In the late 1960s, physicists argued that singularities might be surrounded by a region of churning chaos, where space and time haphazardly grow and shrink. It was dubbed a “Mixmaster universe,” after a line of kitchen appliances. https://buff.ly/4kaLDWZ

How quickly are you ageing? What molecular ‘clocks’ can tell you about your health Armed with an influx of cash and public enthusiasm, researchers are looking to improve how ageing is measured.

Armed with an influx of cash and public (and celebrity) enthusiasm, researchers are looking to improve how ageing is measured

https://go.nature.com/4bf2GTK

Percolation thresholds and connectivity in quantum networks We study entanglement percolation in qubit-based planar quantum network models of arbitrary topology, where neighboring nodes are initially connected by pure states with quenched disorder in their ent...

arxiv.org/abs/2502.17191
/Percolation thresholds and connectivity in quantum networks/
Andrea De Girolamo, Giuseppe Magnifico, Cosmo Lupo

Figure comparing automatic differentiation (AD) and automatic sparse differentiation (ASD). (a) Given a function f, AD backends return a function computing vector-Jacobian products (VJPs). (b) Standard AD computes Jacobians row-by-row by evaluating VJPs with all standard basis vectors. (c) ASD reduces the number of VJP evaluations by first detecting a sparsity pattern of non-zero values, coloring orthogonal rows in the pattern and simultaneously evaluating VJPs of orthogonal rows. The concepts shown in this figure directly translate to forward-mode, which computes Jacobians column-by-column instead of row-by-row.

You think Jacobian and Hessian matrices are prohibitively expensive to compute on your problem? Our latest preprint with @gdalle.bsky.social might change your mind!
arxiv.org/abs/2501.17737
🧵1/8

🎉 Happy to share that my longest Ph.D. project, “A fully-integrated lattice Boltzmann method for fluid–structure interaction”, is online! We develop a fully Eulerian method to simulate many squishy solids in fluids. (1/3)
📑 Paper: authors.elsevier.com/c/1kWjb508I1-63
👩🏻‍💻 Code: github.com/yue-sun/lbrmt

schematic of neural recordings from mouse V1, whole-brain, and hippocampus; neural activity traces from the population, showing more correlated activity in V1 and whole-brain recordings versus more decorrelated activity in hippocampus

What if… spontaneous neural activity 🧠 reflects the baseline rumblings of a brainwide dynamical system initialized for learning? We find that the rumblings have macroscopic properties like those emerging from linear symmetric, critical systems 🧵 #neuroscience #neuroAI www.biorxiv.org/content/10.1...

Transport kinetics across interfaces between coexisting liquid phases We investigate the kinetics of material transport across interfaces in phase-separated mixtures. Using non-equilibrium thermodynamics we derive the interfacial kinetics, describing the movement of the...

1/6 🧪 Preprint-Alert!
We looked at how molecules move across phase boundaries, e.g., in liquid droplets, taking into account that chemical potentials inside and outside the boundary can be different!

This unites recent work with stuff from the 60s and has cool consequences 👇
shorturl.at/j0U6i

Looks to be a really nice read; clear that the man enjoys writing!

arxiv.org/abs/2501.00925
'Fisher Information in Kinetic Theory'
- Cédric Villani

Splendid:

arxiv.org/abs/2501.01304
'Cutoff for non-negatively curved diffusions'
- Justin Salez

The Dimensions of dimensionality Cognitive scientists often infer multidimensional representations from data. Whether the data involve text, neuroimaging, neural networks, or human judgments, researchers frequently infer and analyze latent representational spaces (i.e., embeddings). However, the properties of a latent representation (e.g., prediction performance, interpretability, compactness) depend on the inference procedure, which can vary widely across endeavors. For example, dimensions are not always globally interpretable and the dimensionality of different embeddings may not be readily comparable. Moreover, the dichotomy between multidimensional spaces and purportedly richer representational formats, such as graph representations, is misleading. We review what the different notions of dimension in cognitive science imply for how these latent representations should be used and interpreted.

The Dimensions of dimensionality
www.cell.com/trends/cogni...
#neuroscience

Towards kinetic equations of open systems of active soft matter
https://arxiv.org/pdf/2412.09137
V.I. Gerasimenko

Metastability demystified — the foundational past, the pragmatic present and the promising future

Dynamic systems theory review paper with Fran Hancock, Fernando Rosas & friends

rdcu.be/d3bh9

Structurally informed models of directed brain connectivity - Nature Reviews Neuroscience The influence anatomy exerts on communication between brain regions remains unclear. In this Review, Greaves et al. synthesize how methods of structural connectivity integration constrain inference-ba...

Nature Reviews Neuroscience

Structurally informed models of directed brain connectivity
www.nature.com/articles/s41...

The birth of fruit fly's central nervous system imaged with multicolor #adaptive #lightsheet microscopy. The microscope self-aligns to a signal that appears during imaging.

www.nature.com/articles/nbt...

Self-organized patterning of crocodile head scales by compressive folding - Nature Crocodile head scales self-organize through purely mechanical compressive skin folding rather than a patterning process controlled by gene interactions.

🚨Hyped to share our new article in @natureportfolio.bsky.social! We show that crocodile head scales develop from compressive folding that arises from constrained skin growth 🐊🔬
Really proud of this one - it's cool 😎
Please read & share! 🧪
@genevunige.bsky.social
www.nature.com/articles/s41...

YouTube video by The Julia Programming Language All that's new and improved in Optimization.jl | Dixit | JuliaCon 2024

Discover the latest advancements in Optimization.jl! Learn about the EnsembleProblem interface for multistart strategies, uniform solver states, and advanced symbolic capabilities like automatic solver selection. youtu.be/1JWJpQ8pxys #JuliaLang #Optimization #SciML #JuliaCon #Machinelearning

go.bsky.app/Gf4uKHG

Let me know if you want to be added.

Fascinating 🧵!!

Happy to share link to pdf/video of lecture at College de France on « Encoding, decoding & representations of space». I present how length scales are defined in biology, Shannon information theory, positional information & patterning in guided + self-organised systems. Enjoy!

tinyurl.com/y85ft5nj

“Model-free“ analysis of a complex system. Part II Or: when you don't even see what your model is

The second part of the #ComplexityThoughts on “model-free” analysis of #ComplexSystems. As usual you have the:

Post: open.substack.com/pub/manlius/...

Podcast: creators.spotify.com/pod/show/com...

RSS: manlius.substack.com/feed

Enjoy! 🙏

Ångström-resolution fluorescence microscopy - Nature The authors introduce a single-molecule DNA-barcoding method, resolution enhancement by sequential imaging, that improves the resolution of fluorescence microscopy down to the Ångström scale using off...

ÅNGSTRÖM-RESOLUTION FLUORESCENCE MICROSCOPY.

Can we do structural biology with an optical microscope? Yes!

Check out how we resolved *single bases of DNA* and much more using fluorescence microscopy, out on 24.05.2023 in Nature! @natureportfolio.bsky.social

[re-post from Twitter]

This is beautiful 😄

YouTube video by The Julia Programming Language A fast and flexible CFD solver with heterogeneous execution | Weymouth, Font | JuliaCon 2024

Discover the power of WaterLily.jl! 🚀 A fast, flexible CFD solver now supports multi-threading & GPUs with backend-agnostic execution. Learn more!
youtu.be/FwMh2rq9kOU?...
#julialang #CFDSolvers #programming #HighPerformanceComputing #GPU #MachineLearning #JuliaCon

Cover of textbook. Photo of path in a forest. Text overlaid saying 'Introducing Mathematical Biology, An Open Education Resource by Alex Best'

As my follower count creeps towards that of the old place, an unashamed plug for the FREE online textbook I wrote for #mathbio students. 'Introducing Mathematical Biology' is FREE, interactive, accessible and FREE. Please feel free to share with students. sheffield.pressbooks.pub/introducingm...

V is the moment of inertia of a system with n particles with mass 1, the relationship between V and D can be proven quickly by rewriting the moment of inertia wrt every particle using Steiner's theorem

Analysis of a Single Cell RNA-seq Workflow by Random Matrix Theory Methods - Bulletin of Mathematical Biology Single cell RNA-seq (scRNAseq) workflows typically start with a count matrix and end with the clustering of sampled cells. While a range of methods have been developed to cluster scRNAseq datasets, no...

New #BulletinMathBio paper by Sivan Leviyang on Analysis of a Single Cell RNA-seq Workflow by Random Matrix Theory Methods.

link.springer.com/article/10.1...

Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts - Nature Microbiology Coffee consumption is associated with the presence and abundance of a specific member of the human gut microbiome, Lawsonibacter asaccharolyticus, and changes to the plasma metabolome.

Good news for coffee drinkers! ☕☕

A recent study in Nature Microbiology shows that drinking coffee has a positive effect on the health and composition of the gut microbiome and can help reduce blood sugar and blood pressure

Enjoy your cup of coffee today!

dx.doi.org/10.1038/s415...

VisualPDE VisualPDE brings interactive science and mathematics to the web. Explore topics including waves, viruses and reaction—diffusion patterns, or create your own simulation.

Ever wanted an interactive lightning-fast solver for models in physics, chemistry, or biology? Do you have a web browser?
I'm thrilled to share our website visualpde.com, built explicitly to create interactive spatial models on most devices.

Follow @visualpde.com for cool updates!

Biological origami at molecular level: Cytosolic interactome protects against protein unfolding Human cells are protecting their proteins from unfolding and aggregating. That's what biophysicist Alireza Mashaghi and his team discovered after seven years of in-depth research into the folding mech...

We recently reported the first single molecule protein folding analysis using optical tweezers inside cytosol! This allows for including the full complexity of cellular chaperone network & beyond.

#SingleMolecule #Biophysics #Protein #Chaperone #OpticalTweezers #ChemSky

phys.org/news/2023-08...