Anamnesis: Phase-1 (The Beginning)

As the title suggests, I’m done with phase 0, aka some prep and basic backbone of the project.
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Tho I tried adding a graph using matplotlib, but it looked quite bland n didn’t serve any useful purpose… so I’ve kept the UI for the end ( at least for now ), and removed the existing graph…
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So, from now on, I shall be working on phase-1, which includes:

• Protein sequence collection
• Phylogenetic reconstruction
• Ancestral sequence reconstruction
• Evolutionary uncertainty
• Ancient protein candidates

And that, ladies and gentlemen, is the real beginning of Anamnesis…
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P.S. Till now development was slower as I needed to focus on my studies and stuff, but from now on, things should be swifter…. :)

Anamnesis: The Beginning

This project shall serve as my endgame.
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This idea of Anamnesis is simple:

1. Reconstruct ancestral proteins from hundreds of millions of years ago, reconstruct their structures, simulate their molecular dynamics, and trace how mutations transformed their stability, flexibility, and function.

2. Then extend the evolutionary framework to cancer: model how mutations reshape cellular dynamics and search for previously overlooked dynamical states that may make cancer cells unusually vulnerable.
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And as you can tell by the time I’ve logged this, I’ve already started working on the basics, that is, I’m still a newbie at biology, and need to learn quite a few things while building it.
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Either way, the program can now read the protein, its data and its individual amino acids while knowing which letter corresponds to which amino acid…
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A weird incident, that is, I literally wrote my own parser start to end, to read the data related to protein,, only to then realize I could’ve used Biopython instead…. (genius Ik 🥀)
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But yeah,, I’ll try to develop the project as fast as I can while learning the biology underneath it (a rare moment in life where you genuinely feel thankful for naturally being a really quick learner).
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Soo… that’s it for today?
Have a great evening..! 🕯️

Final Devlog of Light

yep, as the title suggests, this is it.
I have somehow, despite being an INTP, been able to complete the project before the deadline ( or perhaps I should say, exactly at the deadline 😭)
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But anyways,

• Completed the Readme
• Fixed minor issues (console errors)
• Fixed responsiveness issues
• Added a favicon

And yeah, that’s all ig…??
It has been an honor tbh,
I’ve learnt soooo many things while making this site… and revised soooo many concepts…. I was lwk a beginner in web-dev before this, and now, well a bit better I suppose? 😭
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Either way,,,
It was fun…. :)
Thank you for everything..!!! ❤️‍🩹
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P.S. Idk what to add as screenshot for this one, so just added the About page of my site 🗿🤷🏻‍♂️

Day-9 Light

I think I’ve officially reached the stage where this project is consuming me 😭💔
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I couldn’t really write devlogs that often ‘cause I’ve been just TOO busy trying to make this thing look pretty 😭
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And unfortunately, having a creative perfectionist brain while also trying to keep everything minimalist is an awful combination. I kept wanting to add stuff, removing it because it was “too much”, adding it again, moving things around, staring at it for 20 min, and realizing that it looked 4% worse than before 🗿
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Anyways…
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I’ve made some pretty major progress today.
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The biggest one: Light is basically complete.
Added all the content, finished the different sections, and finally got the whole thing to feel like an actual part of the site instead of an empty page with suspicious amounts of negative space 🥀
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I also finally added and polished the About page, w a bunch of minor design fixes along the way.
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Completed:

• Unfinished
• Graveyard
• Now
• Curiosities

And I also added snow interaction, which is probably one of those completely unnecessary things that somehow took way longer than it had any business to… ;-;
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The funny part is, that the actual feature list doesn’t even look THAT insane. (compared to my mental health rn 💔)
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But every single little design decision took FOREVER, because I wanted the site to feel minimal, without feeling empty.. Interesting, without feeling overloaded.. And slightly uncanny without just looking like I discovered CSS animations yesterday 🤷🏻‍♂️
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At this point, I’m lwk happy w how it’s coming together tho.
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The site has WAYY more personality now.
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The next goal is basically finishing whatever tiny things are still bothering me, and then SHIP EM before I lose the remaining fragments of my sanity 😭
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And nvm,, that’s it for today ;-;;;
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Ig this could be the last devlog? Or nvm, I still have to write the Readme, GG, that should be the last one lol..
Whatever,,,, 
Good Evening 🦋

Day-8 Light

At this point, I think Im lwk about to crash out because of how long this is taking me 😭💔 (plus a bad headache)
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I’ve added a new page to my site, called Light’s Lab, something way more interesting than the home page fs.
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Also Added a cool glitchy effect as a transition, to give it that uncanny feel…
And DAMN it took me soo longg to learn how to do ts 😭😭
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After this, I’m done with adding animations/transitions 🥀
Aghh my head hurts so badd 😭
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I think the next goal for me is to design the Lab page properly… then think of adding something new…
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Initially I planned to complete it by Sept 30… but let’s see if I can 🫠
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Anyways, that’s it for todayyy
Dobroye utroo!!!

Day-7 Light

It appears as if somoene’s genuinely addicted to this project 🗿
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Because my productivity is PEAK right now 🕯️
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I’ve lwk changed the entire base design of Light, simply because I felt like it 😭 (I wanted it to look better)
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Here’s a list:

• Added Basic fade-in animation when site is loaded
• Added a leaning hero-figure and changed typography (Some fonts, sizes, colors, etc)
• Added a glitch effect for the Hero sub-text
• Added Snow, as it smhow fits the theme beautifully

There were sm things that people suggested me to add, but I was like: Nah ;-;
For eg: Arrow key navigation
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But someone discovering that R jumps to Archive would be mildly amusing for approximately 4 seconds… So I scrapped that idea 🤷🏻‍♂️
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The snowflakes one was particularly interesting… because….
to animate the snowflakes I used:

new position = old position + velocity

Which is basically a tiny Euler integration step 🗿
So, my snowflakes, accidentaly became a physics simulation… 🥀
For some reason, I really cannot escape ts 💔
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And then the tiny intricacies like giving them close but random velocities for realism (yeah, close, because if not: that would look like the snowflakes had all received contradictory weather reports 😭)
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and once they leave the screen, make them re-enter from the right and top (70:30 :: Top:right % of snowflakes generated),
which is what turns this into a continuous wind field rather than 80 flakes having a one-way death march 🗿
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And yeah, that’s basically it, for today…!!
and as usual,, Ohayoo!!! (Good Morningg, not Ohio 😭💔)

Day-6 Light

HOLYYY Productivity!! 🔥
Added SOOOOO many things today
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Here’s the list:

• Polished the Archive section
• Added “About signature” and href links
• Added content to Contact section and footer- Polished them too
• Made the site responsive
• Added selection option (selecting a text)

Soo, when selecting a text, instead of the default blue color, it’d use another color that respects the color scheme of the site…
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With that, Phase-1 of the Site is over… We have a site that’s essentially complete in itself start to end.And so, Phase-2 of Light has started, which is mostly all about JavaScript and additional sections/features. (Lwk Exciting as hell)
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Also, I decided to add “AUTONOMY · TRANSCENDENCE · ERUDITION” as the “About Signature”, because these are the 3 things that I value THE MOST… Especially Autonomy………….
Is it a bit grandiose? Yeah… but my site’s called Light (Alchemic Eclipse), so we’re not exactly filing taxes here 🤷🏻‍♂️🥀
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But anyways,, that’s it for todayy!!
Have a beautiful morning 🍀

Day-5 Light

• Added content to About section
• Added a few projects to Archive section
• Added basic design to Archive section.

Next goal:

• Polish Archive’s design
• Add content to Contact section and design that too

got big plans ahead..!!

Day-4 Light

Guess who’s back?
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Seems someone’s back from his hiatus 🗿
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yep, so now that’s Aporia’s done and dusted, I realized I need to also complete my site, so here I am…
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I’ve merged Gravitas into Light because it’s apparently Aporia turned out to be too big, but small enough that I could actually finish it before Light comes knocking with a deadline shaped baseball bat 🤷🏻‍♂️
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I’ll add a special section for it on my site, as a mystery or a puzzle of some kind..? perhaps…
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And in the meantime, while I was working on Aporia, I tried testing/changing some bits and features of Light, at once almost changed the entire style upside down… but turns out none of them could beat my original vision… So with some bits of tweaks, I added the About page a month ago… I know I’m a bit early here,, but whatever 😭
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And that’s it for this devlog 🦋
Bbyeee..!!
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P.S. Idk what screenshot to add here as I’ve just restarted working on it so no major updates yet,, let me just add a page of my physics notes which would anyway be on my site 🐈

Final of the final devlog

yep, turns out the build file had quite a few errors and things I should’ve fixed earlier but somehow never crossed my mind,,
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along with the fact that I don’t have Apple verification or whatever it’s called 😭
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Anyways, fixed all the issues I could see, and as far as Ik, none of them are left anymore (hopefully)… And now I can finally ship Aporia after some additional testing on other devices
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Thank you once againn…!!
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(Also as I don’t have any specific attachments, I’ll just add the home-page of aporia as the attachment this time…)

Final Devlog

Functions I added today:

• Mute / Unmute
• Navigation
• Controls menu

And finally completed the Readme, that took the most time out of all…
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And now I can ship the project 🙃
I’ll keep it short as I’m in a bit of rush right now… but yeah…
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It has been an incredible journey..!!
Thank you for being a part of it..!! 🦋

UI Improvements

The UI speaks for itself 🗿 (ifykyk, chess)

Sonification

yes….! now you can hear your life chaos through the positions and the angular speeds of the double pendulums…
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Specifically, the angular position determines the pitch and the angular speed determines the volume of the sound.
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With that, all the core features of Aporia are completely in working condition.
That is, now the only things left are:

• Making the design/typography better.
• Making the sonification pleasant 🗿

Because, even though you can hear the pendulums diverge through the difference in pitch, the sound it creates is a bit…… uhh…… mathematical? 😭
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Let me clarify, the sounds it generate are derived from a Sine wave… but two simultaneous sine waves can become unpleasant surprisingly quickly, because apparently even mathematics needs a volume limit 🗿🤷🏻‍♂️
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So it sounds just like two aliens attempting to negotiate a treaty through a malfunctioning fax machine 💔…
Which can lead to a headache pretty quickly if not cautious… so that is another thing I need to work on…
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And that’s it for today? There’s no attachment as the Mac screen recorder doesn’t support system audio… so it’d be redundant to attach it without audio anyways…. (let me just attach a meme lol)
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Anyways.. thank you for reading this through…!! and
as always,
Good morning 🍀❤️‍🩹

Interactive Screen

As the title suggests I added:

• A home page
• An experiment page
• Made the exp. page interactive

Even though Ik the UI looks awful, but that wasn’t my priority atm, it was to make it interactive, to make sure the changes we do in the values reflect in the simulation….
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Given the fact you know how much of a design freak I am, only I know how much I controlled myself from spending the entire night trying to fix the design… because apparently, projects like these have an instinctive desire to consume their creators…🗿
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But anyways, the next step would be to add proper sonification to Aporia, and then fix the design…
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I took me an awful lot to do all that yesterday,,,
Have you ever faced the thing, where you project becomes so huge, that you, yourself start getting confused about what things did what and why and stuff like that? 😭
Because now it has started happening to me, so from now on, I’ve decided to add comments to my code, for the sake of my future self 🤷🏻‍♂️.
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And yeah, that’s it for today, I believe?
Guten Morgen anyways..!! 🥱👋🏻

Atomic Difference

Ladies and gentlemen,
Both the pendulums started out only an “atom” apart.
I don’t think I need to provide any more context 🐱
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They should always follow the same path, right? RIGHT? 😶‍🌫️
Let’s see….
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Saw the video?
yep, they started only an “atom” apart, yet couldn’t even last a minute together….💔🥀 lol
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Shows us how extremely small differences compound overtime in chaotic systems (like weather prediction systems, double pendulums, etc)
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But anyways, the changes I made are too visible to list down, so I’ll let it be for now…. 🗿
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Good Evening 🦋🤷🏻‍♂️

Small updates

Hello there,, quite tired today, so I don’t think I’ll be able to write much in today’s devlog… let me just start by writing down the things I added in Aporia today:

• Max Energy Error (helpful in comparing different integrators for a fixed amount of time)
• Pause/ Play / Reset using keys
• Increment the simulation by 1 step when paused by pressing N

I believe I shall complete this project this week if things go according to the plan, even though, I can also do the same in next 3 days, but I genuinely don’t love the idea of me working day in and day out like a caffeinated squirrel whose rent is due the next day…
So I’m trying to be a ‘bit’ reasonable here 😭
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And, that’s it for the day, I believe..?
Happy Tuesday ig 🤷🏻‍♂️
& Good Morning 🥀
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P.S. btw sorry if I sound a bit tired, many reasons, but a bad day doesn’t imply a bad life, so I’ll just keep moving 🙃
If you genuinely take time out to read my entire devlogs, then you’re the best lol (for me, at least)
❤️‍🩹 Thank you ❤️‍🩹

Adding RK4 to the simulation

And guess what?
The Energy error dropped from roughly 10^(-1)% to
10^(-6)% orders of magnitude 💀
(Literally FIVE orders of magnitude lower 🫎)
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When I first tried running the program after writing the code for RK4, the best I expected was like 10^(-2) ngl 🥀
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Tho the problem is, I’m running both the versions for an arbitrary amount of time, and then trying to compare the error,
which lwk reminds me of atomic bomb vs coughing baby 😭💔
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So my next goal shall be to script a comparer or some sort, which may output things like :

• maximum energy error
• final energy error
• average energy error
• number of steps
• simulated time
• etc

Should be fun lol,,
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Also also, I tried one more thing, that is, I changed dt to 1 sec 💀
and guess what was the error % of RK4? 60% 💀
(literally 10^(-6) to 60% 💔)
which is basically the numerical equivalent of telling the laws of physics, “I have a better idea” 🗿✌🏻
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But nevertheless, learned a lotttt today..!!
Holy productivity~~~ 🦋🥹
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But anyways, that’s it for today,
Good Morning~!!

P.S. I think this project is lwk going in the right direction, the experimentation, the research, the learnings, new future features, all these things mean way more to me than making a random copy-paste project saying “I made a double pendulum go brrr” 😭
lol

Rendering the Euler Hypothesis of Aporia

yeah, fancy title innit? 🥀 (sorry 😭💔)
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but as the title suggests, I finally was able to render a basic simulation of Aporia with a single, double pendulum, that renders using the Euler Integration method (for now).
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This is the first major step of the simulator… which shall become clear as we move towards the future with the speed of 1 sec per second (🗿)
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Alr, keeping that aside, if you pay some attention to the stuff printing out in the console (in the video), that,,, is the energy difference oscillating (and the Energy Error), which ideally should be 0 (as energy is conserved in a closed system).
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Which shows us that Euler integrator doesn’t just inject extra energy into the system, but also lets some of it bleed out (which shall become important later on as we compare different integrators).
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And, that’s it for the day ig?
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Thank you for reading it through..!!
Have a nice dayyy…!! 🌙