Ideal model thermodynamics (isometric)
- class Ideal(number_of_links, link_length, hinge_mass)
The ideal chain model thermodynamics in the isometric ensemble.
- number_of_links
The number of links in the chain.
- link_length
The length of each link in the chain in units of nm.
- hinge_mass
The mass of each hinge in the chain in units of kg/mol.
- force(end_to_end_length, temperature)
The expected force as a function of the applied end-to-end length and temperature,
\[f(\xi, T) = \frac{\partial\psi}{\partial\xi} = \frac{3kT\xi}{N_b\ell_b^2}.\]- Parameters:
end_to_end_length (numpy.ndarray) – The end-to-end length \(\xi\).
temperature (float) – The temperature \(T\).
- Returns:
The force \(f\).
- Return type:
numpy.ndarray
- nondimensional_force(nondimensional_end_to_end_length_per_link)
The expected nondimensional force as a function of the applied nondimensional end-to-end length per link,
\[\eta(\gamma) = \frac{\partial\vartheta}{\partial\gamma} = 3\gamma.\]- Parameters:
nondimensional_end_to_end_length_per_link (numpy.ndarray) – The nondimensional end-to-end length per link \(\gamma\equiv \xi/N_b\ell_b\).
- Returns:
The nondimensional force \(\eta\equiv\beta f\ell_b\).
- Return type:
numpy.ndarray
- helmholtz_free_energy(end_to_end_length, temperature)
The Helmholtz free energy as a function of the applied end-to-end length and temperature,
\[\psi(\xi, T) = -kT\ln Q(\xi, T).\]- Parameters:
end_to_end_length (numpy.ndarray) – The end-to-end length \(\xi\).
temperature (float) – The temperature \(T\).
- Returns:
The Helmholtz free energy \(\psi\).
- Return type:
numpy.ndarray
- helmholtz_free_energy_per_link(end_to_end_length, temperature)
The Helmholtz free energy per link as a function of the applied end-to-end length and temperature.
- Parameters:
end_to_end_length (numpy.ndarray) – The end-to-end length \(\xi\).
temperature (float) – The temperature \(T\).
- Returns:
The Helmholtz free energy per link \(\psi/N_b\).
- Return type:
numpy.ndarray
- relative_helmholtz_free_energy(end_to_end_length, temperature)
The relative Helmholtz free energy as a function of the applied end-to-end length and temperature,
\[\Delta\psi(\xi, T) = kT\ln\left[\frac{P_\mathrm{eq}(0)}{P_\mathrm{eq}(\xi)}\right] = \frac{3kT\xi^2}{2N_b\ell_b^2}.\]- Parameters:
end_to_end_length (numpy.ndarray) – The end-to-end length \(\xi\).
temperature (float) – The temperature \(T\).
- Returns:
The relative Helmholtz free energy \(\Delta\psi\equiv\psi(\xi,T)-\psi(0,T)\).
- Return type:
numpy.ndarray
- relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
The relative Helmholtz free energy per link as a function of the applied end-to-end length and temperature.
- Parameters:
end_to_end_length (numpy.ndarray) – The end-to-end length \(\xi\).
temperature (float) – The temperature \(T\).
- Returns:
The relative Helmholtz free energy per link \(\Delta\psi/N_b\).
- Return type:
numpy.ndarray
- nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
The nondimensional Helmholtz free energy as a function of the applied nondimensional end-to-end length per link and temperature.
- Parameters:
nondimensional_end_to_end_length_per_link (numpy.ndarray) – The nondimensional end-to-end length per link \(\gamma\equiv \xi/N_b\ell_b\).
temperature (float) – The temperature \(T\).
- Returns:
The nondimensional Helmholtz free energy \(\beta\psi=N_b\vartheta\).
- Return type:
numpy.ndarray
- nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
The nondimensional Helmholtz free energy per link as a function of the applied nondimensional end-to-end length per link and temperature.
- Parameters:
nondimensional_end_to_end_length_per_link (numpy.ndarray) – The nondimensional end-to-end length per link \(\gamma\equiv \xi/N_b\ell_b\).
temperature (float) – The temperature \(T\).
- Returns:
The nondimensional Helmholtz free energy per link \(\vartheta\equiv\beta\psi/N_b\).
- Return type:
numpy.ndarray
- nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
The nondimensional relative Helmholtz free energy as a function of the applied nondimensional end-to-end length per link,
\[\beta\Delta\psi(\gamma) = \ln\left[\frac{\mathscr{P}_\mathrm{eq}(0)}{\mathscr{P}_\mathrm{eq}(\gamma)}\right] = \frac{3}{2}\,N_b\gamma^2.\]- Parameters:
nondimensional_end_to_end_length_per_link (numpy.ndarray) – The nondimensional end-to-end length per link \(\gamma\equiv \xi/N_b\ell_b\).
- Returns:
The nondimensional relative Helmholtz free energy \(\beta\Delta\psi=N_b\Delta\vartheta\).
- Return type:
numpy.ndarray
- nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)
The nondimensional relative Helmholtz free energy per link as a function of the applied nondimensional end-to-end length per link,
\[\Delta\vartheta(\gamma) = \ln\left[\frac{\mathscr{P}_\mathrm{eq}(0)}{\mathscr{P}_\mathrm{eq}(\gamma)}\right]^{1/N_b} = \frac{3}{2}\,\gamma^2.\]- Parameters:
nondimensional_end_to_end_length_per_link (numpy.ndarray) – The nondimensional end-to-end length per link \(\gamma\equiv \xi/N_b\ell_b\).
- Returns:
The nondimensional relative Helmholtz free energy per link \(\Delta\vartheta\equiv\beta\Delta\psi/N_b\).
- Return type:
numpy.ndarray
- equilibrium_distribution(end_to_end_length)
The nondimensional equilibrium probability density of nondimensional end-to-end vectors per link as a function of the nondimensional end-to-end length per link,
\[P_\mathrm{eq}(\xi) = \frac{e^{-\beta\psi(\xi, T)}}{4\pi\int e^{-\beta\psi(\xi', T)} \,{\xi'}{}^2 d\xi'} = \left(\frac{3}{2\pi N_b\ell_b^2}\right)^{3/2}\exp\left(-\frac{3\xi^2}{2N_b\ell_b^2}\right).\]- Parameters:
end_to_end_length (numpy.ndarray) – The end-to-end length \(\xi\).
- Returns:
The equilibrium probability density \(P_\mathrm{eq}\).
- Return type:
numpy.ndarray
- nondimensional_equilibrium_distribution(nondimensional_end_to_end_length_per_link)
The nondimensional equilibrium probability density of nondimensional end-to-end vectors per link as a function of the nondimensional end-to-end length per link,
\[\mathscr{P}_\mathrm{eq}(\gamma) = \frac{e^{-\Delta\vartheta(\gamma)}}{4\pi\int e^{-\Delta\vartheta(\gamma')} \,{\gamma'}{}^2 d\gamma'} = \left(\frac{3}{2\pi N_b}\right)^{3/2}\exp\left(-\frac{3}{2}\,N_b\gamma^2\right).\]- Parameters:
nondimensional_end_to_end_length_per_link (numpy.ndarray) – The nondimensional end-to-end length per link \(\gamma\equiv \xi/N_b\ell_b\).
- Returns:
The nondimensional equilibrium probability density \(\mathscr{P}_\mathrm{eq}\equiv (N_b\ell_b)^3 P_\mathrm{eq}\).
- Return type:
numpy.ndarray
- equilibrium_radial_distribution(end_to_end_length)
The equilibrium probability density of end-to-end lengths as a function of the end-to-end length,
\[g_\mathrm{eq}(\xi) = 4\pi\xi^2 P_\mathrm{eq}(\xi).\]- Parameters:
end_to_end_length (numpy.ndarray) – The end-to-end length \(\xi\).
- Returns:
The equilibrium probability density \(g_\mathrm{eq}\).
- Return type:
numpy.ndarray
- nondimensional_equilibrium_radial_distribution(nondimensional_end_to_end_length_per_link)
The nondimensional equilibrium probability density of nondimensional end-to-end lengths per link as a function of the nondimensional end-to-end length per link,
\[\mathscr{g}_\mathrm{eq}(\gamma) = 4\pi\gamma^2 \mathscr{P}_\mathrm{eq}(\gamma).\]- Parameters:
nondimensional_end_to_end_length_per_link (numpy.ndarray) – The nondimensional end-to-end length per link \(\gamma\equiv \xi/N_b\ell_b\).
- Returns:
The nondimensional equilibrium probability density \(\mathscr{g}_\mathrm{eq}\equiv N_b\ell_b g_\mathrm{eq}\).
- Return type:
numpy.ndarray