polymers 0.3.7

Polymers Modeling Library
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142

#[cfg(feature = "extern")]
pub mod ex;

#[cfg(feature = "python")]
pub mod py;

mod test;

use super::
{
    nondimensional_force,
    nondimensional_helmholtz_free_energy
};
use crate::physics::BOLTZMANN_CONSTANT;
use crate::physics::single_chain::ZERO;

/// The structure of the thermodynamics of the WLC model in the isometric ensemble approximated using a Legendre transformation.
pub struct WLC
{
    /// The mass of each hinge in the chain in units of kg/mol.
    pub hinge_mass: f64,

    /// The length of each link in the chain in units of nm.
    pub link_length: f64,

    /// The number of links in the chain.
    pub number_of_links: u8,

    /// The persistance length of the chain in units of nm.
    pub persistance_length: f64,

    nondimensional_persistance_length: f64
}

/// The Gibbs free energy as a function of the applied end-to-end length and temperature, parameterized by the number of links, link length, hinge mass, and persistance length.
pub fn gibbs_free_energy(number_of_links: &u8, link_length: &f64, hinge_mass: &f64, persistance_length: &f64, end_to_end_length: &f64, temperature: &f64) -> f64
{
    let contour_length = (*number_of_links as f64)*link_length;
    nondimensional_gibbs_free_energy(number_of_links, link_length, hinge_mass, &(persistance_length/contour_length), &(end_to_end_length/contour_length), temperature)*BOLTZMANN_CONSTANT*temperature
}

/// The Gibbs free energy per link as a function of the applied end-to-end length and temperature, parameterized by the number of links, link length, hinge mass, and persistance length.
pub fn gibbs_free_energy_per_link(number_of_links: &u8, link_length: &f64, hinge_mass: &f64, persistance_length: &f64, end_to_end_length: &f64, temperature: &f64) -> f64
{
    let contour_length = (*number_of_links as f64)*link_length;
    nondimensional_gibbs_free_energy_per_link(number_of_links, link_length, hinge_mass, &(persistance_length/contour_length), &(end_to_end_length/contour_length), temperature)*BOLTZMANN_CONSTANT*temperature
}

/// The relative Gibbs free energy as a function of the applied end-to-end length and temperature, parameterized by the number of links, link length, and persistance length.
pub fn relative_gibbs_free_energy(number_of_links: &u8, link_length: &f64, persistance_length: &f64, end_to_end_length: &f64, temperature: &f64) -> f64
{
    let contour_length = (*number_of_links as f64)*link_length;
    nondimensional_relative_gibbs_free_energy(number_of_links, &(persistance_length/contour_length), &(end_to_end_length/contour_length))*BOLTZMANN_CONSTANT*temperature
}

/// The relative Gibbs free energy per link as a function of the applied end-to-end length and temperature, parameterized by the number of links, link length, and persistance length.
pub fn relative_gibbs_free_energy_per_link(number_of_links: &u8, link_length: &f64, persistance_length: &f64, end_to_end_length: &f64, temperature: &f64) -> f64
{
    let contour_length = (*number_of_links as f64)*link_length;
    nondimensional_relative_gibbs_free_energy_per_link(number_of_links, &(persistance_length/contour_length), &(end_to_end_length/contour_length))*BOLTZMANN_CONSTANT*temperature
}

/// The nondimensional Gibbs free energy as a function of the nondimensional end-to-end length per link and temperature, parameterized by the number of links, link length, hinge mass, and nondimensional persistance length.
pub fn nondimensional_gibbs_free_energy(number_of_links: &u8, link_length: &f64, hinge_mass: &f64, nondimensional_persistance_length: &f64, nondimensional_end_to_end_length_per_link: &f64, temperature: &f64) -> f64
{
    nondimensional_helmholtz_free_energy(number_of_links, link_length, hinge_mass, nondimensional_persistance_length, nondimensional_end_to_end_length_per_link, temperature) - nondimensional_force(number_of_links, nondimensional_persistance_length, nondimensional_end_to_end_length_per_link)*nondimensional_end_to_end_length_per_link*(*number_of_links as f64)
}

/// The nondimensional Gibbs free energy per link as a function of the applied nondimensional end-to-end length per link and temperature, parameterized by the number of links, link length, and nondimensional persistance length.
pub fn nondimensional_gibbs_free_energy_per_link(number_of_links: &u8, link_length: &f64, hinge_mass: &f64, nondimensional_persistance_length: &f64, nondimensional_end_to_end_length_per_link: &f64, temperature: &f64) -> f64
{
    nondimensional_gibbs_free_energy(number_of_links, link_length, hinge_mass, nondimensional_persistance_length, nondimensional_end_to_end_length_per_link, temperature)/(*number_of_links as f64)
}

/// The nondimensional relative Gibbs free energy as a function of the nondimensional end-to-end length per link, parameterized by the number of links and nondimensional persistance length.
pub fn nondimensional_relative_gibbs_free_energy(number_of_links: &u8, nondimensional_persistance_length: &f64, nondimensional_end_to_end_length_per_link: &f64) -> f64
{
    nondimensional_gibbs_free_energy(number_of_links, &1.0, &1.0, nondimensional_persistance_length, nondimensional_end_to_end_length_per_link, &300.0) - nondimensional_gibbs_free_energy(number_of_links, &1.0, &1.0, nondimensional_persistance_length, &ZERO, &300.0)
}

/// The nondimensional relative Gibbs free energy as a function of the nondimensional end-to-end length per link, parameterized by the number of links and nondimensional persistance length.
pub fn nondimensional_relative_gibbs_free_energy_per_link(number_of_links: &u8, nondimensional_persistance_length: &f64, nondimensional_end_to_end_length_per_link: &f64) -> f64
{
    nondimensional_gibbs_free_energy_per_link(number_of_links, &1.0, &1.0, nondimensional_persistance_length, nondimensional_end_to_end_length_per_link, &300.0) - nondimensional_gibbs_free_energy_per_link(number_of_links, &1.0, &1.0, nondimensional_persistance_length, &ZERO, &300.0)
}

/// The implemented functionality of the thermodynamics of the WLC model in the isometric ensemble approximated using a Legendre transformation.
impl WLC
{
    /// Initializes and returns an instance of the thermodynamics of the WLC model in the isometric ensemble approximated using a Legendre transformation.
    pub fn init(number_of_links: u8, link_length: f64, hinge_mass: f64, persistance_length: f64) -> Self
    {
        WLC
        {
            hinge_mass,
            link_length,
            number_of_links,
            persistance_length,
            nondimensional_persistance_length: persistance_length/(number_of_links as f64)/link_length
        }
    }
    /// The Gibbs free energy as a function of the applied end-to-end length and temperature.
    pub fn gibbs_free_energy(&self, end_to_end_length: &f64, temperature: &f64) -> f64
    {
        gibbs_free_energy(&self.number_of_links, &self.link_length, &self.hinge_mass, &self.persistance_length, end_to_end_length, temperature)
    }
    /// The Gibbs free energy per link as a function of the applied end-to-end length and temperature.
    pub fn gibbs_free_energy_per_link(&self, end_to_end_length: &f64, temperature: &f64) -> f64
    {
        gibbs_free_energy_per_link(&self.number_of_links, &self.link_length, &self.hinge_mass, &self.persistance_length, end_to_end_length, temperature)
    }
    /// The relative Gibbs free energy as a function of the applied end-to-end length and temperature.
    pub fn relative_gibbs_free_energy(&self, end_to_end_length: &f64, temperature: &f64) -> f64
    {
        relative_gibbs_free_energy(&self.number_of_links, &self.link_length, &self.persistance_length, end_to_end_length, temperature)
    }
    /// The relative Gibbs free energy per link as a function of the applied end-to-end length and temperature.
    pub fn relative_gibbs_free_energy_per_link(&self, end_to_end_length: &f64, temperature: &f64) -> f64
    {
        relative_gibbs_free_energy_per_link(&self.number_of_links, &self.link_length, &self.persistance_length, end_to_end_length, temperature)
    }
    /// The nondimensional Gibbs free energy as a function of the applied nondimensional end-to-end length per link and temperature.
    pub fn nondimensional_gibbs_free_energy(&self, nondimensional_end_to_end_length_per_link: &f64, temperature: &f64) -> f64
    {
        nondimensional_gibbs_free_energy(&self.number_of_links, &self.link_length, &self.hinge_mass, &self.nondimensional_persistance_length, nondimensional_end_to_end_length_per_link, temperature)
    }
    /// The nondimensional Gibbs free energy per link as a function of the applied nondimensional end-to-end length per link and temperature.
    pub fn nondimensional_gibbs_free_energy_per_link(&self, nondimensional_end_to_end_length_per_link: &f64, temperature: &f64) -> f64
    {
        nondimensional_gibbs_free_energy_per_link(&self.number_of_links, &self.link_length, &self.hinge_mass, &self.nondimensional_persistance_length, nondimensional_end_to_end_length_per_link, temperature)
    }
    /// The nondimensional relative Gibbs free energy as a function of the applied nondimensional end-to-end length per link.
    pub fn nondimensional_relative_gibbs_free_energy(&self, nondimensional_end_to_end_length_per_link: &f64) -> f64
    {
        nondimensional_relative_gibbs_free_energy(&self.number_of_links, &self.nondimensional_persistance_length, nondimensional_end_to_end_length_per_link)
    }
    /// The nondimensional relative Gibbs free energy per link as a function of the applied nondimensional end-to-end length per link.
    pub fn nondimensional_relative_gibbs_free_energy_per_link(&self, nondimensional_end_to_end_length_per_link: &f64) -> f64
    {
        nondimensional_relative_gibbs_free_energy_per_link(&self.number_of_links, &self.nondimensional_persistance_length, nondimensional_end_to_end_length_per_link)
    }
}