You have to put energy into a system to make it cyclize (form a ring). We found, using QM calculations, the amount of energy you need was proportional to how far apart the atoms start out.

My first presentation at a regional ACS meeting! April 2006!

new year’s resolution: be like sharks

My condolences Alex. I know how much he meant to you and the other Charmm developers. He’ll be missed by the compchem community at large.

An intact antibody

A half exploded antibody

A fully exploded antibody

😒 (🩶protein 🧡disulfides 💜glycans)

During lab meeting: "I don't even have time to tell you how wrong you are" Also during lab meeting: "Actually, it's gonna bug me if I don't"

🧪

The thing about working with nucleic acids is that you’ll forget proteins can carry positive charge and need anions to neutralize 🤦🏻‍♀️

This picture of Neptune was produced from the last whole planet images taken through the green and orange filters on NASA's Voyager 2 narrow-angle camera. The images were taken at a range of 4.4 million miles from the planet, 4 days and 20 hours before closest approach. CREDIT: NASA

Uranus and Neptune don’t have magnetic poles, according to data from NASA Voyager. The disordered magnetic field could be created by mantles with two liquid layers: one water layer and another carbon, nitrogen, and hydrogen layer. In PNAS: www.pnas.org/doi/10.1073/...

A close up of an IgG1 Fc domain glycan (blue) and its attachment point (green)

An IgG1 antibody shown in secondary structure ribbon with coarse grained beads overlapping

Using SIRAH to coarse grain my glycosylayed antibody! Hooray for (1) tutorials that work, and (2) my first foray into CG! Can I join the #glycotime club?

Fleece lined tights! Wool and cashmere where possible - the latter is lightweight but warm

A picture of a Baltimore oriole from the national zoo

Messing around with pyrophosphates, hopefully adding them to modXNA in the near future. Then off to tackle termini mods. Then Thanksgiving prep begins. 👏🏻 checking 👏🏻those 👏🏻boxes

We are looking for a #CompChem postdoc to implement MELD (Modeling Employing Limited Data) into the AMBER suite of programs and test new applications in integrative modeling. Work with
@adrianroitberg.bsky.social
and me at #UFChemistry! Apply here explore.jobs.ufl.edu/en-us/job/53...

A quantitative framework for structural interpretation of DMS reactivity Dimethyl sulfate (DMS) chemical mapping is widely used for probing RNA structure, with low reactivity interpreted as Watson-Crick (WC) base pairs and high reactivity as unpaired nucleotides. Despite i...

🧬 Excited to share our new preprint! DMS chemical mapping, a key technique for studying RNA structure. Everyone assumes low DMS reactivity = Watson-Crick , high = non-WC. However, analyzing 7,500 RNA structures containing known 3D structures reveals it's not that simple. doi.org/10.1101/2024...

Zero slow down for the projects I use a fixed charge FF for. I need more sampling, not less. If something I’m investigating needs to include polarizeability, then the price is the price. Tagging @justinlemkulvt.bsky.social because this is something we discuss a lot!

Worm logo 4ever 💪

I read Dr. No: a novel for book club and loved it, James is on my TBR!! Check it out if you like spy thrillers :)

My students decided to try running MD with a 100 fs timestep today so we’re going to read the Ryckaert SHAKE paper

Updated ff94 atom types AND ran a 5k. The atom types were more exhausting 😩

Album cover from The Miseducation of Lauryn Hill

upload.wikimedia.org/wikipedia/en...

Solomon R. Guggenheim Museum, New York Solomon R. Guggenheim Founding Collection, By gift © 2016 Artists Rights Society (ARS), New York/ADAGP, Paris

Several Circles by Vasily Kandinsky, 1926

https://botfrens.com/collections/212/contents/137491

Looks great! There’s a yarn saying, “make a mistake to let your soul escape,” and I like to think it applies to both intentional and unintentional ones 😜

Each co-author on this paper individually has, in the past, spent days-weeks coming up with a single modification - annoying! Now we can get good parameters in minutes, that are built on top of the *very good* Amber nucleic acid force fields. ✌️🧬💻

modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense olig...

I do molecular dynamics simulations of biopharmaceutical molecules, both protein and nucleic acid (RNA 4ever). Here’s a link to a recent project, modXNA, which parameterizes any combo of base/sugar/bb nucleic acid modification for an MD sim: pubs.acs.org/doi/10.1021/...

Hello! Im a research chemist working at NIST. This means my work supports US commerce through improving measurements of molecules. I work in a group of all types of structural biologists.

Two pumpkins with bear faces painted to look like pandas. Celebrating the new pandas at the National Zoo!

Im proud of my research, sure, but we WON THE PUMPKIN CARVING COMPETITION this year

I love a good pick up meeting.

Hahahahaha amazing, don’t we all ✌️