There are several ways to calculate the PMF in |Gromacs|, probably the most common of which is to make use of the pull code. The steps for obtaining a PMF using umbrella sampling, which allows for sampling of statistically-improbable states, are: * Generate a series of configurations along...
Additionally, the Lorentz force equation can be used to calculate the deflection of a plasma jet by a magnetic field, taking into consideration factors such as electric fields and self-induced magnetic fields. The kinetic energy density of the plasma must overcome the magnetic energy density of ...
These are biologically important questions because the answer to the first two questions could impact our understanding of how protein homeostasis is maintained in cells. The answer to the final question would help to explain how synonymous mutations can have long term impacts on protein structure and...
The centrifugal force (Fcent) on the side of wells was used to calculate the parameters of contact mechanics (r′, L′, pcent; Fig. 6 A), instead of the buoyant and gravitational forces:(6)Fcent=mω2l,where ω is the angular velocity of the rotating bead (360 rpm = 0.11 m/s),...
We next asked how it is possible that long-lived misfolded proteins are able to bypass the post-translational cellular chaperone machinery. To address this question we used coarse-grained Langevin dynamics to calculate the dissociation constant between the chaperone GroEL and three distinct conformational...
(G, N, P, Q, S, T) and hydrophobic (A, C, I, L, M, V) amino acid residues (hydrophobic and polar, respectively), and fractions of residues of A, L, and S. Notably, except for the pLDDT of AF2 models, the experimental ProS structures were employed to calculate the structural ...