In order to investigate the confined SPP modes, we calculated the cavity modes for the cavities with L values of 40 and 120 nm, respectively.
To analyze displacements associated with these three modes, we calculated normalized square atomic displacement for each mode, which is the square of the displacement of each Cα atom, normalized, so that the sum over all the DDX3X Cα atoms equals one.
To further characterize these two Myc-induced regulatory modes, we calculated changes in transcripts' translation efficiency (TE) and compared them with alterations in mRNA level (Fig 1C).
The reader should note, however, that we calculate vibrational modes in the molecule (in a frozen gold junction) rather than propagating phonon modes in some large crystal.
The analysis is based on an inverse vibration problem: Given a candidate mode shape and density distribution, we calculate the plate stiffness so that the governing equation for the plate mode shape is identically satisfied.
To determine if the conservation ratio is the same for motif modes of the same topology, we calculated the conservation ratio for one million motif modes.
For comparisons between measurements in transport and at the urban background location and between two modes that were measured simultaneously, we calculated ratios for each sampling day and calculated median and interquartile ranges of the daily ratios.
To understand these properties, we calculated the plasmonic modes (E z ) by using 3D-FDTD method.
Furthermore, we calculated the normal modes for selected snapshots from the AA-MD simulation.
We choose the top 20 AC modes to calculate the feature vector, and the parameter used for determining the size of sub-image is n = 1.
