Infrequent metadynamics study of rare-event electrostatic channeling

We are glad to share that Yan’s first paper has been published online. In this work, we employed infrequent metadynamics (InMetaD) to study the slow hopping process of the intermediate glucose-6-phosphate (G6P) on a poly-arginine peptide. We estimated the hopping rates and hopping activation energy with (InMetaD) and quantified the desorption energy of G6P with umbrella sampling. By comparing the transfer efficiency with the previously studied poly-lysine bridge, our results indicate that arginine could be more efficient than lysine in electrostatically transferring G6P.
Ref: Xie, Y.; Calabrese Barton, S., “Infrequent Metadynamics Study of Rare-Event Electrostatic Channeling”, Phys. Chem. Chem. Phys.  23, 13381 (2021). doi:10/gkgmtf
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Kanchan Chavan’s Defense


Congratulations to Kanchan Chavan who defended her dissertation titled “Multi Scale Simulations for Efficient Multi-Step Reaction Cascades” today. Kanchan is finishing her Ph.D. in Chemical Engineering, and has build deep capabilities in our group for multiscale simulations of electrocatalytic materials, using the finite element method, molecular dynamics, DFT and microkinetics. Below are her two papers as lead author, with another in preparation. Congrats Kanchan!

  • K. S. Chavan and S. C. Barton, “Confinement and Diffusion of Small Molecules in a Molecular-Scale Tunnel”, J. Electrochem. Soc., 167, 023505 (2020). doi:10.1149/1945-7111/ab6dd2
  • K. S. Chavan and S. Calabrese Barton, “Simulation of Intermediate Channeling by Nanoscale Confinement”, J. Phys. Chem. C, 122, 14474–14480 (2018). doi:10.1021/acs.jpcc.8b01922

Kanchan zooming with her committee, clockwise from top left, Dr. Tim Hogan, Dr. Calabrese Barton, Dr. David Hickey, and Dr. Alexei Bazavov.

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Welcome to Kat Hummer

Welcome to Kat Hummer, who has joined our group as an undergraduate Professorial Assistant. Kat is an undergraduate student studying chemical engineering and Spanish, and is a member of the Honors College at MSU, which offers the professorial assistant program. She also participates in the Women in Engineering program and the Environmental Engineering Student Society.

Kat will begin by working with some of our computational tools that we build to analyze experimental data. Welcome aboard, Kat!

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Welcome to Mindy Lee

We’re happy to welcome Mindy Lee to the group. Mindy is pursuing her MS in Chemical Engineering and will be doing a research on an electrochemical hydrogenation of biomass. She started her BS-MS dual degree program in January 2020 and finished her BS in Chemical Engineering last May. Welcome aboard, Mindy!

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Welcome to Christina Wark

UPDATE (10/15/20): Christina is now a permanent member of the group! Hooray!

Christina Wark has joined the group this summer on an Early Start Fellowship. A Michigan native from the Detroit area, Christina completed dual bachelor’s degrees in chemical engineering and mechanical engineering at Kettering University in Flint, MI. Christina will start her formal Ph.D. program in Chemical Engineering at MSU this Fall. This summer, she’ll work on modeling of SECM systems using the finite element method in python. She says, “I like to enjoy all seasons of the natural beauty that Michigan has which supports my passion for sustainability and ‘being green’.” Welcome to the MSU family, Christina!

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Molecular Dynamics Inside a Nanotube

Here’s a new paper by Kanchan detailing the trajectories that small molecules can take inside a nanotube. This can be considered the MD version of Kanchan’s previous work, which was a continuum model.  We show how the residence time of a molecule (or how long it stays inside the nanotube) depends on nanotube geometry for two different molecule types. We also show that you can increase the residence time by modification of the NT termini- by applying static charge at the end of the tube. Surprisingly, this applied charge affects neutral molecules like ethanol more than charged oxalate.

Reference: K. S. Chavan and S. Calabrese Barton, “Confinement and Diffusion of Small Molecules in a Molecular-Scale Tunnel”, J. Electrochem. Soc., 167, 023505 (2020). doi:10.1149/1945-7111/ab6dd2

Cool video after the jump.. Continue reading

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Bon Voyage Muhammad!

Spartans Will

Spartans Will

We bid farewell to Muhammad Gul, who visited with us for six months to conduct electrochemical characterization experiments on his oxide nanoparticles. A graduate student working with Khalida Akhtar at the National Center of Excellence in Physical Chemistry, Peshawar Pakistan, Muhammad has expertise in hydrothermal synthesis of oxide nanoparticles suitable for capacitor and battery applications. You can check out some of his synthesis work here:

M. Gul and K. Akhtar, “Effect of various technological parameters on particle morphology and uniformity of α-Ni(OH) 2 synthesized via surfactant-free hydrothermal route”, J. Dispers. Sci. Technol. (2019). doi:10.1080/01932691.2019.1703733.

We enjoyed Muhammad’s visit and look forward to working with him again!

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Markov-State Transition Path Analysis of Electrostatic Channeling

Congrats to Yuanchao on his new paper in J. Phys. Chem.  This was a great collaboration our friends in Shelley Minteer’s group at U. Utah and Alex Dickson of MSU’s Biochemistry and Molecular Biology Dept. Alex helped us analyze pathways for intermediate transport over enzyme surfaces.  We were able to use this analysis to accurately predict transport efficiency over heterogeneous enzymatic cascades.

Ref: Y. Liu, D. P. Hickey, S. D. Minteer, A. Dickson and S. Calabrese Barton, “Markov-State Transition Path Analysis of Electrostatic Channeling”, J. Phys. Chem. C, 123, 15284–15292 (2019). doi:10.1021/acs.jpcc.9b02844

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Yuanchao Liu’s Defense

Congratulations to Yuanchao Liu, who on Thursday defended his dissertation titled “Multi-Scale Simulation of Electrostatic Channeling”. Yuanchao is finishing his Ph.D. in Materials Science and Engineering, and has lead our group in building capabilities in molecular modeling of bio reaction systems. He has two papers published with another on the way.

Well done, Yuanchao!

  1. Y. Liu, I. Matanovic, D. P. Hickey, S. D. Minteer, P. Atanassov and S. Calabrese Barton, “Cascade Kinetics of an Artificial Metabolon by Molecular Dynamics and Kinetic Monte Carlo”, ACS Catalysis, 8, 7719–7726 (2018). doi:10.1021/acscatal.8b01041
  2. Y. Liu, D. P. Hickey, J.-Y. Guo, E. Earl, S. Abdellaoui, R. D. Milton, M. S. Sigman, S. D. Minteer and S. Calabrese Barton, “Substrate Channeling in an Artificial Metabolon: A Molecular Dynamics Blueprint for an Experimental Peptide Bridge”, ACS Catalysis, 7, 2486–2493 (2017). doi:10.1021/acscatal.6b03440
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Presentations at ECS Seattle

We’ll be attending the the 233rd meeting of the Electrochemical Society in Seattle this week.  Two of us will be presenting our work:
We are also participating in the ECS Hack Week. Look for Kanchan, Yuanchao, and Alex starting on Wednesday. Looking forward to seeing you there!
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