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Center of mass distance between asODN and each dendrimer is a way to evaluate the formation of a complex between two molecules, or in this case, the degree of penetration of asODN inside the dendrimer.
Here, the center of mass distance between the two peptide chains was large, and indeed a chain separation mode was the one mostly described by the third eigenvector.
(D) Comparative Gaussian distribution of the center mass distance between Cav1.3 and ribbon in controls (black, n = 71 active zones) and latrunculin-treated (orange, n = 102 active zones) IHCs.
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We consider the following potential which is a generalization of the Wood Saxon potential and it is given by [19]: V r = - V 1 exp - r - R a 1 + exp - r - R a + V 2 exp - 2 r - R a 1 + exp - 2 r - R a, (28 where r stands for the center-of-mass distance between the projectile nucleus and the target nucleus.
Here the hydrophobic interactions were measured by the center-of-mass distance between two hydrophobic groups [17].
A hydrogen bond is identified if the distance between donor D and acceptor A is ≤3.5 Å and the angle D−H···A is ≤120°, while a side chain contact is defined if the center-mass-distance between sidechains is less than 6.5 Å.
In its standard B-form orientation (starting conformation for state I), the center-of-mass distances between C1 G5, G2 G5, and C3 G5 should be around 15.2, 11.6, and 8.3 Å, respectively.
A simple measure of strand slippage (shown in Figure 3), which can be applied to all three cytosine unstacking scenarios, can be obtained by combining two center-of-mass distances between template strand non-hydrogen base atoms: (1) G2:C4 and C1 C4 for C3 unstacking, (2) C3:C5 and G2 C5 for C4 unstacking, and (3) C4:G6 and C3 G6 for C5 unstacking.
Fig. 3 a Center of mass distance (y axis) between PAMAM NH2/PAMAM-OH dendrimers and asODN and b radius of gyration (y axis) of the dendrimer in presence of asODN as a function of simulation time (x axis) Fig. 4 a Binding energy of the complex formation between PAMAM-NH2 and PAMAM-OH and asODN, obtained from MM-GBSA method.
The plot profile tool of Image J was used to determine the mean distance between the ribbon and the Cav.3 patch (center mass distance).
Correspondingly, the center of mass (COM) distance between Tretinoin and CNT (10, 7) rapidly decreases with time up to nearly 5 ns in water.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com