Not a bad rant, sounds like Nick´s emergent book club, but that is not the rant I was looking for.
Yah, found the references the hard way. The paper from LANL was https://journals.aps.org/prb/abstract/10.1103/PhysRevB.57.R13985, pretty bad job on producing the date and author name. Parallel replica method for dynamics of infrequent eventsArthur F. VoterPhys. Rev. B 57, R13985(R) – Published 1 June 1998 The Pande lab paper was https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.86.4983 Mathematical Analysis of Coupled Parallel SimulationsMichael R. Shirts and Vijay S. PandePhys. Rev. Lett. 86, 4983 – Published 28 May 2001 i found the first from the second, found the second as #181/260 in the Pubmed listing for "pande vs" which the Pande lab uses as its list of publications. I originally picked up on the topic in https://science.sciencemag.org/content/290/5498/1903 Screen Savers of the World Unite! 1. Michael Shirts <https://science.sciencemag.org/content/290/5498/1903#aff-1>, 2. Vijay S. Pande* <https://science.sciencemag.org/content/290/5498/1903#aff-1> See all authors and affiliations Science 08 Dec 2000: Vol. 290, Issue 5498, pp. 1903-1904 DOI: 10.1126/science.290.5498.1903 So the original rant might have been on a BiosGroup mailing list or just in my head. -- rec -- On Mon, Aug 30, 2021 at 2:33 PM Marcus Daniels <mar...@snoutfarm.com> wrote: > This week's Science has an article on predicting RNA structure using deep > learning. The other approach you mention sounds like Rosetta. > > -----Original Message----- > From: Friam <friam-boun...@redfish.com> On Behalf Of u?l? ?>$ > Sent: Monday, August 30, 2021 11:27 AM > To: friam@redfish.com > Subject: Re: [FRIAM] Weighted Ensemble > > The below is the only thing my search turns up (via $ grep -i folding > $(grep -li protein $(grep -l "From: [\"]*Roger Critchlow[\"]* <r...@elf.org>" > *))) I found nothing if I include "parallel" in the and. If you have other > keywords, maybe it'll be more apparent. (Header still includes Google. So > it's not clear to me when you started using GMail.) > > > On 9/14/09 7:48 PM, Roger Critchlow wrote: > > As I read it, the issue isn't whether structures and/or configurations > > are/aren't important, the question is whether they operate according > > to emergent or resultant rule sets. > > > > The Emergentists were betting heavily on the emergent rule set. They > > believed that the variety of chemistry couldn't possibly be the result > > of protons and electrons operating according to physics as they knew > > it. They were right, it wasn't physics as they knew it, but the > > answer turned out to be the result of configurational physics rather > > than emergent principles of chemistry. They also bet that the variety > > of biology couldn't be the result of chemical molecules operating > > according to the chemistry they knew. And they were right again, it > > wasn't chemistry as they knew it, but the answer turned out to be the > > result of configurational chemistry rather than emergent priniciples > > of biology. > > > > Chemistry and biology turn out to be ever more complicated > > configurations of protons and electrons, with some neutron ballast, > > operating according to the principles of quantum mechanics and > > statistical mechanics. It's all physics, same particles, same forces, > > same laws, no emergent forces. There are configuration forces, but > > they're not emergent forces, they're subtle results of electrons > > packing themselves into quantized energy levels in increasingly > > complicated configurations of nuclei. > > > > The structure of DNA and the elaboration of molecular biology was the > > last straw because it provided a purely physical mechanism for > > inheritance. > > > > But you're right to see it as a bit of a conundrum. The Emergentists, > > as McLaughlin summarizes them, were substantially correct: > > configurations of atoms in molecules are the key to understanding > > chemistry, there are all sorts of chemically distinctive things that > > happen because of those configurations, none of those chemically > > distinctive things are obvious when you play around with protons and > > electrons in the physics lab. But it all turned out to be part of the > > resultant of quantum mechanics, not emergent in the sense the > > Emergentists had painted themselves into, so they were wrong in the > > one sense they really cared about. > > > > > On 8/30/21 10:43 AM, Roger Critchlow wrote: > > This sounds like an algorithm for parallel protein folding that I > > ranted about a long time ago. Start with some collection of > > conformations; perform many different molecular dynamics simulations > > from your starting points in parallel; continue with the most > > promising subset. As molecular dynamics on proteins tends to find > > lots of deadends, you can get a lot of improvement by tabu'ing the > > known deadends and extending into conformations which don't double > > back into visited regions. Seems I remember it went back to some > monte-carlo work at LANL in the 1950's, Goodfellow? > > > > It also sounds a lot like Monte Carlo Tree search as used, for > > instance, in AlphaGo. > > > > It boils down to how well you can distinguish promising and > > unpromising branches. > > > > Whatever, it was in Friam before gmail, so I can't search for it. > > There doesn't appear to be any search in the Friam archives, and the > > years before > > 2017 at https://redfish.com/pipermail/friam_redfish.com/ are all 404 > anyway. > > > > -- rec -- > > > > On Mon, Aug 30, 2021 at 12:39 PM uǝlƃ ☤>$ <geprope...@gmail.com> wrote: > > > >> In my ignorance, I've thought of weighted ensemble (WE) as a specific > >> kind of novelty search. E.g. weighting toward trajectories that > >> exhibit anomalies. Is that what you mean by it? > >> > >> Also, for each of the 5 you're interested in, do you have convenient > >> example cites for each/any of them? In particular, (2) and (3)? Or > >> are these just ideas of places where you think WE should apply? > >> > >> For my part, no. I haven't used WE in particular. I have a friend > >> who's worked on identifying mechanical anomalies from audio > >> (recordings of machines as they hum). He may have used it. I'll ask. > >> > >> On 8/29/21 1:07 PM, Jon Zingale wrote: > >>> I am presently working on learning weighted ensemble < > >> https://arxiv.org/pdf/1906.00856.pdf> sampling techniques and was > >> curious if any here have worked with them before. The technique seems > >> promising and has enjoyed quite a bit of success (even above MCMC < > >> https://en.wikipedia.org/wiki/Markov_chain_Monte_Carlo>) in circles > >> concerned with reaction rates for rare events. > >>> > >>> Some points of interest for me include: > >>> > >>> 1. A better sampling of fringe-outlier works/art from streaming > >> services. > >>> 2. An alternative (bin-based sampling) to globally defined "fitness" > >> measures in evolutionary modeling. > >>> 3. An application of diffusion-limited aggregation to general > >>> search > >> (especially in the face of limited resources) > >>> 4. An application of linear logic to optimization problems in > >> conformation prediction < > >> https://en.wikipedia.org/wiki/Protein_structure_prediction>. > >>> 5. Investigation of dynamical properties, such as distribution of > >> trajectories with "high winding number", on strange attractors. > >>> > >>> > >>> While I am just beginning to grok the technique, I thought it might > >>> be > >> fruitful to ask here. > > > -- > ☤>$ uǝlƃ > > - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam un/subscribe > http://redfish.com/mailman/listinfo/friam_redfish.com > FRIAM-COMIC http://friam-comic.blogspot.com/ > archives: http://friam.471366.n2.nabble.com/ > - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam > un/subscribe http://redfish.com/mailman/listinfo/friam_redfish.com > FRIAM-COMIC http://friam-comic.blogspot.com/ > archives: http://friam.471366.n2.nabble.com/ >
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