multi_locus_analysis.analytical

For computing analytical results relevant to diffusing loci.

When possible, prefer the functions in the WLCSIM module instead, as they have been more recently tested.

multi_locus_analysis.analytical.frac_cv(t, alpha, kbT=1, xi=1)

Velocity autocorrelation of a fractionally-diffusing particle. Weber, Phys Rev E, 2010 (Eq 32)

multi_locus_analysis.analytical.frac_discrete_cv(t, delta, alpha, kbT=1, xi=1)

Discrete velocity autocorrelation of a fractionally-diffusing particle. Weber, Phys Rev E, 2010 (Eq 33)

multi_locus_analysis.analytical.frac_discrete_cv_normalized(t, delta, alpha)

Normalized discrete velocity autocorrelation of a fractionally-diffusing particle. Should be equivalent to

frac_discrete_cv(t, delta, 1, 1)/frac_discrete_cv(0, delta, 1, 1)

Lampo, BPJ, 2016 (Eq 5)

multi_locus_analysis.analytical.frac_msd(t, alpha, kbT=1, xi=1)

MSD of fractionally diffusing free particle.

Weber, Phys Rev E, 2010 (Eq 10)

multi_locus_analysis.analytical.rouse_cv_mid(t, alpha, b, N, kbT=1, xi=1, min_modes=1000)

Velocity autocorrelation of midpoint of a rouse polymer.

Weber Phys Rev E 2010, Eq. 33.

multi_locus_analysis.analytical.rouse_cvv_ep(t, delta, p, alpha, b, N, kbT=1, xi=1)

Term in parenthesis in Lampo, BPJ, 2016 Eq. 10.

multi_locus_analysis.analytical.rouse_large_cvv_g(t, delta, deltaN, b, kbT=1, xi=1)

Cvv^delta(t) for infinite polymer.

Lampo, BPJ, 2016 Eq. 16.

multi_locus_analysis.analytical.rouse_mid_msd(t, alpha, b, N, kbT=1, xi=1, num_modes=1000)

Weber Phys Rev E 2010, Eq. 24.

multi_locus_analysis.analytical.rouse_mode(p, n, N=1)

Eigenbasis for Rouse model.

Indexed by p, depends only on position n/N along the polymer of length N. N=1 by default.

Weber, Phys Rev E, 2010 (Eq 14)

multi_locus_analysis.analytical.rouse_mode_coef(p, b, N, kbT=1)

k_p: Weber Phys Rev E 2010, after Eq. 18.

multi_locus_analysis.analytical.rouse_mode_corr(p, t, alpha, b, N, kbT=1, xi=1)

Weber Phys Rev E 2010, Eq. 21.

multi_locus_analysis.analytical.simple_rouse_mid_msd(t, b, N, kbT=1, xi=1, num_modes=1000)

modified from Weber Phys Rev E 2010, Eq. 24.

multi_locus_analysis.analytical.tDeltaN(n1, n2, alpha, b, kbT, xi)

Lampo et al, BPJ, 2016, eq 11

multi_locus_analysis.analytical.tR(alpha, b, N, kbT=1, xi=1)

Lampo et al, BPJ, 2016, eq 8