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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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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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Quantification of Cascade Kinetics by Molecular Dynamics and Kinetic Monte Carlo Methods

Look for our new paper in ACS Catalysiscombining of Molecular Dynamics (MD) and Kinetic Monte Carlo (KMC) methods to quantify kinetics and transport in a two-step artificial cascade.

Written by Ph.D. student Yuanchao Liu in collaboration with Dr. Ivana Matanovic of th3 University of New Mexico and Dr. David P. Hickey of the Minteer group at the University of Utah, MD simulation was used to study surface interactions and related energy-determined rate constants in a cascade comprised of hexokinase and glucose-6-phosphate dehydrogenase bridged by an electrostatic peptide. The KMC model was used to estimate product evolution on experimental time scales. This paper builds on our previous collaborative work combining MD and experiment.

A polylysine peptide was used as an electrostatic bridge to transport glucose 6-phosphate (G6P) from HK to G6PDH. After traversing the bridge, G6P hops from the bridge to the downstream binding pocket on G6PDH. With explicit event sites and rate constants, KMC model was used to integrate all elementary steps by stochastic selection. Finally, the overall kinetics can be quantified to be compared with experimental results on real world time scales.

Please look below the fold for videos from this paper!

Reference: 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, (2018). doi:10.1021/acscatal.8b01041

Continue reading

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Buffer Calculator

After a long absence, our buffer calculator has finally returned. This new calculator works for phosphate and citrate buffers and calculates the formulation needed to achieve a given pH. It also provides enhanced information on buffer strength, including a titration plot and capacity plot.

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Summer Poster Session

Congratulations to Beryl Zhang ’18 who presented her poster, on Enzymatic hydrogel thickness measurements by AFM, at the at the Mid-Michigan Symposium for Undergraduate Research Experiences (Mid-SURE). Beryl helped Alex getting our new AFM-SECM system off the ground, measuring the thickness of hydrogels made using the slide coating technique. This approach will be used for electrochemical microscopy studies of single and multi-enzyme cascades.

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Congratulations Professor Gallaway

Congrats to former group member Josh Gallaway who is starting a new tenure-track position in the Dept. of Chemical Engineering at Northeastern University.  Josh’s research in our group was on redox complexes for mediating enzymatic reactions, but his recent studies have combined spectroscopic and electrochemical techniques to understand battery chemistry, especially zinc alkaline batteries. We can’t wait to see what Josh does at NEU!

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New article on nanofiber bioelectrodes

Former postdoc Cenk Gumeci and Duyen Do have published new work on electrospun nanofiber-based bioelectrodes in Electrocatalysis. Electrospinning allows for the control of fiber diameter and density, and allow for very thin and highly efficient biocatalytic films. Current density reaching 10 mA cm−2 was observed for glucose oxidation, rivaling that of commercial carbon nanomaterials. This work was featured as cover art for the July 2017 issue.

  • C. Gumeci, D. Do and S. C. Barton, “Electrospun Carbon Nanofibers as Supports for Bioelectrodes”, Electrocatalysis, 8, 321–328 (2017). link
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Intermediate Transport at the Nanoscale

A new paper by Erica Earl is available now in Physical Chemistry Chemical Physics (PCCP). In this paper, Erica uses a continuum model to demonstrate the effectiveness of channeling strategies in reaction cascades. She studied proximity, physisorption, and electrostatic interactions, three modes discussed in a recent review paper by our collaborators and us. The paper clearly demonstrates the effectiveness of electrostatic interactions for channelling of intermediates between active sites.

The continuum approach is useful for studying long-range interactions, but interactions specific to molecular structure must be assessed using molecular-scale modeling such as molecular dynamics. Our collaborative MD study, recently published in ACS Catalysis, complements this paper well.

Electrostatic interactions are capable of channeling reaction intermediates in catalytic
cascades, but simulations predict this is true only for sufficiently high kinetic rates.

  • E. Earl and S. Calabrese Barton, “Simulation of intermediate transport in nanoscale scaffolds for multistep catalytic reactions”, Phys. Chem. Chem. Phys., 19, 15463–15470 (2017). doi:10.1039/C7CP00239D
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