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Justin Lemkul

@justinlemkulvt.bsky.social

Associate Professor of Biochemistry at Virginia Tech. Comp Chem, CADD, and Drude FF contributor. Opinions my own. Go Hokies!

66 Posts1130 Follower328 Folgt
Justin Lemkul@justinlemkulvt.bsky.social · 7mo ago

Another new article from former Ph.D. student Julia Montgomery on the electrostatics of the beta-2 adrenergic receptor. Very cool cooperative dynamics and polarization effects in microswitch residues! Link below provides free access for 50 days: www.sciencedirect.com/science/auth...

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sciencedirect.com

Justin Lemkul@justinlemkulvt.bsky.social · 7mo ago

First article of 2026! Happy to have our first real foray into carbohydrates out in J Phys Chem B. Excellent work by PhD candidate Esmat Mohammadi. pubs.acs.org/doi/full/10....

Insights into the Electronic and Structural Properties of Cellulose and Amylose: A Comparative Force Field Study

Amylose and cellulose are important biopolymers with diverse applications in biotechnology and materials science. Understanding their structural, dynamic, and solvation properties at the molecular level is critical for harnessing their potential. This study investigates the electronic and structural properties of single-chain cellulose and single- and double-chain amylose in aqueous solution using molecular dynamics simulations with both nonpolarizable (CHARMM) and polarizable (Drude) force fields. CHARMM simulations show stable hydrogen bonding between amylose and water, higher glucose ring dipole moments, increased rigidity, adoption of chair conformations, and less variation in dihedral angles. In contrast, Drude simulations captured dynamic electronic polarization, enhanced conformational flexibility, and resulted in heterogeneous inter- and intramolecular hydrogen bonds. For cellulose, structural and solvation behaviors were largely similar between CHARMM and Drude. These findings highlight molecular interactions and solvation dynamics of amylose and cellulose, with potential relevance in materials science and biotechnology.

pubs.acs.org

Stand Up for Science!@standupforscience.net · last yr.

(10/11) 75 years of scientific discovery—now on the chopping block. Trump’s 2025 budget proposes a 56% cut to the NSF. Over 1,000 grants terminated. 37 divisions abolished. Funding frozen. This isn’t just reckless—it’s a war on knowledge, a war on progress.

A bold graphic with the headline ‘75 Years of Incredible Discovery. Now Under Attack.’ displays four visuals representing threats to the National Science Foundation (NSF). A pie chart shows a proposed 56% budget cut, a ‘CANCELLED’ stamp is over a document to represent over 1,000 grants terminated, chained lab equipment symbolizes freezes on new and existing funding, and a person packing a box reflects the abolishment of 37 internal divisions.
Ardem Patapoutian@ardemp.bskyverified.social · last yr.

Published an op-ed for @cnn.com: “Nobel laureate: I owe America my success. Today, its scientific future is in danger.” A personal reflection on what’s at stake as science funding gets slashed. I’d be grateful if you could amplify both in and beyond the science world. www.cnn.com/2025/04/09/h...

Nobel laureate: I owe America my success. Today, its scientific future is in danger | CNN

Dr. Ardem Patapoutian says he watches “with deep sadness as the United States’ remarkable scientific enterprise, which took generations of hard work and national investment to build, faces a concerted...

cnn.com

@darcy-davidson.bsky.social · last yr.

@biophysicalsoc.bsky.social you need to be sharing at the conference this week like our lives depend on it. Because they do. Speak up. Stand up. Get out there and protect out democracy

Stand Up for Science!@standupforscience.net · last yr.

Welcome to the Bluesky account for Stand Up for Science 2025! Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide! #scienceforall #sciencenotsilence

Justin Lemkul@justinlemkulvt.bsky.social · 2y ago

@biochem-anne.bsky.social and I are looking for a home for a perspective we wrote on current technical challenges in biomolecular simulations. Preprint linked here; we aren't sure of the best venue. Shopped around a bit, so far rejected each time for "poor fit." #compchem doi.org/10.26434/che...

Robustness in Biomolecular Simulations: Addressing Challenges in Data Generation, Analysis, and Curation

Computational simulations of biomolecules provide a wealth of information about the thermodynamic landscape of biologically important systems, kinetics of important cellular processes, and the biophys...

doi.org

Marcelo D. Polêto@mdpoleto.bsky.social · 2y ago

Excited to finally share that our work is featured as the front cover of ACS Macromolecules' new issue! Image was powered by the one and only MolecularNodes (thx @bradyajohnston.bsky.social) while I was playing around with surface transparency 😁 #chemsky #compchem

Front cover of the journal ACS Macromolecules. A single chain of PET polymer on the left. An amorphous phase of PET embedded in a box of transparent water surface on the right. A crystal PET unit on the bottom right, with a protein bound to it. PET atoms are shown in green. Lightnings are falling from a cloudy sky above. The word MACROMOLECULES in white on the center top of the page.
Marcelo D. Polêto@mdpoleto.bsky.social · 2y ago

Our paper found a permanent home at ACS Macromolecules 🎉 Very happy with the final results 😁 #chemsky #compchem pubs.acs.org/doi/10.1021/...

Michael Bauer@michaeldbauer.bsky.social · 2y ago

"If we don't feel stupid it means we are not really trying" Very encouraging quote from this inspiring article. The other two are also excellent! I'll add this piece of advice, which a friendly ultramarathoner once gave me: "Enjoy the highs, manage the lows!" #econsky

Science News@scinews.bsky.social · 2y ago

Three must read papers for PhD students. #scisky #PhD #science #research #academicsky 1. The importance of stupidity in scientific research Open Access journals.biologists.com/jcs/article/...

Rommie Amaro@rommieamaro.bsky.social · 2y ago

🚨Announcing NetSci: a super fast tool to compute correlated motion in biomolecules pubs.acs.org/doi/10.1021/... @pabloarantes.bsky.social & team also made it into a Colab notebook: colab.research.google.com/drive/1GGJKr... Give it a try & send feedback!

NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation

We present the NetSci program–an open-source scientific software package designed for estimating mutual information (MI) between data sets using GPU acceleration and a k-nearest-neighbor algorithm. This approach significantly enhances calculation speed, achieving improvements of several orders of magnitude over traditional CPU-based methods, with data set size limits dictated only by available hardware. To validate NetSci, we accurately compute MI for an analytically verifiable two-dimensional Gaussian distribution and replicate the generalized correlation (GC) analysis previously conducted on the B1 domain of protein G. We also apply NetSci to molecular dynamics simulations of the Sarcoendoplasmic Reticulum Calcium-ATPase (SERCA) pump, exploring the allosteric mechanisms and pathways influenced by ATP and 2′-deoxy-ATP (dATP) binding. Our analysis reveals distinct allosteric effects induced by ATP compared to dATP, with predicted information pathways from the bound nucleotide to the calcium-binding domain differing based on the nucleotide involved. NetSci proves to be a valuable tool for estimating MI and GC in various data sets and is particularly effective for analyzing intraprotein communication and information transfer.

pubs.acs.org

Marcelo D. Polêto@mdpoleto.bsky.social · 2y ago

Our paper found a permanent home at ACS Macromolecules 🎉 Very happy with the final results 😁 #chemsky #compchem pubs.acs.org/doi/10.1021/...

Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations

The environmental and economic challenges posed by the widespread use and disposal of plastics, particularly poly(ethylene terephthalate) (PET), require innovative solutions to mitigate their impact. ...

pubs.acs.org

Marcelo D. Polêto@mdpoleto.bsky.social · 2y ago

It’s finally out! 🥳 We extended the Drude polarizable force field to model PET polymer and demonstrated interesting applications in modeling protein-PET interactions. Feel free to check it out! DMs are open for feedback 😁