Publications

Through a combination of classical molecular dynamics simulations and atomic resolution Brownian dynamics, we determine the permeability for carboxysomes to photosynthetic metabolites and the rate of leakage from the carbon concentrating mechanism in cyanobacteria.

D Sarkar, C Maffeo, M Sutter, A Aksimentiev, CA Kerfeld, JV Vermaas

PNAS 121 e2402277121 (2024)

Kara did a fantastic news story on this work!

Comparing molecular simulation to x-ray footprinting mass spectrometry, we determine that flat and curved BMC protein assemblies have similar pore dynamics.

S Raza, D Sarkar, LJG Chan, J Mae, M Sutter, CJ Petzold, CA Kerfeld, CY Ralston, S Gupta, JV Vermaas

ACS Omega 9 35503-35514 (2024)

This paper was selected for a cover! We also have a news story to go along with the paper.

Using NMR together with molecular simulations, we can quantify how fungal cell walls change in response to drug exposure.

M Dickwella Widanage, I Gautam, D Sarkar, F Mentink-Vigier, JV Vermaas, SY Ding, AS Lipton, T Fontaine, JP Latgé, P Wang, and T Wang

Nature Communications 15 6382 (2024)

This paper has a high-level overview written by the MSU communications team!

Using higher level theory than prior papers, we get the order of magnitude but not the temperature dependence right for electron transfer within a nanocrystal.

W Parson, J Huang, M Kulke, JV Vermaas, and DM Kramer

Journal of Chemical Physics 160 065101 (2024)

This article was chosen for the journal cover, and the PRL has a great story about this research!

Based on molecular simulation, we find that sorgoleone, a small molecule made by sorghum, is readily able to transfer from cell to cell using passive membrane permeation.

S Raza, TH Sievertsen, S Okumoto, and JV Vermaas

Phytochemistry 217 113891 (2024)

In this research article, we determine how PLAFP binds to biological membranes, and picks up a lipid, eventually transporting signaling lipids elsewhere in the cell.

M Kulke, E Kurtz, DM Boren, DM Olson, AM Koenig, S Hoffmann-Benning, and JV Vermaas

Plant Science 338 111900 (2024)

In this paper, we analyze how nanoscale vibrations in a cytochrome nanowire can influence the current carrying ability of these nanowires. Longer than normal distances that electrons need to “hop” create bottlenecks along large chains, which is ameliorated by having a wider wire for electron transfer to take place along.

M Kulke, DM Olson, J Huang, DM Kramer, and JV Vermaas

Small 19 (52) 2304013 (2023)

This research was picked up by MSU Today.

This work discusses the dynamic nature of the thylakoid membrane in response to temperature changes and its lipid composition. The study investigates the effects of temperature and isoprene content on the structure and dynamics of the membrane using molecular dynamics simulations. The results suggest that temperature affects various properties of the membrane, while isoprene concentration does not have a significant thermoprotective effect, and isoprene easily permeates the membrane.

M Kulke, SM Weraduwage, TD Sharkey, and JV Vermaas

Plant Cell & Environment 46 (8) 2273-2589 (2023)

This work was featured as a PRL news article.

In collaboration with a diverse research group from NREL and the Forest Products Lab, we measured diffusion for ions and cell wall components within models for secondary cell walls at different hydration levels. Unsurprisingly, more water to lubricate the cell wall raises diffusion. However, we predict a moisutre-induced glass transition at around 10-15% water content in secondary plant cell walls.

D Sarkar, L Bu, JE Jakes, JK Zieba, ID Kaufman, MF Crowley, PN Ciesielski, and JV Vermaas

The Cell Surface 9 100105 (2023)

With this research, we explore how diterpenes permeate across biological membranes. We find that diterpenes permeate passively at large rates across bilayers. Intriguingly, we think that the permeation may be optimized for plant-like membranes.

S Raza, M Miller, B Hamberger, and JV Vermaas

Journal of Physical Chemistry B 127 (5) 1144-1157 (2023)

This is a cool tool to help relax away ring penetration artifacts that might arise when assembling a molecular simulation system.

D Sarkar, M Kulke, and JV Vermaas

Biomolecules 13 (1) 107 (2023)

Together with collaborators at MTU, we studied how lignin nanoparticles would form under different solvent conditions.

RCA Ela, S Raza, PA Heiden, JV Vermaas, and RG Ong

ACS Applied Polymer Materials 4 (10) 6925-6935 (2022)

Together with collaborators in Germany, we refined a model for an intrinsicly disordered protein involved in Huntington’s disease.

SM Ayala Mariscal, ML Pigazzini, Y Richter, M Özel, IL Grothaus, J Protze, K Ziege, M Kulke, M ElBediwi, JV Vermaas, L Colombi Ciacchi, S Köppen, F Liu, and J Kirstein

Nature Communications 13, 4692 (2022)

Nature has a companion article that is less technical than a full-blown journal article.

We developed a new scheme for doing PBC unwrapping, which is correct even for long simulations. We develop code implementations to apply this to qwrap, pbctools, and fastpbc.

M Kulke and JV Vermaas

Journal of Chemical Theory and Computation 18 (10) 6161-6171 (2022)

Using experimental Cryo-EM data, we built a better model for the viral vector used in the AstraZeneca COVID-19 vaccine. Our collaborators linked its structure to rare blood clotting side effects for the vaccine.

AT Baker, RJ Boyd, D Sarkar, A Teijeria-Crespo, CK Chan, E Bates, K Waraich, J Vant, E Wilson, CD Truong, M Lipka-Lloyd, P Fromme, J Vermaas, D Williams, L Machiesky, M Heurich, BM Nagalo, L Coughlan, S Umlauf, P-L Chui, PJ Rizkallah, TS Cohen, AL Parker, A Singharoy, and MJ Borad

Science Advances 7, 49 (2021)

This work has been featured by the BBC, EurekaAlert, and MSU.