1 # Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
3 # This program is free software: you can redistribute it and/or modify
4 # it under the terms of the GNU General Public License as published by
5 # the Free Software Foundation, either version 3 of the License, or
6 # (at your option) any later version.
8 # This program is distributed in the hope that it will be useful,
9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11 # GNU General Public License for more details.
13 # You should have received a copy of the GNU General Public License
14 # along with this program. If not, see <http://www.gnu.org/licenses/>.
16 # The author may be contacted at <wking@drexel.edu> on the Internet, or
17 # write to Trevor King, Drexel University, Physics Dept., 3141 Chestnut St.,
18 # Philadelphia PA 19104, USA.
20 """Test a Hookian chain with Bell model unfolding rate.
22 With the constant velocity experiment and a Hookian domain, the
23 unfolding force is proportional to time, so we expect a peaked
26 Analytically, with a spring constant
30 and a pulling velocity
34 we have a loading rate
36 .. math:: df/dt = df/dx dx/dt = kv \\;,
40 .. math:: f = kvt + f_0 \\;.
42 Assuming :math:`f_0 = 0` and an unfolding rate constant :math:`K`, the
46 dp/dt = -K_0 p = -p K_0 exp(f \\Delta x/k_B T)
47 dp/df = dp/dt dt/df = -p K_0/kv exp(f \\Delta x/k_B T)
48 = -p/\\rho exp(-\\alpha/\\rho) exp(f/\\rho)
49 = -p/\\rho exp((f-\\alpha)/\\rho)
51 Where :math:`\\rho \\equiv k_B T/\\Delta x` and
52 :math:`\\alpha \\equiv \\rho log(kv/K_0\\rho)`.
54 Events with such an exponentially increasing "hazard function" follow
55 the Gumbel (minimum) probability distribution
57 P(f) = K_0 p(f) = 1/\\rho exp((f-\\alpha)/\\rho - exp((f-\\alpha)/\\rho))
59 which has a mean :math;`\\langle f \\rangle = \\alpha - \\gamma_e \\rho`
60 and a variance :math:`\\sigma^2 = \pi^2 \\rho^2 / 6`, where
61 :math:`\\gamma_e = 0.577\\ldots` is the Euler-Mascheroni constant.
64 >>> test(num_domains=5)
65 >>> test(unfolding_rate=5)
66 >>> test(unfolding_distance=5)
67 >>> test(spring_constant=5)
70 Now use reasonable protein parameters.
72 >>> test(num_domains=1, unfolding_rate=1e-3, unfolding_distance=1e-9,
73 ... temperature=300, spring_constant=0.05, velocity=1e-6)
74 >>> test(num_domains=50, unfolding_rate=1e-3, unfolding_distance=1e-9,
75 ... temperature=300, spring_constant=0.05, velocity=1e-6)
77 Problems with 50_1e-6_0.05_1e-3_1e-9_300's
78 z = K0/kv: 17106.1 (expected 20000.0)
79 Strange banded structure too. Banding most pronounced for smaller
80 forces. The banding is due to the double-unfolding problem. Reducing
81 P from 1e-3 to 1e-5 (which takes a lot longer to run), gave
82 50_1e-6_0.05_1e-3_1e-9_299, which looks much nicer.
85 from numpy import arange, exp, log, pi, sqrt
87 from ..constants import gamma_e, kB
88 from ..histogram import Histogram
89 from ..fit import HistogramModelFitter
90 from ..manager import get_manager
91 from ..sawsim import SawsimRunner
92 from ..sawsim_histogram import sawsim_histogram
95 def probability_distribution(x, params):
96 """Gumbel (minimum) probability distribution.
98 .. math:: 1/\\rho exp((x-\\alpha)/\\rho - exp((x-\\alpha)/\\rho))
100 p = params # convenient alias
101 p[1] = abs(p[1]) # cannot normalize negative rho.
102 xs = (x - p[0]) / p[1]
103 return (1.0/p[1]) * exp(xs - exp(xs))
106 class GumbelModelFitter (HistogramModelFitter):
107 """Gumbel (minimum) model fitter.
109 def model(self, params):
110 """A Gumbel (minimum) decay model.
114 .. math:: y \\propto exp((x-\\alpha)/\\rho - exp((x-\\alpha)/\\rho))
116 self._model_data.counts = (
117 self.info['binwidth']*self.info['N']*probability_distribution(
118 self._model_data.bin_centers, params))
119 return self._model_data
121 def guess_initial_params(self):
122 rho = sqrt(6) * self._data.std_dev / pi
123 alpha = self._data.mean + gamma_e * rho
126 def guess_scale(self, params):
129 def model_string(self):
130 return 'p(x) ~ exp((x-alpha)/rho - exp((x-alpha)/rho))'
132 def param_string(self, params):
134 for name,param in zip(['alpha', 'rho'], params):
135 pstrings.append('%s=%g' % (name, param))
136 return ', '.join(pstrings)
140 def bell_rate(sawsim_runner, num_domains=1, unfolding_rate=1,
141 unfolding_distance=1, temperature=1/kB, spring_constant=1,
143 loading_rate = float(spring_constant * velocity)
144 rho = kB * temperature / unfolding_distance
145 alpha = rho * log(loading_rate / (unfolding_rate * rho))
146 w = 0.1 * rho # calculate bin width (in force)
147 force_mean = alpha - gamma_e * rho
149 theory.bin_edges = arange(start=0, stop=3*force_mean, step=w)
150 theory.bin_centers = theory.bin_edges[:-1] + w/2
151 theory.counts = w*num_domains*N*probability_distribution(
152 theory.bin_centers, [alpha, rho])
155 max_force_step = w/10.0
156 max_time_step = max_force_step / loading_rate
158 '-d %(max_time_step)g -F %(max_force_step)g -v %(velocity)g '
159 '-s cantilever,hooke,%(spring_constant)g -N1 '
160 '-s folded,null -N%(num_domains)d -s unfolded,null '
161 '-k "folded,unfolded,bell,{%(unfolding_rate)g,%(unfolding_distance)g}" '
162 '-T %(temperature)g -q folded '
165 sim = sawsim_histogram(sawsim_runner, param_string, N=N,
166 bin_edges=theory.bin_edges)
168 e = GumbelModelFitter(sim)
170 sim_alpha = params[0]
171 sim_rho = abs(params[1])
172 for s,t,n in [(sim_alpha, alpha, 'alpha'), (sim_rho, rho, 'rho')]:
173 assert (s - t)/t < 0.1, 'simulation %s = %g != %g = %s' % (n,s,t,n)
174 return sim.residual(theory)
177 def test(threshold=0.2, **kwargs):
179 sr = SawsimRunner(manager=m)
181 residual = bell_rate(sawsim_runner=sr, **kwargs)
182 assert residual < threshold, residual