Sentence examples for mean force profiles from inspiring English sources

Further, we computed the energy landscape of association as PMF (Potential of Mean Force) profiles within a reasonable agreement to experiment.

Calculation of the potential of mean force profiles for the initial separation of the first few terminal basepairs in a DNA oligomer revealed that forces ranging between 130 and 230 pN are needed to disrupt the first basepair, and these values are an order of magnitude larger than those needed to disrupt basepairs in partially unzipped DNA.

To understand the underlying mechanism, the potential mean force profile, water density distribution and hydrogen bonding dynamics are analyzed to investigate both the diffusion of the water molecules near the membrane and in the bulk salt solution.

(D ) Potential of mean force profile calculated from ABF simulations using the height of the D3 region (specifically the red sphere) as the reaction coordinate.

Two different ABF runs were performed: first with a distance range between the aforementioned centers-of-mass of 1.5 Å and then piecing together these results as the initial potential of mean force profile for calculations with distance ranges of 5 Å.

The potential of mean force (PMF) profiles of amino acids revealed qualitative differences, resulting into altered orientation and the choice of preferential interacting site with the metal surface.

The simulations in each window were continued for up to 0.8 or 1.4 ns, yielding a total of 232 ns for all three cytosine unstacking potential of mean force (PMF) profiles.

The potential of mean force (PMF) or free energy profiles for cytosine unstacking were therefore obtained using explicit solvent umbrella sampling MD simulations with the original pseudodihedral restraint and are shown in Figure 2. The starting state for all these umbrella sampling simulations was the fully stacked state I shown in Figure 1.

Intermediate structures in the base flipping of the target cytosine (underlined in Figure 1A) are shown in Figure 1B with the associated free energy profiles or potentials of mean force (PMF) shown in Figure 1C.

A molecule that starts from z M descends down the W z) profile pushed by a mean force F = − dW z dz which favors its exit from the channel in either direction.

We obtained a set of profiles of the potential of mean force between protofilaments in a periodic two-dimensional sheet in aqueous solution.