Three ways people handle this now, and some thoughts on the future.| corinwagen.github.io
The Moneylender and his Wife, Quentin Matsys (1514)Inspired by relatedwritings from Scott Alexander, who is funnier than me. TW: fiction, but barely. AlphaProteinStructure-2 is a deep learning model that can predict the structure of mesoscale protein complexes like amyloid fibrils. AlphaProteinStructure-2 is free for academic usage. Typically this means researchers at universities can use the model for free, while researchers at for-profit institutions are banned from using the model without ...| Corin Wagen
What I learned from finally reading some Girard.| corinwagen.github.io
(This post is copied from some notes I gave to our summer interns at Rowan almost without modification. Hopefully people outside Rowan find this useful too!) This is a brief and opinionated guide on how to give a research talk to an external audience. Some initial points of clarification—this guide is for a research talk, not a sales call or a VC pitch. Research talks have their own culture and norms; treating a research talk as a sales call is likely to backfire disastrously. When is a res...| Corin Wagen
Learning about the daily lives of peasants in 14th-century France.| corinwagen.github.io
On the vibe shift that's happening across computational chemistry.| corinwagen.github.io
What I found to be helpful in learning quantum chemistry.| corinwagen.github.io
Recently, Kelsey Piper shared that o3 (at time of writing, one of the latest reasoning models from OpenAI) could guess where outdoor images were taken with almost perfect accuracy. Scott Alexander and others have since verified this claim. I’ve been playing around with this too: with the prompt linked in Scott’s post, o3 can guess where my photos were taken almost every time, even when I intentionally avoid anything that looks like it might be too helpful. After inspecting the reasoning, ...| Corin Wagen
Why I did not like The Ruthless Elimination of Hurry.| corinwagen.github.io
Why physics- and ML-based scientific simulation will converge.| corinwagen.github.io
Just a weird poem parody.| corinwagen.github.io
In 2007, John Van Drie wrote a perspective on what the next two decades of progress in computer-assisted drug design (CADD) might entail. Ash Jogalekar recently looked back at this list, and rated the progress towards each of Van Drie’s goals on a scale from one to ten. There’s a lot in Jogalekar’s piece that’s interesting and worth discussing, but I was particularly intrigued by the sixth item on the list (emphasis added): Outlook 6: today’s sophisticated CADD tools only in the han...| Corin Wagen
A Hofstadter-style dialogue about protein–ligand binding-affinity prediction.| corinwagen.github.io
A literature review, of sorts.| corinwagen.github.io
All the books I read in 2024.| corinwagen.github.io
This post assumes some knowledge of molecular dynamics and forcefields/molecular mechanics. For readers unfamiliar with these topics, Abhishaike Mahajan has a great guide to these topics on his blog. Although forcefields are commonplace in all sorts of biomolecular simulation today, there’s a growing body of evidence showing that they often give unreliable results. For instance, here’s Geoff Hutchison criticizing the use of forcefields for small-molecule geometry optimizations: The use of...| Corin Wagen
Abhishaike Mahajan recently wrote an excellent piece on how generative ML in chemistry is bottlenecked by synthesis (disclaimer: I gave some comments on the piece, so I may be biased). One of the common reactions to this piece has been that self-driving labs and robotics will soon solve this problem—this is a pretty common sentiment, and one that I’ve heard a lot. Unfortunately, I think that the strongest version of this take is wrong: organic synthesis won’t be “solved” by just rep...| Corin Wagen
Finding different conformations, made easy.| corinwagen.github.io
Wading through the quagmire of biological packages as an organic chemist.| corinwagen.github.io
Some thoughts about why I like the DiffLinker paper, and where this work could go.| corinwagen.github.io
Sharing some open-source computational chemistry work.| corinwagen.github.io
SolidWorks as archetype of simulation software for experimentalists, and how life scientists can learn from this.| corinwagen.github.io
In Wednesday’s post, I wrote that “traditional physical organic chemistry is barely practiced today,” which attracted some controversy on X. Here are some responses: “POC has evolved in many directions and its concepts are widely used, e.g., in host-guest chem, org syn, materials sci, drug discovery.” - Bill Jorgensen “There is still a lot of absolutely gorgeous classical phys org done with organometallic and enzymatic reactions. The molecules have changed, the ideas are the same....| Corin Wagen
In this post, I’m trying something new and embedding calculations on Rowan alongside the text. You can view the structures and energies right in the page, or you can follow a link and view the full data in a new tab. While PDFs and printed journals are limited to displaying 2D renditions of 3D structures, there’s no reason why websites should follow suit—and now that all my calculations are already on the web, it’s simple to share the primary data. The 2-norbornyl cation has a special...| Corin Wagen
All the books I read in 2023.| corinwagen.github.io
What Richard Sutton has to say about computational chemistry today.| corinwagen.github.io
Six koans from Amazon.| corinwagen.github.io
Following Michaeleen Doucleff on her journey to learn ancient parenting wisdom.| corinwagen.github.io
Promising, but is it investable?| corinwagen.github.io
Sometimes our problems are not as hard as they seem.| corinwagen.github.io
Or; how I stopped worrying and learned to love networking.| corinwagen.github.io
A summary of recent developments in low-cost quantum chemistry.| corinwagen.github.io
Why I'm always nervous about energy decomposition analysis.| corinwagen.github.io
Two papers looking at an interesting, and distinctive, property of all transition states.| corinwagen.github.io
A breakdown of the Mcule building blocks database.| corinwagen.github.io
The divide between the QM tribe and the MD tribe, and why it's bad for science.| corinwagen.github.io
Summarizing some recent work in an exciting area of the literature.| corinwagen.github.io
A new form of research organization.| corinwagen.github.io
Why the pKa scale stops working in nonpolar solvents, and what it means for practicing organic chemists.| corinwagen.github.io
Some advice I frequently give, collected.| corinwagen.github.io
Why peer review is the only place that scientists get proper feedback on their work, and why that's good (and bad).| corinwagen.github.io
Reflections on a decade studying organic chemistry.| corinwagen.github.io
The most- and least-read posts, and some reflections| corinwagen.github.io
Exploring the science behind Varda Space Industries.| corinwagen.github.io
Anyone can screen for generality; you just have to believe in yourself.| corinwagen.github.io
Why it is easier to be a chemist today than it ever has been, and what that means for the field.| corinwagen.github.io
A gonzo guide to the world of Silicon Valley, explained through three literary allusions.| corinwagen.github.io
Reflecting on recent events at JCIM.| corinwagen.github.io
A master class from Richard Hamming, one of the fathers of modern computing.| corinwagen.github.io
Isotope-ratio mass spectrometry was once used to measure KIEs to insane precision. Why has it fallen out of favor?| corinwagen.github.io
A literature study discovers a curious result, and I try to get to the bottom of it.| corinwagen.github.io
What we can learn from Silicon Valley.| corinwagen.github.io
The past, present, and future of journals, and some creative ideas for the new world order.| corinwagen.github.io
PCA, tSNE, and UMAP - distance preservation, local structure, and precision–recall tradeoff| corinwagen.github.io
For those who dislike relying on social media.| corinwagen.github.io
The Arrow replacement effect, Richard Hamming, and why so many new ideas come from startups/assistant professors.| corinwagen.github.io
Looking for 'diamonds in the rough.'| corinwagen.github.io
Why, how, and what to read.| corinwagen.github.io
Taking ideas from one discipline to another for scientific progress.| corinwagen.github.io
Predicting experimental NMR spectra for fun and profit.| corinwagen.github.io
How to make a very slow language slightly less slow.| corinwagen.github.io
Two views on how practical applications can lead to innovations in basic research.| corinwagen.github.io
On the predictive power of calculations, and why we still need human intuition.| corinwagen.github.io
In science, if you know what you are doing, you should not be doing it. In engineering, if you do not know what you are doing, you should not be doing it.| corinwagen.github.io
My favorite papers from 2022.| corinwagen.github.io
Quantum chemists and their sneaky tricks, part 1 of infinity.| corinwagen.github.io
Surveying a year in chemical meta-optimization.| corinwagen.github.io
An example of a KIE experiment that seems more informative than it is.| corinwagen.github.io
All the books I read in 2022.| corinwagen.github.io
Are relative energies good enough to make Boltzmann weighting worth it?| corinwagen.github.io
A simple recipe for running a conformational search.| corinwagen.github.io
A few responses to thoughtful critiques of my previous post.| corinwagen.github.io
Why 13C NMR is, generally, a waste of time and should not be required.| corinwagen.github.io
How poor institutions prevent scientific progress, by analogy to the Canadian tech scene.| corinwagen.github.io
A tiny program to estimate ion-pair dissociation constants.| corinwagen.github.io
Last week's business card, broken down.| corinwagen.github.io
A simulation of liquid Ar small enough to fit on a business card.| corinwagen.github.io
I summarize Michael Nielsen and Kanjun Qiu's argument for why starting new scientific institutions can drive progress.| corinwagen.github.io
Thoughts on how to respond to decline and injustice.| corinwagen.github.io
Different approaches for studying dissociation of the water dimer.| corinwagen.github.io
How to be better at recognizing talented people.| corinwagen.github.io
A quick guide to some introductory cheminformatics.| corinwagen.github.io
Quick-and-dirty comparison of the accuracy of different computational methods.| corinwagen.github.io
Still-fresh insights from the legendary business book, and applications to academia.| corinwagen.github.io
A deep dive into predicting correct regiochemical outcomes using molecular dynamics, and the shortcomings of transition-state theory.| corinwagen.github.io
'They have passed like rain on the mountain... The days have gone down in the West behind the hills into shadow.'| corinwagen.github.io
Creating smooth potential energy surfaces using Python.| corinwagen.github.io
How the project started, the challenges we faced, and what I've learned from it.| corinwagen.github.io
A simple mathematical demonstration that the existence of a low-energy intermediate has no impact on rate.| corinwagen.github.io
How to increase trust in our field.| corinwagen.github.io
How acid-catalyzed reactions behave as intermediate lifetime approaches zero.| corinwagen.github.io
Graphical comparison of different ultrafast processes.| corinwagen.github.io
Using new spectroscopic tools to probe solvation dynamics in a variety of systems.| corinwagen.github.io
A few useful commands for computational chemists.| corinwagen.github.io
What we can learn from femtosecond observation of benzhydryl cation solvolysis.| corinwagen.github.io
What I learned from computing extremely large transition states, and a cheap way to study explicit solvation of complex systems.| corinwagen.github.io
Similarities and differences between management consulting and graduate school in the physical sciences, and what we can learn from the comparison.| corinwagen.github.io