bookmark | Chris Aldrich

🔖 Self-Organized Resonance during Search of a Diverse Chemical Space

Bookmarked Self-Organized Resonance during Search of a Diverse Chemical Space (Physical Review Letters)

ABSTRACT Recent studies of active matter have stimulated interest in the driven self-assembly of complex structures. Phenomenological modeling of particular examples has yielded insight, but general thermodynamic principles unifying the rich diversity of behaviors observed have been elusive. Here, we study the stochastic search of a toy chemical space by a collection of reacting Brownian particles subject to periodic forcing. We observe the emergence of an adaptive resonance in the system matched to the drive frequency, and show that the increased work absorption by these resonant structures is key to their stabilization. Our findings are consistent with a recently proposed thermodynamic mechanism for far-from-equilibrium self-organization.

Suggested by First Support for a Physics Theory of Life in Quanta Magazine.

🔖 Spontaneous fine-tuning to environment in many-species chemical reaction networks | PNAS

Bookmarked Spontaneous fine-tuning to environment in many-species chemical reaction networks (Proceedings of the National Academy of Sciences)

Significance A qualitatively more diverse range of possible behaviors emerge in many-particle systems once external drives are allowed to push the system far from equilibrium; nonetheless, general thermodynamic principles governing nonequilibrium pattern formation and self-assembly have remained elusive, despite intense interest from researchers across disciplines. Here, we use the example of a randomly wired driven chemical reaction network to identify a key thermodynamic feature of a complex, driven system that characterizes the “specialness” of its dynamical attractor behavior. We show that the network’s fixed points are biased toward the extremization of external forcing, causing them to become kinetically stabilized in rare corners of chemical space that are either atypically weakly or strongly coupled to external environmental drives. Abstract A chemical mixture that continually absorbs work from its environment may exhibit steady-state chemical concentrations that deviate from their equilibrium values. Such behavior is particularly interesting in a scenario where the environmental work sources are relatively difficult to access, so that only the proper orchestration of many distinct catalytic actors can power the dissipative flux required to maintain a stable, far-from-equilibrium steady state. In this article, we study the dynamics of an in silico chemical network with random connectivity in an environment that makes strong thermodynamic forcing available only to rare combinations of chemical concentrations. We find that the long-time dynamics of such systems are biased toward states that exhibit a fine-tuned extremization of environmental forcing.

Suggested by First Support for a Physics Theory of Life in Quanta Magazine.

An Introduction to the IndieWeb | AltPlatform

Bookmarked An Introduction to the IndieWeb by Chris Aldrich (AltPlatform)

Whether you're starting a blog, building your personal brand, posting a resume, promoting a hobby, writing a personal journal, creating an online commonplace book, sharing photos or content with friends, family, or colleagues, writing reviews, sharing recipes, podcasting, or any one of the thousand other things people do online it all starts with having a presence and an identity online.

I remember some of the difficulties I had in understanding, comprehending, and coming to grasp with the overall concept of the IndieWeb. Then I contended with strategies for navigating my way through the wiki and deciding in what order to do things and finding my way into the rich and diverse community of help and additional resources.

I’ve written an introduction–aimed at beginners (and non-developers)–on AltPlatform.org that I hope might help out others who are thinking about or starting their own journey.

Editor’s Note:
As of December 2017, the AltPlatform.org site which originally published this article has shut down. I’ve smartly kept a private archived copy of the original of this post here on my personal site and manually syndicated a copy of it to AltPlatform for just such a possibility. (Hooray for PASTA (Publish Anywhere, Save to (Private) Archive)!) As a result of the shutdown, I’m making the original public here and you can now read it below.

If you wish, you can also read a copy of the original as it appeared on AltPlatform on the Internet Archive.

Introduction to Algebraic Geometry | UCLA Extension in Fall 2017

Bookmarked MATH X 451.42 Introduction to Algebraic Geometry (UCLA Extension)

Algebraic geometry is the study, using algebraic tools, of geometric objects defined as the solution sets to systems of polynomial equations in several variables. This introductory course, the first in a two-quarter sequence, develops the basic theory of the subject, beginning with seminal theorems—the Hilbert Basis Theorem and Hilbert’s Nullstellensatz—that establish the dual relationship between so-called varieties—both affine and projective—and certain ideals of the polynomial ring in some number of variables. Topics covered in this first quarter include: algebraic sets, projective spaces, Zariski topology, coordinate rings, the Grassmannian, irreducibility and dimension, morphisms, sheaves, and prevarieties. The theoretical discussion will be supported by a large number of examples and exercises. The course should appeal to those with an interest in gaining a deeper understanding of the mathematical interplay among algebra, geometry, and topology. Prerequisites: Some exposure to advanced mathematical methods, particularly those pertaining to ring theory, fields extensions, and point-set topology.

Dr. Michael Miller has announced the topic for his Fall math class at UCLA Extension: Algebraic Geometry!!

Yes math fans, as previously hinted at in prior conversations, we’ll be taking a deep dive into the overlap of algebra and geometry. Be sure to line up expeditiously as registration for the class won’t happen until July 31, 2017.

While it’s not yet confirmed, some sources have indicated that this may be the first part of a two quarter sequence on the topic. As soon as we have more details, we’ll post them here first. As of this writing, there is no officially announced textbook for the course, but we’ve got some initial guesses and the best are as follows (roughly in decreasing order):

Ideals, Varieties, and Algorithms: An Introduction to Computational Algebraic Geometry and Commutative Algebra (Undergraduate Texts in Mathematics) 4th ed. by David A. Cox, John Little, and Donal O’Shea
Algebraic Geometry: An Introduction (Universitext) by Daniel Perrin
An Invitation to Algebraic Geometry (Universitext) by Karen E. Smith, Lauri Kahanpää, Pekka Kekäläinen, William Traves
Algebraic Geometry (Dover Books on Mathematics) by Solomon Lefschetz (Less likely based on level and age, but Dr. Miller does love inexpensive Dover editions)

For those who are new to Dr. Miller’s awesome lectures, I’ve written some hints and tips on what to expect.

Most of his classes range from about 20-30 people, many of them lifelong regulars. (Yes, there are dozens of people like me who will take almost everything he teaches–he’s that good. This class, my 22nd, will be the start of my second decade of math with him.)

🔖 Communication complexity of approximate Nash equilibria | arXiv

Bookmarked Communication complexity of approximate Nash equilibria (arXiv)

For a constant ϵ, we prove a poly(N) lower bound on the (randomized) communication complexity of ϵ-Nash equilibrium in two-player NxN games. For n-player binary-action games we prove an exp(n) lower bound for the (randomized) communication complexity of (ϵ,ϵ)-weak approximate Nash equilibrium, which is a profile of mixed actions such that at least (1−ϵ)-fraction of the players are ϵ-best replying.

Suggested by In Game Theory, No Clear Path to Equilibrium by Erica Klarreich (Quanta Magazine)

🔖 A Mind at Play: How Claude Shannon Invented the Information Age by Jimmy Soni, Rob Goodman

Bookmarked A Mind at Play: How Claude Shannon Invented the Information Age (Simon & Schuster)

The life and times of one of the foremost intellects of the twentieth century: Claude Shannon—the neglected architect of the Information Age, whose insights stand behind every computer built, email sent, video streamed, and webpage loaded. Claude Shannon was a groundbreaking polymath, a brilliant tinkerer, and a digital pioneer. He constructed a fleet of customized unicycles and a flamethrowing trumpet, outfoxed Vegas casinos, and built juggling robots. He also wrote the seminal text of the digital revolution, which has been called “the Magna Carta of the Information Age.” His discoveries would lead contemporaries to compare him to Albert Einstein and Isaac Newton. His work anticipated by decades the world we’d be living in today—and gave mathematicians and engineers the tools to bring that world to pass. In this elegantly written, exhaustively researched biography, Jimmy Soni and Rob Goodman reveal Claude Shannon’s full story for the first time. It’s the story of a small-town Michigan boy whose career stretched from the era of room-sized computers powered by gears and string to the age of Apple. It’s the story of the origins of our digital world in the tunnels of MIT and the “idea factory” of Bell Labs, in the “scientists’ war” with Nazi Germany, and in the work of Shannon’s collaborators and rivals, thinkers like Alan Turing, John von Neumann, Vannevar Bush, and Norbert Wiener. And it’s the story of Shannon’s life as an often reclusive, always playful genius. With access to Shannon’s family and friends, A Mind at Play brings this singular innovator and creative genius to life.

I can’t wait to read this new biography about Claude Shannon! The bio/summer read I’ve been waiting for.

With any luck an advanced reader copy is speeding it way to me! (Sorry you can’t surprise me with a belated copy for my birthday.) A review is forthcoming.

You have to love the cover art by Lauren Peters-Collaer.

Resources from Domains 2017

Bookmarked Domains 2017 Conference (Reclaim Hosting)

Indie EdTech and Other Curiosities, June 5-6, 2017 at University of Oklahoma

Twitter Stream for #Domains17

Keynote: Neither Locked out nor locked in by Martha Burtis

Live-streamed videos from Virtually Connecting

DoOO Curriculum on Github

JBJ blogpost: Looking back at #Domains17

🔖 Feed reader revolution: it’s time to embrace open & disrupt social media

Bookmarked Feed reader revolution: it’s time to embrace open & disrupt social media

By supporting Micropub, indie-config, and/or action URLs, current feed readers can make it far easier for people on the open web to not only read content the way they currently do on siloed social media services like Facebook, Twitter, Instagram, et al. Increased ease-of-use to allow these functionalities with beautiful user interface will help to move users out of walled-gardens where they’re trapped into the larger universe of the free and open internet. Individuals with their own websites can support the acceptance of these posts to save their interactions with what they’ve read, be they comments, likes, bookmarks, or other interactions. They can also close the loop by supporting Webmentions so that their comments can be sent to (and potentially displayed) on others’ websites. All of these pieces combined make for a more open and democratic web.

The article about feed readers that I wrote for the new AltPlatform tech blog is out now. I hope everyone will take a look.

When this publication from Richard MacManus (the founder of ReadWriteWeb.com, one of my old favorite standbys) popped up a few weeks ago with the tagline “A non-profit tech blog about the open web”, I immediately bookmarked it and knew it would be at the top of my subscription list. When I read his founding manifesto for the blog, I was hooked and bumped it to the top of my list and tipped off others:

This looks like a must-read blog for #Indieweb proponents.https://t.co/pVvG1h34nb

— ChrisAldrich (@ChrisAldrich) May 31, 2017

There’s also some great articles up by Emre Sokullu, Brian Hendrickson, and Richard MacManus on a variety of other great topics. I hope you’ll take a look at what they’re doing and subscribe.

I’m pleased that they’ve taken something I was planning on posting here on my site and are giving it some wider exposure.

If you’re a journalist, blogger, or writer in the space, do feel free to connect with them to pitch ideas.

Twitter List from #Domains17

Bookmarked Twitter List from #Domains17 by Chris Aldrich (Twitter)

Teachers, educators, researchers, technologists using open technologies in education #openEd, #edTech, #DoOO, #IndieWeb

I’ve compiled a twitter list of people related to #openEd, #edTech, #DoOO, #indieweb, and related topics who tweeted about #domains17 in the past week. The list has multiple views including members and by tweets.

Feel free to either subscribe to the list (useful when adding streams to things like Tweetdeck), or for quickly scanning down the list and following people on a particular topic en-masse. Hopefully it will help people to remain connected following the conference. I’ve written about some other ideas about staying in touch here.

If you or someone you know is conspicuously missing, please let me know and I’m happy to add them. Hopefully this list will free others from spending the inordinate amount of time to create similar bulk lists from the week.

🔖 dokieli

Bookmarked dokie.li (dokie.li)

dokieli is a clientside editor for decentralised article publishing, annotations and social interactions.

dokieli envisions research results, analysis and data all being produced interactively on the Web and seamlessly linked to and from articles. Through annotations and notifications, the academic process of peer-review can be open, transparent and decentralised for researchers.