Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains

Table 1 Evaluation of the measurement accuracy using synthetic polymers with known persistence lengths as test samples

^*Sample	N chains	Persistence length according to all 3 measures (nm)^†(C_D)^‡[interval; nm]
^*Sample	N chains	^▲ < R² > = f(ℓ)	^▲ < cos θ > = f(ℓ)	^▲ < δ² > = f(ℓ)
^§SP50	38	^§68 ± 3 (0.996)	^§70 ± 6 (0.927)	–
^§SP50	38	[0; 500]	[20; 500]	–
SP750	78	777 ± 114 (0.999)	728 ± 32 (0.968)	538 ± 28 (0.961)
SP750	78	[0; 1900]	[50; 1000]	[0; 300]
^¶SP2500-1	44	2867 ± 372 (0.999)	2599 ± 506 (0.947)	2986 ± 914 (0.923)
^¶SP2500-1	44	[0; 600]	[20; 500]	[0; 600]
^¶SP2500-2	35	3047 ± 496 (0.999)	3015 ± 590 (0.966)	2894 ± 608 (0.991)
^¶SP2500-2	35	[0; 2500]	[40; 2500]	[0; 1200]
^¤SP2500-2	35	2525 ± 191 (0.999)	2542 ± 214 (0.960)	2441 ± 318 (0.966)
^¤SP2500-2	35	[0; 600]	[40; 600]	[0; 600]
SP8000	41	7280 ± 1060 (0.999)	6669 ± 494 (0.789)	8262 ± 1083 (0.949)
SP8000	41	[0; 1200]	[20; 700]	[0; 800]
SP1e5	48	64264 ± 5514 (0.999)	–	86475 ± 14480 (0.985)
SP1e5	48	[0; 3500]	–	[0; 3500]
SP5.2e6	70	1.49e5 ± 0.13e5 (0.999)	–	5.64e6 ± 0.85e6 (0.994)
SP5.2e6	70	[0; 19500]	–	[0; 18000]

Refer to Additional file1: Note S4 and Table S1 for details on how the data in this table was generated with Synchains and analyzed with Easyworm.
^*Each number in the sample names corresponds to the persistence length P (in nm) that was used to generate one particular synthetic polymer (SP), e.g. for SP50, P was set to 50 nm.
^†C_D is the coefficient of determination (usually noted "R²" but not here because R is already used to refer to the end-to-end distance).
^‡[interval] is the range of distance ℓ (along the chain contour) on which each fit was made.
^▲Mean square of the end-to-end distance R, tangent-tangent correlations < cos θ > and mean square of the deviations δ to secant midpoint, as described in Eqs. 1–3.
^§We excluded chains displaying non-self-avoiding random walk from the analysis of SP50 chains (see Additional file1: Figure S5). Therefore the value of 70 nm for P was expected[3].
^¶SP2500-1 and SP2500-2 differ by their contour length (respectively 0.4 ± 0.2 and 5.3 ± 2.8 μm).
^¤The calculated value for P is closer to the theoretical value than in the same sample in the above line. This is probably due a larger amount of data available for the shortest ℓ distances, hence rendering statistical analysis more reliable.

ISSN: 1751-0473