The Science Motivation
I dropped out of a Ph.D. program 4 years ago and joined the start-up tech world a brash change for a synthesist. But now I’m back, committing a “financial martyr” as I’ve been told before, so why am I here?
When I was 20 I wanted to start putting chemistry into the computer, a lot of my friends were programmers and I thought this was the most amazing thing. It started off with trying to put the periodic table as class objects and their attributes labeled. The minute we got to different organic compounds the project crumbled….we were not ready.
For example, our code was our best understanding at the time:
class Atom():
neutrons = ?
electrons = ?class Hydrogen(Atom): mass = 1.008
electrons = 1
So I began my journey into cheminformatics (The keyword I found later). We are organic chemists that also delved into the coding world as we try to put our skeletal perception language into the computer to help us because we are struggling as a community.
We understand the functional groups and how they relate to each other but it can be hard to prove since our science is based on what we see in the lab:
I’ve seen these molecules, I know how they think, I guess on what they will do but sometimes strange things like this happen and it’s just very beautiful. Here is where my brain stops and I just enjoy the nature of life because to me this is mathematically ineffable.
But we need to predict this stuff so maybe the computer will figure it out? For a long time I studied IUPAC nomenclature and then I started picking up a language during my mid 20s to help me translate to the computer the molecule in a 1-D fashion:
"alanine": "C",
"arginine": "CCCCNC(N)=N",
"asparagine": "CCC(N)=O",
"aspartic acid": "CC(O)=O",
"cysteine": "CS",
"glutamic acid": "CCC(O)=O",
"glutamine": "CCC(N)=O",I was able to start reading what this meant and I started finding patterns. Eventually, I found a pattern for peptides, and circular peptides and was able to publish it as a rogue scientist working from my home. Well, I needed to find other Cheminformaticians away from my home in Austin plus there was a layer missing. Each of the atoms of the universe I didn’t know how to describe.
From scraping twitter I found that University of Maryland was using the key word “Cheminformatics”, it picked up on my radar. So quit the start-up that I helped build for 3 years, and I joined the University of Maryland PhD Program to find out what these guys were up to. I joined these Molecular Dynamic folk to find out how they were simulating these molecules and why have I never seen Molecular Dynamics in the industrial world. It ultimately comes down to a trust of the forcefields that govern these guys simulations — for example, they watch the movement of atoms in the universe and make correlations:
Turns out these forcefields one of them is written here (there are multiple), CHARMM. And it’s based on the energy equations of some underlying physics but validated by NMR. They did it, they cataloged the atoms of the universe. That’s my bridge….
Then I found this:
CGenFF aims to be a general force field for drug-like molecules developed to be compatible with the CHARMM all-atom additive biomolecular force fields.
This is their tree, a lot of computer science friends might know this design. This is called an atom-type engine, something I wasn’t able to do when I was younger but it existed here.
This is the source of my passion for coming back. Us Cheminformaticians need this so we can relate to the real and the computational chemist world. This is our lexical key and by inheritance, I now believe in the CHARMM General Forcefield. I believe in this architecture and I’m going to prove it works, with my newfound scientist friends. I am being judged constantly but who gives a fuck, I understand what I gave up and what I have to do.
The People Motivation
In graduate school, I listen to all the depression and sadness that comes with being in academia. We need to care about each other. Science is very hard and it’s not something we can do alone. I knew it was going to be intense coming to Maryland and into the heart of Baltimore. I knew our school was in the Shock Critical Care Unit, here’s one of our buildings:
It is not easy where I work. Our problems are not the hardest problems of the universe but they are the most impactful to the people here to make sure our medical center can help.
I realized I want and need to do my part within the center in making this easier for the patient. This is what I’ve seen in my past. I tell myself I need to give up a part of my life because if my skills will be useful they should be applied here — for the patient. That is often forgotten. I am going broke, I miss my girlfriend, friends, and family but I am chasing my dream to what I think will help the world and become what I want to be: a Drug Hunter. Hopefully, it pays off in the future.
