Nutsch2005_phototaxis_noncyc_repellent_light

A quantitative model of the switch cycle of an archaeal flagellar motor and its sensory control, Nutsch et al, Biophys. J. 2005 ( 16192281
) and
del Rosario et al, IET Syst. Biol. 2007 ( 17708428
). This is the non-cyclic model for
spontaneous simulations used in creating Figure 5C of del Rosario 2007.
The value plotted in the figure is ks*A_43(t)/max(ks*A_43(t)),
where ks is a model parameter. In the figure, the asymmetric model with
10% and 50% increase in parameter R_cw are compared with data for
spontaneous, repellent and attractant stimuli.

There are 5 SBML models provided:
spontaneous simulations (all light parameters Iuv, Ibl and Ior are zero)
repellent dark (sensor via SRII but with Ibl = 0)
repellent light (sensor via SRII)
attractant dark (sensor via SRI but with Iuv=Ior=0)
attractant light (sensor via SRI)
The 5 SBML files are "symmetric" models since the parameters in the
clockwise and counter-clockwise directions are equal. For the asymmetric
simulations in Figure 5c, parameter R_cw must be increased 10% and
50%.

We provide the following Matlab code to plot figure 5c using the
Systems Biology Toolbox:
---- begining of Matlab code
myodeoptions = odeset('AbsTol', 1e-10, 'RelTol', 1e-8);

dark1 = linspace(0, 2, 1000);
lighton = linspace(2, 2+0.02, 100);
dark2 = linspace(2+0.02, 60, 1000);
%for spontaneous, no need to separate since all dark
tspan = [dark1,lighton(2:end),dark2(2:end)];

sbmodspont = SBmodel('Nutsch2005_phototaxis_noncyc_spont.xml');
sbmodrepdark = SBmodel('Nutsch2005_phototaxis_noncyc_rep_dark.xml');
sbmodreplight = SBmodel('Nutsch2005_phototaxis_noncyc_rep_light.xml');
sbmodattdark = SBmodel('Nutsch2005_phototaxis_noncyc_att_dark.xml');
sbmodattlight = SBmodel('Nutsch2005_phototaxis_noncyc_att_light.xml');

R_cw_nominal = SBparameters(sbmodspont, 'R_cw');
R_cw_10inc = R_cw_nominal + 0.1*R_cw_nominal;
R_cw_50inc = R_cw_nominal + 0.5*R_cw_nominal;

sbmodspont10 = SBparameters(sbmodspont, 'R_cw', R_cw_10inc);
sbmodspont50 = SBparameters(sbmodspont, 'R_cw', R_cw_50inc);
clear sbmodspont

sbmodrepdark10 = SBparameters(sbmodrepdark, 'R_cw', R_cw_10inc);
sbmodreplight10 = SBparameters(sbmodreplight, 'R_cw', R_cw_10inc);
sbmodrepdark50 = SBparameters(sbmodrepdark, 'R_cw', R_cw_50inc);
sbmodreplight50 = SBparameters(sbmodreplight, 'R_cw', R_cw_50inc);
clear sbmodrepdark sbmodreplight

sbmodattdark10 = SBparameters(sbmodattdark, 'R_cw', R_cw_10inc);
sbmodattlight10 = SBparameters(sbmodattlight, 'R_cw', R_cw_10inc);
sbmodattdark50 = SBparameters(sbmodattdark, 'R_cw', R_cw_50inc);
sbmodattlight50 = SBparameters(sbmodattlight, 'R_cw', R_cw_50inc);
clear sbmodattdark sbmodattlight

%Asymmetric Spontaneous Simulations, 10% increase in parameter R_cw
sboutput_spont_Rcw10 = SBsimulate(sbmodspont10, 'ode15s', tspan, [], myodeoptions);
%Asymmetric Spontaneous Simulations, 50% increase in parameter R_cw
sboutput_spont_Rcw50 = SBsimulate(sbmodspont50, 'ode15s', tspan, [], myodeoptions);

%Asymmetric Repellent Simulations, 10% increase in parameter R_cw
sboutput_rep_dark1_Rcw10 = SBsimulate(sbmodrepdark10, 'ode15s', dark1, [], myodeoptions);
initcondafterdark1 = sboutput_rep_dark1_Rcw10.statevalues(end,:);

sboutput_rep_light_Rcw10 = SBsimulate(sbmodreplight10, 'ode15s', lighton, initcondafterdark1, myodeoptions);
initcondafterlight = sboutput_rep_light_Rcw10.statevalues(end,:);

sboutput_rep_dark2_Rcw10 = SBsimulate(sbmodrepdark10, 'ode15s', dark2, initcondafterlight, myodeoptions);

%Asymmetric Repellent Simulations, 50% increase in parmaeter R_cw
sboutput_rep_dark1_Rcw50 = SBsimulate(sbmodrepdark50, 'ode15s', dark1, [], myodeoptions);
initcondafterdark1 = sboutput_rep_dark1_Rcw50.statevalues(end,:);

sboutput_rep_light_Rcw50 = SBsimulate(sbmodreplight50, 'ode15s', lighton, initcondafterdark1, myodeoptions);
initcondafterlight = sboutput_rep_light_Rcw50.statevalues(end,:);

sboutput_rep_dark2_Rcw50 = SBsimulate(sbmodrepdark50, 'ode15s', dark2, initcondafterlight, myodeoptions);

%Asymmetric Attractant Simulations, 10% increase in parameter R_cw
sboutput_att_dark1_Rcw10 = SBsimulate(sbmodattdark10, 'ode15s', dark1, [], myodeoptions);
initcondafterdark1 = sboutput_att_dark1_Rcw10.statevalues(end,:);

sboutput_att_light_Rcw10 = SBsimulate(sbmodattlight10, 'ode15s', lighton, initcondafterdark1, myodeoptions);
initcondafterlight = sboutput_att_light_Rcw10.statevalues(end,:);

sboutput_att_dark2_Rcw10 = SBsimulate(sbmodattdark10, 'ode15s', dark2, initcondafterlight, myodeoptions);

%Asymmetric Attractant Simulations, 50% increase in parameter R_cw
sboutput_att_dark1_Rcw50 = SBsimulate(sbmodattdark50, 'ode15s', dark1, [], myodeoptions);
initcondafterdark1 = sboutput_att_dark1_Rcw50.statevalues(end,:);

sboutput_att_light_Rcw50 = SBsimulate(sbmodattlight50, 'ode15s', lighton, initcondafterdark1, myodeoptions);
initcondafterlight = sboutput_att_light_Rcw50.statevalues(end,:);

sboutput_att_dark2_Rcw50 = SBsimulate(sbmodattdark50, 'ode15s', dark2, initcondafterlight, myodeoptions);

A44cwindex = stateindexSB(sbmodspont10, 'A_cw43');
A44ccwindex = stateindexSB(sbmodspont10, 'A_ccw43');
ks_cw = SBparameters(sbmodspont10, 'ks_cw');
ks_cc = SBparameters(sbmodspont10, 'ks_cc');

yfig5cspontRcw10 = (sboutput_spont_Rcw10.statevalues(:, A44cwindex)*ks_cw + sboutput_spont_Rcw10.statevalues(:, A44ccwindex)*ks_cc) / ...
max(sboutput_spont_Rcw10.statevalues(:, A44cwindex)*ks_cw + sboutput_spont_Rcw10.statevalues(:, A44ccwindex)*ks_cc);
yfig5cspontRcw50 = (sboutput_spont_Rcw50.statevalues(:, A44cwindex)*ks_cw + sboutput_spont_Rcw50.statevalues(:, A44ccwindex)*ks_cc) / ...
max(sboutput_spont_Rcw50.statevalues(:, A44cwindex)*ks_cw + sboutput_spont_Rcw50.statevalues(:, A44ccwindex)*ks_cc);

A44cwindex = stateindexSB(sbmodrepdark10, 'A_cw43');
A44ccwindex = stateindexSB(sbmodrepdark10, 'A_ccw43');
ks_cw = SBparameters(sbmodrepdark10, 'ks_cw');
ks_cc = SBparameters(sbmodrepdark10, 'ks_cc');

tfig5crepRcw10 = [sboutput_rep_dark1_Rcw10.time(:)', sboutput_rep_light_Rcw10.time(:)', sboutput_rep_dark2_Rcw10.time(:)'];
A44cwrepRcw10 = [sboutput_rep_dark1_Rcw10.statevalues(:, A44cwindex);
sboutput_rep_light_Rcw10.statevalues(:, A44cwindex);
sboutput_rep_dark2_Rcw10.statevalues(:, A44cwindex)];
A44ccwrepRcw10 = [sboutput_rep_dark1_Rcw10.statevalues(:, A44ccwindex);
sboutput_rep_light_Rcw10.statevalues(:, A44ccwindex);
sboutput_rep_dark2_Rcw10.statevalues(:, A44ccwindex)];
yfig5crepRcw10 = (A44cwrepRcw10*ks_cw + A44ccwrepRcw10*ks_cc) / ...
max(A44cwrepRcw10*ks_cw + A44ccwrepRcw10*ks_cc);

tfig5crepRcw50 = [sboutput_rep_dark1_Rcw50.time(:)', sboutput_rep_light_Rcw50.time(:)', sboutput_rep_dark2_Rcw50.time(:)'];
A44cwrepRcw50 = [sboutput_rep_dark1_Rcw50.statevalues(:, A44cwindex);
sboutput_rep_light_Rcw50.statevalues(:, A44cwindex);
sboutput_rep_dark2_Rcw50.statevalues(:, A44cwindex)];
A44ccwrepRcw50 = [sboutput_rep_dark1_Rcw50.statevalues(:, A44ccwindex);
sboutput_rep_light_Rcw50.statevalues(:, A44ccwindex);
sboutput_rep_dark2_Rcw50.statevalues(:, A44ccwindex)];
yfig5crepRcw50 = (A44cwrepRcw50*ks_cw + A44ccwrepRcw50*ks_cc) / ...
max(A44cwrepRcw50*ks_cw + A44ccwrepRcw50*ks_cc);

A44cwindex = stateindexSB(sbmodattdark10, 'A_cw43');
A44ccwindex = stateindexSB(sbmodattdark10, 'A_ccw43');
ks_cw = SBparameters(sbmodattdark10, 'ks_cw');
ks_cc = SBparameters(sbmodattdark10, 'ks_cc');

tfig5cattRcw10 = [sboutput_att_dark1_Rcw10.time(:)', sboutput_att_light_Rcw10.time(:)', sboutput_att_dark2_Rcw10.time(:)'];
A44cwattRcw10 = [sboutput_att_dark1_Rcw10.statevalues(:, A44cwindex);
sboutput_att_light_Rcw10.statevalues(:, A44cwindex);
sboutput_att_dark2_Rcw10.statevalues(:, A44cwindex)];
A44ccwattRcw10 = [sboutput_att_dark1_Rcw10.statevalues(:, A44ccwindex);
sboutput_att_light_Rcw10.statevalues(:, A44ccwindex);
sboutput_att_dark2_Rcw10.statevalues(:, A44ccwindex)];
yfig5cattRcw10 = (A44cwattRcw10*ks_cw + A44ccwattRcw10*ks_cc) / ...
max(A44cwattRcw10*ks_cw + A44ccwattRcw10*ks_cc);

tfig5cattRcw50 = [sboutput_att_dark1_Rcw50.time(:)', sboutput_att_light_Rcw50.time(:)', sboutput_att_dark2_Rcw50.time(:)'];
A44cwattRcw50 = [sboutput_att_dark1_Rcw50.statevalues(:, A44cwindex);
sboutput_att_light_Rcw50.statevalues(:, A44cwindex);
sboutput_att_dark2_Rcw50.statevalues(:, A44cwindex)];
A44ccwattRcw50 = [sboutput_att_dark1_Rcw50.statevalues(:, A44ccwindex);
sboutput_att_light_Rcw50.statevalues(:, A44ccwindex);
sboutput_att_dark2_Rcw50.statevalues(:, A44ccwindex)];
yfig5cattRcw50 = (A44cwattRcw50*ks_cw + A44ccwattRcw50*ks_cc) / ...
max(A44cwattRcw50*ks_cw + A44ccwattRcw50*ks_cc);

figure
plot(tfig5crepRcw10, yfig5crepRcw10, 'y', 'linewidth', 2)
hold on
plot(tfig5crepRcw50, yfig5crepRcw50, 'k')
legend('R_{cw} increased 10%', 'R_{cw} increased 50%')
plot(sboutput_spont_Rcw10.time, yfig5cspontRcw10, 'y', 'linewidth', 2)
plot(sboutput_spont_Rcw50.time, yfig5cspontRcw50, 'k')
plot(tfig5cattRcw10, yfig5cattRcw10, 'y', 'linewidth', 2)
plot(tfig5cattRcw50, yfig5cattRcw50, 'k')
grid on
myaxis = axis; axis([0 60 0 1.2])
text(1, 1.1, 'repellent'); text(10, 1.1, 'spontaneous'); text(25, 1.1, 'attractant')
xlabel('time, s'); ylabel('reversals per time interval (1/s)')

---- end of Matlab code
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.