only a snapshot of a highly flexible molecule. Biomolecular Emulator-1 (BioEmu-1) is a deep-learning model that provides scientists with a glimpse into the rich world of different structures each protein can adopt, or structural ensembles, bringing us a step closer to understanding how proteins work. A deeper understanding of proteins enables us to design more effective drugs, as many medications work by influencing protein structures to boost their function or prevent them from causing harm.One way to model different protein structures is through molecular dynamics (MD) simulations. These tools simulate how proteins move and deform over time and are widely used in academia and industry. However, in order to simulate functionally important changes in structure, MD simulations must be run for a long time. This is a computationally demanding task and significant effort has been put into accelerating simulations, going as far as designing custom computer architectures (opens in new tab). Yet, even with these improvements, many proteins remain beyond what is currently possible to simulate and would require simulation times of years or even decades.Enter BioEmu-1 (opens in new tab)a deep learning model that can generate thousands of protein structures per hour on a single graphics processing unit. Today, we are making BioEmu-1 open-source (opens in new tab), following our preprint (opens in new tab) from last December, to empower protein scientists in studying structural ensembles with our model.It provides orders of magnitude greater computational efficiency compared to classical MD simulations, thereby opening the door to insights that have, until now, been out of reach.Spotlight: Microsoft research newsletterMicrosoft Research NewsletterStay connected to the research community at Microsoft.Subscribe todayOpens in a new tab We have enabled this by training BioEmu-1 on three types of data sets: (1) AlphaFold Database (AFDB) (opens in new tab) structures (2) an extensive MD simulation dataset, and (3) an experimental protein folding stability dataset (opens in new tab). Training BioEmu-1 on the AFDB structures is like mapping distinct islands in a vast ocean of possible structures. When preparing this dataset, we clustered similar protein sequences so that BioEmu-1 can recognize that a protein sequence maps to multiple distinct structures. The MD simulation dataset helps BioEmu-1 predict physically plausible structural changes around these islands, mapping out the plethora of possible structures that a single protein can adopt. Finally, through fine-tuning on the protein folding stability dataset, BioEmu-1 learns to sample folded and unfolded structures with the right probabilities.Figure 1: BioEmu-1 predicts diverse structures of LapD protein unseen during training. We sampled structures independently and reordered the samples to create a movie connecting two experimentally known structures.Combining these advances, BioEmu-1 successfully generalizes to unseen protein sequences and predicts multiple structures. In Figure 1, we show that BioEmu-1can predict structures of the LapD protein (opens in new tab) from Vibrio cholerae bacteria, whichcauses cholera.BioEmu-1 predicts structures of LapD when it is bound and unbound with c-di-GMP molecules, both of which are experimentally known but not in the training set.Furthermore, our model offers a view on intermediate structures, which have never been experimentally observed, providing viable hypotheses about how this protein functions. Insights into how proteins function pave the way for further advancements in areas like drug development.Figure 2: BioEmu-1 reproduces the D. E. Shaw research(DESRES) simulation of Protein G accurately with a fraction of the computational cost. On the top, we compare the distributions of structures obtained by extensive MD simulation (left) and independent sampling from BioEmu-1 (right). Three representative sample structures are shown at the bottom.Moreover, BioEmu-1 reproduces MD equilibrium distributions accurately with a tiny fraction of the computational cost. In Figure 2, we compare 2D projections of the structural distribution of D. E. Shaw research (DESRES) simulation of Protein G (opens in new tab) and samples from BioEmu-1. BioEmu-1 reproduces the MD distribution accurately, while requiring 10,000-100,000 times fewer GPU hours.Figure 3: BioEmu-1 accurately predicts protein stability. On the left, we plot the experimentally measured free energy differences G against those predicted by BioEmu-1. On the right, we show a protein in folded and unfolded structures.Furthermore, BioEmu-1 accurately predicts protein stability, which we measure by computing the folding free energiesa way to quantify the ratio between the folded and unfolded states of a protein. Protein stability is an important factor when designing proteins, e.g., for therapeutic purposes. Figure 3 shows the folding free energies predicted by BioEmu-1, obtained by sampling protein structures and counting folded versus unfolded protein structures, compared against experimental folding free energy measurements. We see that even on sequences that BioEmu-1 has never seen during training, the predicted free energy values correlate well with experimental values.Professor Martin Steinegger (opens in new tab) of Seoul National University, who was not part of the study, says With highly accurate structure prediction, protein dynamics is the next frontier in discovery. BioEmu marks a significant step in this direction by enabling blazing-fast sampling of the free-energy landscape of proteins through generative deep learning.We believe that BioEmu-1 is a first step toward generating the full ensemble of structures that a protein can take. In these early days, we are also aware of its limitations. With this open-source release, we hope scientists will start experimenting with BioEmu-1, helping us carve out its potentials and shortcomings so we can improve it in the future. We are looking forward to hearing how it performs on variousproteins you care about.AcknowledgementsBioEmu-1 is the result of highly collaborative team effort at Microsoft Research AI for Science. The full authors: Sarah Lewis, Tim Hempel, Jos Jimnez-Luna, Michael Gastegger, Yu Xie, Andrew Y. K. Foong, Victor Garca Satorras, Osama Abdin, Bastiaan S. Veeling, Iryna Zaporozhets, Yaoyi Chen, Soojung Yang, Arne Schneuing, Jigyasa Nigam, Federico Barbero, Vincent Stimper, Andrew Campbell, Jason Yim, Marten Lienen, Yu Shi, Shuxin Zheng, Hannes Schulz, Usman Munir, Ryota Tomioka, Cecilia Clementi, Frank NoOpens in a new tab

The upgrades being pushed out for AI chatbots arent slowing down, and one of the latest improvements added to Google Gemini is an ability for the AI to remember previous conversations. This allows you to refer back to something youve said the previous day, the previous week, or whenever it was. But do you want that?Gemini can now recall your past chats to provide more helpful responses, explains Google. Whether youre asking a question about something youve already discussed, or asking Gemini to summarize a previous conversation, Gemini now uses information from relevant chats to craft a response.For now, this is exclusive to Gemini Advanced subscribers and those using Gemini in English, though it may roll out to other users in the future. The new memory feature is enabled by default, though you do have some options if you dont want the AI bot remembering everything youve said.How Geminis memory worksConversation history works on top of the existing memory feature. Screenshot: Google The new upgrade is relatively straightforward: It means that chats that stack up in your Gemini app, like files in your Google Drive, can be referred back to whenever you like (ChatGPT recently launched a similar feature). The idea is that the AI will get to know you better, meaning more relevant responses and less repetition.For example, Gemini might remember the sports teams you follow, the music you like, or the hobbies you engage in. When youre asking for news updates or activity ideas, that can be useful information for the bot to havefilm recommendations can skip the titles youve watched already, for example. You dont need to switch this on, as its enabled automatically.It can also be useful for summaries. Maybe you want to summarize the days chats so far, or youve forgotten what youve already talked to Gemini about through the course of the week. You can just make a request using natural language: What were we talking about yesterday? for example, or summarize everything we chatted about last week.Based on our testing, this all works rather well, though its not perfectGemini will sometimes forget details (or more likely, pick out the wrong ones), and give you responses that make no sense. On the whole though, its a useful addition to Geminis features, as long as you dont mind keeping everything on record.Note that this is separate to the information you can tell Gemini about yourself by clicking Settings and Saved info (on the web), or by tapping your profile picture (top right) and Saved info (on mobile). This feature lets you commit key details to Geminis memory, such as what your occupation is, or the foods you like, or how youd like Gemini to respond to you (with simple, informal language, for example).How to manage Geminis memoryYou can auto-delete your Gemini chats if youd prefer. Screenshot: Google The idea of Gemini remembering everything you say to it may be raising a few red flags for you, and its worth remembering that most of the time youre using AI tools, youre also helping to train them. This is the case with Gemini, and your chats might even be reviewed by humans, in order to improve Gemini and its AI models.You can read the full Gemini Privacy policy online, and its worth noting this part of it: Please dont enter confidential information in your conversations, or any data you wouldnt want a reviewer to see or Google to use to improve our products, services and machine learning technologies.Google doesnt let you opt out of having your chats used in this way, but you can specify that the chats arent to be stored at all, or should be deleted after a certain time period. It depends how you want to balance your privacy and digital data trail against the convenience of having all your AI conversations available to review and recall.To find these options on the web, click Activity inside the Gemini app; in the mobile apps, tap your profile picture (top right), then Gemini Apps Activity. On the next screen, you can turn off the Gemini chat history altogetherwhich essentially means conversations are deleted as soon as youre done with them.You can also wipe everything thats been gathered so far, as well as erase individual chats. If youd rather have Gemini automatically delete your conversations after a certain amount of time, youre able to choose between 3 months, 18 months, or 36 months (and you still get the manual deletion options too).

Sex is messy.Its not just about chromosomes. Or reproductive cells. Or any other binary metric. Many genetic, environmental and developmental variations can produce what are thought of as masculine and feminine traits in the same person. And so sex, scientists say, should be viewed in all its complex glory.Sex is a multifaceted trait that has some components that are present at birth and some components that developed during puberty, and each of these components shows variation, says Sam Sharpe, an evolutionary biologist at Kansas State University in Manhattan.Yet a definition of biological sex put forth by U.S. President Donald Trump designates people as either male or female based solely on the size of the reproductive cells they make.Millions of Americans dont fit that narrow definition through no fault of their own and many dont even know it.In an executive order signed January 20, the president asserts that there are two immutable human sexes and that females are defined as persons belonging, at conception, to the sex that produces the large reproductive cell. Males, according to the order, make the smaller cell.On February 19, newly instated Health and Human Services secretary Robert F. Kennedy Jr. announced that the agency, which oversees most federally funded health research, will use these definitions in making policies.In a slight variation from the executive order, HHS defines males as people of the sex characterized by a reproductive system with the biological function of producing sperm. And females as people with reproductive systems that make eggs.For me, the definition is really painful because it reduces a human being to their chance of reproducing, says Anna Biason-Lauber, a pediatric endocrinologist at the University of Fribourg in Switzerland.Whats more, Trumps definition is not biologically accurate and leaves out people who carry certain genetic variants and dont make any reproductive cells, or gametes. The order makes no exceptions for them. What does that mean for people who dont have gametes? Sharpe asks. That is, as of now, an unanswered question. But its an important question to answer, because you cant have a definition of sex that doesnt apply to everyone.Any definition of sex used to determine who can get an identification card or use a public restroom needs to account for variation, they and other researchers say.Sex is complicatedOne thing Trumps order gets right is that there are two sizes of reproductive cells, or gametes, known as eggs and sperm. Egg cells are much larger than sperm. Thats about as close to a true binary as nature gets, says Nathan Lents, a molecular evolutionary biologist at the John Jay College of Criminal Justice in New York City.But sex is much more than the size of reproductive cells, researchers say.Biology doesnt operate in binaries very often, Lents says.Instead, most characteristics ascribed to males and females fall along a spectrum with two peaks, one the average for females and the other the average for males. For instance, on average, males are taller than females and have more muscle mass, more red blood cells and a higher metabolism.But almost nobody fits in the peak for all those measures for their sex, Lents says. Theres plenty of women who are taller than plenty of men. There are plenty of women who have higher metabolic rates than some men, even though the averages are different.If you define biological sex purely on the gametes, youre going to ignore most of what actually matters to your daily life, including in your social life, he says. Reducing sex to a binary really doesnt make a lot of sense for how we actually live.Sex doesnt start at conceptionNo sex cells are produced at conception. Fertilized eggs cant produce gametes, because theyre single cells, Sharpe says.In fact, sex development doesnt start until several weeks after conception. The exact timing is hard to pinpoint in humans, because it happens in the womb, often before people know theyre pregnant, Biason-Lauber says. About six weeks into gestation, cells appear that will eventually give rise to the gonads: ovaries to make eggs or testes to produce sperm. But for a couple of weeks, she says, those cells are absolutely indistinguishable from each other.Scientists used to think that embryos automatically developed as female unless there were specific instructions to become male. But in the last decade, researchers found that for embryos to develop as females they need to actively dismantle male-producing structures and build ones that support female reproduction.At about eight weeks of gestation, certain cells in what will become the testes begin to make the hormone testosterone, which is important for development of the scrotum and penis and other male reproductive organs. But males still dont produce sperm at this point. Thats partially because testosterone production drops around week 20 of pregnancy and doesnt pick back up again until puberty, when it kicks in once more, allowing immature cells to morph into sperm.Ovaries dont produce any sex hormones in the fetus. And the uterus, fallopian tubes and the vagina develop without any input from hormones, Biason-Lauber says. Females are born with all the eggs they will ever make, though those cells are stuck in suspended animation until puberty, when they can mature and be released.Sex chromosomes differThose developmental processes are partially directed by what are often called sex chromosomes. The name is somewhat of a misnomer because these two chromosomes dubbed X and Y have a wide range of responsibilities beyond sex.The X chromosome contains hundreds of genes including many involved in processes throughout the body such as blood clotting, color vision and brain development. The much smaller Y chromosome contains genes important for male sex development and fertility, but also plays a role in immunity, heart health and cancer.Millions of people are intersex, including model Hanne Gaby Odiele, shown walking the runway during Paris Fashion Week in 2022. Such people dont fit typical binary definitions of sex. Odiele, who has androgen insensitivity that prevents the body from responding to testosterone and similar hormones, speaks out against unconsented surgeries on intersex children to make them conform to a sex binary.Jonas Gustavsson/Sipa USA/Alamy Stock PhotoFemales generally have two X chromosomes, while males typically have an X and a Y chromosome. But there are plenty of variations on that theme, Biason-Lauber says. For instance, inTurner syndrome, women lack one X chromosome. They do not have gametes, she says. Instead, these women have what are called streak gonads. They have a piece of collagen instead of ovaries. They do have a uterus.This leads Biason-Lauber to wonder, if the definition of a woman is the presence of the big cells, what are these [people]? Turner syndrome is not so rare, she says, occurring in 1 of every 2,000 to 2,500 female babies born. Some people are not diagnosed until adulthood or may never be diagnosed.About 1 in every 650 male babies born have two or more X chromosomes and one Y. Those men, who have Klinefelter syndrome, dont produce sperm. Many are unaware that they carry an extra chromosome until they go for fertility treatments, Biason-Lauber says. These people have testes and penises, but they dont make small reproductive cells, and thus dont fit the administrations definition of men.The Y chromosome contains a gene called SRY that is important, but not essential, for male sex development. Sometimes, when chromosomes are divvied up before sperm production, SRY jumps out of the Y chromosome and attaches itself to an X or another chromosome. When the hitchhiking SRY gene, but not the rest of the Y chromosome, is passed on to offspring it may result in people who have two X chromosomes plus a stray SRY gene. Those people often develop as males.Some people have an X and a Y chromosome but carry a version of SRY or other genes that dont spur typical male development. Those people develop as females but dont make gametes.Other people with an X and a Y may have genetic variants that prevent their bodies from responding to testosterone and other male sex hormones, called androgens. Those people with androgen insensitivity have testes inside their abdomens, but the rest of their bodies develop as female. These people would have the small cells, but theyre not men, Biason-Lauber says.Variants in many other genes may also prevent production of either large or small reproductive cells. Some people even have different combinations of sex chromosomes in different cells in their bodies.Being intersex isnt all that rareAbout 1.7 percent of the population is intersex and dont fit neatly into male and female boxes, according to InterAct, an advocacy organization for intersex youth. Thats as common as having naturally red hair. Intersex people may have any of a wide variety of sex development differences including Turner syndrome, androgen insensitivity, Klinefelter syndrome and others.Some may be born with both ovarian and testicular tissue, and thus might be classified as both male and female under the terms of the executive order, says Sylvan Fraser Anthony, InterActs legal and policy director.Intersex individuals often undergo surgeries as infants or young children to make their genitals or internal organs conform to the sex their parents choose. They may also need to take hormones such as estrogen or testosterone to maintain their health, says Sharpe, who worries that a binary definition of sex could be used to deny intersex people access to health care.Such sex hormones also play an important role in many facets of development, including whether your skin is painfully dry or not, or how tall you grow during puberty, or whether youre able to maintain bone density, they say.Choosing any single definer of sex is bound to sow confusion.If [they] use chromosomes, theres a whole lot of individuals who will be quite surprised to learn that theyre male, Lents says. If they use gametes, theyre going to exclude some individuals but theyll also potentially open the door to including people that they didnt intend. For instance, people who have X and Y chromosomes but make female gametes would be eligible under the definition to compete in womens sports.The biology of sex and gender makes it very clear, Lents says. These are not hard categories with clear definitions.

Nature, Published online: 19 February 2025; doi:10.1038/d41586-025-00298-7The mechanism that causes static electricity to build up is a mystery. Experiments now reveal that materials remember past contacts with each other and this determines how electric charge is transferred in future contacts.

Nature, Published online: 19 February 2025; doi:10.1038/d41586-025-00302-0Tumour cells often have problems processing messenger RNA. The finding that these splicing errors result in commonly expressed peptides that are recognized by immune cells offers a target for cancer treatments.

NASA increased the chances of asteroid 2024 YR4 hitting Earth to 1 in 32, or 3.1%, on Tuesday, but they're now back down to 1 in 67, or 1.5%.

A new computer model suggests that the process of evolution can get better at evolving in the face of environmental change.

Arnold 7.3.7.0 is here, featuring improved shadows for glass objects, better global light sampling for glossy materials, faster scene IPR updates, and more.Details: https://80.lv/articles/arnold-7-3-7-0-is-now-available/@arnoldrenderer

.@bman_me is building their own version of procedural environment maker inspired by Tiny Glade.It's powered by Blender and Python: https://80.lv/articles/check-out-this-tiny-glade-like-procedural-environment-tool/

ArnoldAutodesk has released Arnold 7.3.7.0, a feature release of its production renderer that brings improved shadows for glass objects, better global light sampling for glossy materials, faster scene IPR updates, and more enhancements and bug fixes.Transparent objects, such as clear glass, now cast shadows. The new transmission_shadow_density parameter in the openpbr_surface and standard_surface shaders controls the appearance of these shadows.Heres transmission_shadow_density 0 and 1 accordingly with caustics off:ArnoldArnoldWith caustics:ArnoldArnoldGLS now considers material glossiness when sampling, significantly improving quality, especially in scenes with numerous small lights. While this results in minor slowdowns for fixed AA renders, adaptive renders see overall speed improvements. For instance, in the robot scene at the top of the article, a 1.7x speedup was achieved with adaptive rendering. This feature can be toggled on or off using GLS_glossy_enable.Arnold 7.3.7.0 also features better detection of visibility changes for faster scene updates, allows to control motion keys in alembic, load and render OpenVDB points, and has improved compatibility with recent USD versions and Solaris.See the release notes for the full list of changes and join our80 Level Talent platformand ournew Discord server, follow us onInstagram,Twitter,LinkedIn,Telegram,TikTok, andThreads, where we share breakdowns, the latest news, awesome artworks, and more.Source link The post Arnold 7.3.7.0 Is Now Available appeared first on CG SHARES.