https://lamontbiophysics.com/blog daily 0.75 2022-12-05 https://lamontbiophysics.com/blog/symmetries-and-physics monthly 0.5 2022-12-04 https://lamontbiophysics.com/blog/explanations-of-sex-incomplete monthly 0.5 2022-12-05 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/84d06d5a-8027-4069-aef5-3fb7e8ad7d79/sarahotto.png Blog - Explanations of Sex Considered Incomplete - Make it stand out Pithy plot from "Selective Interference and the Evolution of Sex" Sarah P. Otto. The ellipsoid represents the typical state of life. We really have no idea what sign “typical epistasis” should have, but zero seems reasonable, so it’s centered at zero. But due to some weird second order effects in the replicator equations, linkage is usually negative. https://lamontbiophysics.com/blog/redesigning-the-periodic-table monthly 0.5 2022-12-05 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/9fb1407c-5479-495b-ba78-81f04a841ad0/periodsquare2.jpg Blog - Redesigning the Periodic Table - Make it stand out my periodic table https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/ed450d8c-bf9c-4aa6-b5ad-c798d9ca90a8/Simple_Periodic_Table_Chart-en.png Blog - Redesigning the Periodic Table - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://lamontbiophysics.com/blog/classifiers-for-likelihoods-why-logistic monthly 0.5 2022-12-04 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/4f134353-fba5-4964-a421-4ba440fc847a/classifer.png Blog - Classifiers for Likelihoods: Why Logistic? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/c96e34c9-5ff7-4389-9ae3-1f3cb2617c83/bregman.png Blog - Classifiers for Likelihoods: Why Logistic? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://lamontbiophysics.com/blog/fishing-for-the-right-wright-fisher monthly 0.5 2022-12-04 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/3cfa7421-604e-4b16-808a-a972606103e6/swisscheesevector.png Blog - Fishing for the right Wright-Fisher - Make it stand out If you just delete from inside your vector of individuals, your memory starts to look like swiss cheese from the death events. https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/8e234ce9-8610-44dc-9280-c03c3d8506ec/inversecdf.png Blog - Fishing for the right Wright-Fisher - Make it stand out Sampling from a multinomial distribution involves inverting CDF and this requires O(N) comparisons. Shown are two random draws (red diamonds) from a six-outcome multinomial distributions resulting in 2 and 5. https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/39062175-0bb0-4574-a826-0f2005a51822/swapping.png Blog - Fishing for the right Wright-Fisher - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://lamontbiophysics.com/blog/fast-forward-sim-of-populations-in-julia monthly 0.5 2022-12-04 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/fece7d15-7f84-4be4-bf40-ccd1ba35f7f5/Screenshot+2022-09-24+at+13.53.55.png Blog - Fast forward simulations of populations in Julia - Make it stand out These candyland spires are a good sign that the code is tastes good to a CPU, although it doesn’t mean there isn’t a better algorithm that takse advantage of clone counting. This is generated by ProfileViews.jl https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/66f39c9f-c07d-4230-864c-54394b9f95b0/balancedmoranprocess.png Blog - Fast forward simulations of populations in Julia - Make it stand out A visual description of what’s happening in the code below. Virus 103462 with the blue phenotype wins the above battle and becomes the proud parent of 103501 and 103502! https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/28b30ca6-d064-4e9c-b07a-0fdd838f726f/virusshape.png Blog - Fast forward simulations of populations in Julia - Make it stand out How I visualize of the components of Virus{G}. The backward arrows indicate lineage relationships from the child to the parent. From these arrows, we can reconstruct the whole population tree. https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/139c96ac-ac76-432b-81b0-b03a61fc20f9/livingdead.png Blog - Fast forward simulations of populations in Julia - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://lamontbiophysics.com/blog/chemical-kinetics-to-kimura-eqation monthly 0.5 2022-12-05 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/acde0c47-e653-4fc8-ab63-eb75a2362cf4/reaction_coordinate.png Blog - From chemical kinetics to the Kimura Equation - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/9d1beb73-3716-428e-8c02-ead46dd376f5/reaction_volume.png Blog - From chemical kinetics to the Kimura Equation - Make it stand out reaction volumes are imaginary dotted lines in our container that sometimes contain enough particles to start a chemical reaction https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/abf57398-2d6e-41f1-bec2-aeafc21a8469/box_plot.png Blog - From chemical kinetics to the Kimura Equation - Make it stand out IMO, not exactly on the same level as the FFT (or k-statistics for that matter) https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/110bd1ff-e5ed-4294-9c06-bab86dc1aa26/simplex_diffusion.png Blog - From chemical kinetics to the Kimura Equation - Make it stand out The Kimura equation defines a diffusion confined to the simplex over all population types https://lamontbiophysics.com/blog/tag/Julia monthly 0.5 https://lamontbiophysics.com/blog/tag/pop-gen monthly 0.5 https://lamontbiophysics.com/blog/tag/population+genetics monthly 0.5 https://lamontbiophysics.com/blog/tag/diffusion monthly 0.5 https://lamontbiophysics.com/blog/tag/genetics monthly 0.5 https://lamontbiophysics.com/blog/tag/wright-fisher monthly 0.5 https://lamontbiophysics.com/blog/tag/forward+simulation monthly 0.5 https://lamontbiophysics.com/blog/tag/evolution monthly 0.5 https://lamontbiophysics.com/blog/tag/kimura+equation monthly 0.5 https://lamontbiophysics.com/blog/tag/chemical-reaction monthly 0.5 https://lamontbiophysics.com/about daily 1.0 2022-08-25 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/b0a969a6-4ac7-4616-804f-46a2b4d7a643/profile.jpg https://lamontbiophysics.com/publications daily 0.75 2022-12-05 https://images.squarespace-cdn.com/content/v1/5ec321c2af33de48734cc929/1607694644871-IC85FNH781UNZSZEGHDR/Aro+Ha_0428.jpg Publications https://lamontbiophysics.com/research daily 0.75 2022-11-23 https://lamontbiophysics.com/research/agent-based-modeling monthly 0.5 2022-12-04 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/fcdfc6a0-7a9b-4299-a55a-38e377897e53/4ways.jpg https://lamontbiophysics.com/research/predicting-genotypic-substitutions monthly 0.5 2022-08-25 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/9763554f-22e7-4e1a-9516-58fd1ef4997b/codons%3Dtable.png https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/b43f968a-139a-4b7e-99b2-2fa13b916ce6/physicsofmesure.png https://lamontbiophysics.com/research/treatment-design-with-dynamic-programming monthly 0.5 2022-08-29 https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/2e4d98fb-ef2f-43e9-8d43-61e8170bc9b1/dynamicprogramming.png https://images.squarespace-cdn.com/content/v1/62f26850d5df0b3c0fd3956a/7d9ba438-fbd5-4884-afd1-b66d68cb3bd3/workingbackwardsmarkov.png