Background

Josh is now a computational biophysicist within the scientific computing group. During his PhD training at the University of Illinois, Josh performed and analyzed molecular dynamics simulations at all scales. This time included graduate research opportunities throughout the national lab system at the National Renewable Energy Laboratory, Oak Ridge National Laboratory, and Sandia National Lab. This membrane-focused research was expanded during his postdoctoral tenure at the National Renewable Energy Laboratory to encompass biomass materials, with a particular focus on lignin. Josh is now applying this experience towards adapting molecular dynamics codes to trends in HPC architecture and enable advances at the bleeding edge of computational science.

Education

2010
Arizona State University
Physics, Biochemistry, Computational Math
Bachelor of Science (B.S.)
2016
University of Illinois at Urbana-Champaign
Biophysics
Doctor of Philosophy (Ph.D.)

R&D Activities Contributions

Center for Accelerated Application Readiness (CAAR) - In preparation for next-generation supercomputer Summit, the Oak Ridge Leadership Computing Facility (OLCF) selected 13 partnership projects into its Center for Accelerated Application Readiness (CAAR)…

Awards

2018 — Wiley Computing in Chemistry Outstanding Postdoc Award

2016 — Director’s Postdoctoral Fellow, National Renewable Energy Laboratory

2014 — Sandia National Laboratories Excellence in Science and Engineering Research Program Fellowship

2011 — DOE Computational Sciences Graduate Fellowship

Publications

2014 - Vermaas, J. V.; Tajkhorshid, E. A Microscopic View of Phospholipid Insertion Into Biological Membranes. J. Phys. Chem. B 2014, 118, 1754–1764, DOI: 10.1021/jp409854w.

2014 - Pogorelov, T. V.; Vermaas, J. V.; Arcario, M. J.; Tajkhorshid, E. Partitioning of Amino Acids Into a Model Membrane: Capturing the Interface. J. Phys. Chem. B 2014, 118, 1481–1492, DOI: 10.1021/jp4089113.

2014 - Vermaas, J. V.; Tajkhorshid, E. Conformational Heterogeneity of α-Synuclein in Membrane. Biochim. Biophys. Acta - Biomembr. 2014, 1838, 3107–3117, DOI: 10.1016/j.bbamem.2014.08.012.

2015 - Vermaas, J. V.; Crowley, M. F.; Beckham, G. T.; Payne, C. M. Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases. J. Phys. Chem. B 2015, 119, 6129–6143, DOI: 10.1021/acs.jpcb.5b00778.

2009 - Chamberlin, R. V.; Vermaas, J. V.; Wolf, G. H. Beyond the Boltzmann Factor for Corrections to Scaling in Ferromagnetic Materials and Critical Fluids. Eur. Phys. J. B 2009, 71, 1–6, DOI: 10.1140/epjb/e2009-00278-0.

2015 - Qi, Y.; Cheng, X.; Lee, J.; Vermaas, J. V.; Pogorelov, T. V.; Tajkhorshid, E.; Park, S.; Klauda, J. B.; Im, W. CHARMM-GUI HMMM Builder for Membrane Simulations With the Highly Mobile Membrane-Mimetic Model. Biophys. J. 2015, 109, 2012–2022, DOI: 10.1016/j.bpj.2015.10.008.

2015 - Vermaas, J. V.; Petridis, L.; Qi, X.; Schulz, R.; Lindner, B.; Smith, J. C. Mechanism of Lignin Inhibition of Enzymatic Biomass Deconstruction. Biotechnol. Biofuels 2015, 8, 217, DOI: 10.1186/s13068-015-0379-8.

2016 - Trebesch, N.; Vermaas, J. V.; Tajkhorshid, E. In Comput. Biophys. Membr. Proteins, Domene, C., Ed.; Royal Society of Chemistry: Cambridge, 2016; Chapter 7, pp 197–236, DOI: 10.1039/9781782626695-00197.

2016 - Vermaas, J. V.; Hardy, D. J.; Stone, J. E.; Tajkhorshid, E.; Kohlmeyer, A. TopoGromacs: Automated Topology Conversion From CHARMM to GROMACS Within VMD. J. Chem. Inf. Model. 2016, 56, 1112–1116, DOI: 10.1021/acs.jcim.6b00103.

2016 - Baylon, J. L.; Vermaas, J. V.; Muller, M. P.; Arcario, M. J.; Pogorelov, T. V.; Tajkhorshid, E. Atomic-Level Description of Protein–Lipid Interactions Using an Accelerated Membrane Model. Biochim. Biophys. Acta - Biomembr. 2016, 1858, 1573–1583, DOI: 10.1016/j.bbamem.2016.02.027.

2016 - Sun, C.; Taguchi, A. T.; Vermaas, J. V.; Beal, N. J.; O’Malley, P. J.; Tajkhorshid, E.; Gennis, R. B.; Dikanov, S. A. Q-Band Electron-Nuclear Double Resonance Reveals Out-Of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 From Escherichia coli. Biochemistry 2016, 55, 5714–5725, DOI: 10.1021/acs.biochem.6b00669.

2016 - Mayne, C. G.; Arcario, M. J.; Mahinthichaichan, P.; Baylon, J. L.; Vermaas, J. V.; Navidpour, L.; Wen, P.-C.; Thangapandian, S.; Tajkhorshid, E. The Cellular Membrane as a Mediator for Small Molecule Interaction With Membrane Proteins. Biochim. Biophys. Acta - Biomembr. 2016, 1858, 2290–2304, DOI: 10.1016/j.bbamem.2016.04.016.

2016 - Vermaas, J. V.; Tajkhorshid, E. Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail. Biochemistry 2017, 56, 281–293, DOI: 10.1021/acs.biochem.6b00468.

2017 - Vermaas, J. V.; Beckham, G. T.; Crowley, M. F. Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation. J. Phys. Chem. B 2017, 121, 11311–11324, DOI: 10.1021/acs.jpcb.7b08233.

2018 - Vermaas, J. V.; Bentley, G. J.; Beckham, G. T.; Crowley, M. F. Membrane Permeability of Terpenoids Explored With Molecular Simulation. J. Phys. Chem. B 2018, 122, 10349–10361, DOI: 10.1021/acs.jpcb.8b08688.

2019 - Zheng, F.; Vermaas, J. V.; Zheng, J.; Wang, Y.; Tu, T.; Wang, X.; Xie, X.; Yao, B.; Beckham, G. T.; Luo, H. Activity and Thermostability of GH5 Endoglucanase Chimeras From Mesophilic and Thermophilic Parents. Appl. Environ. Microbiol. 2019, 85, e02079–e02018, DOI: 10.1128/AEM.02079-18.

2019 - Vermaas, J. V.; Dellon, L. D.; Broadbelt, L. J.; Beckham, G. T.; Crowley, M. F. Automated Transformation of Lignin Topologies Into Atomic Structures With LigninBuilder. ACS Sustain. Chem. Eng. 2019, 7, 3443–3453, DOI: 10.1021/acssuschemeng.8b05665.

2019 - Vermaas, J. V.; Kont, R.; Beckham, G. T.; Crowley, M. F.; Gudmundsson, M.; Sandgren, M.; Ståhlberg, J.; Väljamäe, P.; Knott, B. C. The Dissociation Mechanism of Processive Cellulases. Proc. Natl. Acad. Sci. 2019, 116, 23061–23067, DOI: 10.1073/pnas.1913398116.

2019 - Vermaas, J. V.; Dixon, R. A.; Chen, F.; Mansfield, S. D.; Boerjan, W.; Ralph, J.; Crowley, M. F.; Beckham, G. T. Passive Membrane Transport of Lignin-Related Compounds. Proc. Natl. Acad. Sci. 2019, 116, 23117–23123, DOI: 10.1073/pnas.1904643116.

2019 - Orella, M. J.; Gani, T. Z. H.; Vermaas, J. V.; Stone, M. L.; Anderson, E. M.; Beckham, G. T.; Brushett, F. R.; Román-Leshkov, Y. Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis. ACS Sustain. Chem. Eng. 2019, 7, 18313–18322, DOI: 10.1021/acssuschemeng.9b03534.

2019 - Vermaas, J. V.; Crowley, M. F.; Beckham, G. T. A Quantitative Molecular Atlas for Interactions Between Lignin and Cellulose. ACS Sustain. Chem. Eng. 2019, 7, 19570–19583, DOI: 10.1021/acssuschemeng.9b04648.

Highlights