Skip to main content
Photo of Joshua Vermaas.

Josh Vermaas

Postdoctoral Researcher-Directors Fellowship | 303-384-6284
Orcid ID
Google Scholar

Research Interests

I use molecular dynamics simulations to explore biological interfaces, such as those found at the cell membrane or in lignocellulosic biomass. In particular, molecular dynamics can see in molecular detail the interactions at these interfaces, which provide mechanistic insight that can inform experiment and guide research toward fruitful results.

Areas of Expertise

  • Molecular dynamics

  • Compound parameterization

  • Scientific visualization


  • Ph.D., Biophysics, University of Illinois Urbana-Champaign, 2016

  • B.S., Physics, Biochemistry, and Computational Math, Arizona State University, 2010

Featured Publications

  1. "Electrostatic Lock in the Transport Cycle of the Multidrug Resistance Transporter EmrE", PNAS (2018)

    EmrE in a membrane context, highlighting specific hydrogen bonds that break protein symmetry.

  2. "Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation," Journal of Physical Chemistry B (2017)

    Translocation of fatty acyl products from aqueous solution across a lipid bilayer to the organic phase, shown with four layers of spheres: yellow, red and white, grey, and red and white. There are five green sphere columns interspersed throughout.

  3. "Mechanism of Lignin Inhibition of Enzymatic Biomass Deconstruction," Biotechnology for Biofuels (2015)
    Simulation snapshot of lignocellulosic biomass along with cellolytic enzymes, shown by a series of three sets of horizontal red girder shapes with blue and green globules intertwined.

  4. "Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases," Journal of Physical Chemistry B (2015)
    Activity summary of lytic polysaccharide monooxygenases, and their effect on the crystallinity of cellulose juxtaposed on top of a forest scene. Cellulose Fibril, LPMO Oxidation, Decrystallization, and Cellulase Action are shown as series of grey and red intertwined rods meshed together and inset in ovals.

  5. "A Microscopic View of Phospholipid Insertion into Biological Membranes," Journal of Physical Chemistry B (2014)
    Lipid insertion (shown as blue, red, black, and yellow intertwined rods in a mesh formation) into a biological membrane (shown as tan intertwined rods with some layers of red and blue rods in a mesh formation).

Awards and Honors

  • National Renewable Energy Laboratory Director’s Postdoctoral Fellowship

  • Sandia National Laboratories Excellence in Science and Engineering Research Program Fellowship

  • U.S. Department of Energy Computational Science Graduate Fellowship