Asymmetric surface potentials induced by Na+ binding to DPPC bilayers surrounded by solutions of (1) 145 mM KCl and 5 mM NaCl and (2) 145 mM NaCl and 5 mM KCl. Na+ ions shown in blue, K+ ions shown in green, and Cl- ions shown in orange.
Asymmetric surface potentials induced by Na+ binding to DPPC bilayers surrounded by solutions of (1) 145 mM KCl and 5 mM NaCl and (2) 145 mM NaCl and 5 mM KCl. Na+ ions shown in blue, K+ ions shown in green, and Cl- ions shown in orange.
Electrostatic surface potential of a POPC membrane calculated by APBS in an investigation of the properties of water surrounding lipid bilayers. More details are available in the publication (Lin et al, 2002).
Collaborative work between the Chivers and Baker groups investigating the molecular dynamics of NikR to better understand the molecular basis of its allosteric activity. This figure shows the principal modes of motion of the NikR molecule (foreground) as obtained by analyzing conformational covariance (background) from a molecular dynamics simulation.
Correlation of polar solvation forces from implicit and explicit solvent simulations. See publication for more details (Wagoner et al, 2004).
Na+ binding site in thrombin from collaborative work with the Di Cera lab to understand the mechanism of Na+ activation of thrombin.
An illustration of the PDB2PQR service, which prepares files for electrostatics calculations (e.g., with APBS) by adding missing atoms, assigning titration states, and assigning parameters. Please see the publication for more details (Dolinsky TJ et al, 2004).
A schematic representation of a new topology-based method for comparing electrostatic potentials developed in collaboration with the Bajaj and Zhang research groups. Please see the publication for more detail (Zhang X, et al, 2006).
Electrostatic isocontours of a microtubule as calculated with the Baker group APBS software. More details are available in the publications (Sept et al, 2003, Baker et al, 2001).
Finite element meshes generated in collaboration with the Bajaj group and used with the FEtk finite element library to solve the diffusion equation and obtain AChE substrate binding rates. More information is available in the publications (Zhang et al, 2005, Song et al, 2004a, Song et al, 2004b).
Computational models for potential paths for single-stranded DNA through the RecBCD helicase. Work done in collaboration with the Lohman and Ju labs. Please see publication for more details (Wong CJ, et al, 2006).
A cartoon of the tetrameric NikR protein, a Ni++-activated repressor studied in collaboration with the Chivers lab.
Salicylate interaction with DPPC membranes, simulated as part of a collaboration with the Brownell and Raphael research groups to understand the effect of amphiphiles on membrane electrostatics and mechanics. Please see the publication for more details (Song Y et al, 2005).