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Effects of counterion valency on the damping of phonons propagating along the axial direction of liquid-crystalline DNA
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10.1063/1.2128702
/content/aip/journal/jcp/123/21/10.1063/1.2128702
http://aip.metastore.ingenta.com/content/aip/journal/jcp/123/21/10.1063/1.2128702

Figures

Image of FIG. 1.
FIG. 1.

The typical fittings of IXS spectra with the GTEE theory at are shown for four different samples with different counterions. Only the lower part of the measured spectra (circles with error bars) and their fitting curves (thick solid line) are shown to illustrate the feature of the collective excitations. The dashed line is the resolution function and the thin solid line is the extracted by the fitting. From the top to the bottom panel, the samples are calf-thymus -DNA with the different extra counterions. They are , , , and spermidine, respectively.

Image of FIG. 2.
FIG. 2.

The extracted at and for four different samples is shown. From the top to the bottom panel, the samples are calf-thymus -DNA with different extra counterions, which are , , , and spermidine, respectively.

Image of FIG. 3.
FIG. 3.

The longitudinal-acoustic-phonon-dispersion relation of calf-thymus -DNA in is shown in the top panel. The extracted sound speed is about . In the bottom panel, the approximate structure factor (blue circles) calculated through the fitted parameters is compared with the measured structure factor with a scaling factor.

Image of FIG. 4.
FIG. 4.

The longitudinal-acoustic-phonon-dispersion relation of calf-thymus -DNA in is shown in the top panel. The extracted sound speed is about . In the bottom panel, the approximate structure factor (blue circles) calculated through the fitted parameters is compared with the measured structure factor with a scaling factor.

Image of FIG. 5.
FIG. 5.

The longitudinal-acoustic-phonon-dispersion relation of calf-thymus -DNA in is shown in the top panel. The extracted sound speed is about . In the bottom panel, the approximate structure factor (blue circles) calculated through the fitted parameters is compared with the measured structure factor with a scaling factor.

Image of FIG. 6.
FIG. 6.

The longitudinal-acoustic-phonon-dispersion relation of calf-thymus -DNA in spermidine is shown in the top panel. The extracted sound speed is about . In the bottom panel, the approximate structure factor (blue circles) calculated through the fitted parameters is compared with the measured structure factor with a scaling factor.

Image of FIG. 7.
FIG. 7.

The comparison of the phonon-dispersion relation of two samples. The circles with error bars show the dispersion relation of the calf-thymus -DNA in . The solid curve is drawn to guide the eyes. The up triangles with error bars show the dispersion relation of calf-thymus -DNA in . The added divalent counterions clearly overdamped phonons in the intermediate range (12.5–). The star and cross symbols are the phonon-dispersion relations measured by INS (Ref. 7).

Image of FIG. 8.
FIG. 8.

The comparison of the phonon-dispersion relation of two samples. The circles with error bars show the dispersion relation of the calf-thymus -DNA in . The solid curve is drawn to guide the eyes. The stars with error bars show the dispersion relation of calf-thymus -DNA in spermidine. The added trivalent counterions clearly overdamped phonons in the intermediate range (12.5–).

Image of FIG. 9.
FIG. 9.

The phonon damping of different samples at different values is shown. The phonon damping of the samples with extra counterions is always larger than the results without extra counterions (circles). At the same ionic strength, it seems that the trivalent counterions can induce a larger phonon damping than the divalent counterions (see text).

Image of FIG. 10.
FIG. 10.

This figure shows the ratio between the phonon damping and the phonon frequency of DNA samples with different counterions. The circles with error bars are the results of calf-thymus -DNA in . The up triangle, star, and diamond symbols correspond to the results from the , , and samples, respectively. The solid lines are drawn to guide the eyes (see text).

Image of FIG. 11.
FIG. 11.

The intermediate scattering functions are calculated with the fitted parameters of the IXS spectra of calf-thymus -DNA in at (solid line), (dotted line), (dash dotted line), and (long dot-dashed line). The vertical dotted line drawn at shows the time window calculated through the energy resolution of the spectrometer (see text). Below this time line, the calculated is more reliable.

Image of FIG. 12.
FIG. 12.

The intermediate scattering functions are calculated with the fitted parameters of the IXS spectra of calf-thymus -DNA in at (solid line), (dotted line), (dash dotted line), and (long dot-dashed line). The vertical dotted line drawn at shows the time window calculated through the energy resolution of the spectrometer. Below this time line, the result is more reliable.

Image of FIG. 13.
FIG. 13.

The intermediate scattering functions are calculated with the fitted parameters of the IXS spectra of calf-thymus -DNA in spermidine at (solid line), (dotted line), (dash-dotted line), and (long dash-dotted line). The vertical dotted line drawn at shows the time window calculated through the energy resolution of the spectrometer. Below this time line, the result is more reliable.

Tables

Generic image for table
Table I.

Estimated fast relaxation time of DNA samples (unit:picoseconds).

Generic image for table
Table II.

Estimated slow relaxation time of DNA samples (unit:picoseconds).

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/content/aip/journal/jcp/123/21/10.1063/1.2128702
2005-12-08
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Effects of counterion valency on the damping of phonons propagating along the axial direction of liquid-crystalline DNA
http://aip.metastore.ingenta.com/content/aip/journal/jcp/123/21/10.1063/1.2128702
10.1063/1.2128702
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