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Following on from my previous post The Non-Chaotic Duffing Equation, now we will study the chaotic behaviour of the Duffing Equation
P.s:Any comments/advice on improving the code is welcome.
The Original Duffing Equation is the following:
Let 
. This implies that
. This implies thatThen we rewrite it as a System of First-Order Equations
Using the substitution 
for 
, the second-order equation can be transformed into the following system of first-order equations:
for , the second-order equation can be transformed into the following system of first-order equations:
Exploring the Effect of γ.
% Define parameters
gamma = 0.1;
alpha = -1;
beta = 1;
delta = 0.1;
omega = 1.4;
% Define the system of equations
odeSystem = @(t, y) [y(2);
-delta*y(2) - alpha*y(1) - beta*y(1)^3 + gamma*cos(omega*t)];
% Initial conditions
y0 = [0; 0]; % x(0) = 0, v(0) = 0
% Time span
tspan = [0 200];
% Solve the system
[t, y] = ode45(odeSystem, tspan, y0);
% Plot the results
figure;
plot(t, y(:, 1));
xlabel('Time');
ylabel('x(t)');
title('Solution of the nonlinear system');
grid on;
% Plot the phase portrait
figure;
plot(y(:, 1), y(:, 2));
xlabel('x(t)');
ylabel('v(t)');
title('Phase Portrait');
grid on;
% Define the tail (e.g., last 10% of the time interval)
tail_start = floor(0.9 * length(t)); % Starting index for the tail
tail_end = length(t); % Ending index for the tail
% Plot the tail of the solution
figure;
plot(y(tail_start:tail_end, 1), y(tail_start:tail_end, 2), 'r', 'LineWidth', 1.5);
xlabel('x(t)');
ylabel('v(t)');
title('Phase Portrait - Tail of the Solution');
grid on;
% Define parameters
gamma = 0.318;
alpha = -1;
beta = 1;
delta = 0.1;
omega = 1.4;
% Define the system of equations
odeSystem = @(t, y) [y(2);
-delta*y(2) - alpha*y(1) - beta*y(1)^3 + gamma*cos(omega*t)];
% Initial conditions
y0 = [0; 0]; % x(0) = 0, v(0) = 0
% Time span
tspan = [0 800];
% Solve the system
[t, y] = ode45(odeSystem, tspan, y0);
% Plot the results
figure;
plot(t, y(:, 1));
xlabel('Time');
ylabel('x(t)');
title('Solution of the nonlinear system');
grid on;
% Plot the phase portrait
figure;
plot(y(:, 1), y(:, 2));
xlabel('x(t)');
ylabel('v(t)');
title('Phase Portrait');
grid on;
% Define the tail (e.g., last 10% of the time interval)
tail_start = floor(0.9 * length(t)); % Starting index for the tail
tail_end = length(t); % Ending index for the tail
% Plot the tail of the solution
figure;
plot(y(tail_start:tail_end, 1), y(tail_start:tail_end, 2), 'r', 'LineWidth', 1.5);
xlabel('x(t)');
ylabel('v(t)');
title('Phase Portrait - Tail of the Solution');
grid on;
% Define parameters
gamma = 0.338;
alpha = -1;
beta = 1;
delta = 0.1;
omega = 1.4;
% Define the system of equations
odeSystem = @(t, y) [y(2);
-delta*y(2) - alpha*y(1) - beta*y(1)^3 + gamma*cos(omega*t)];
% Initial conditions
y0 = [0; 0]; % x(0) = 0, v(0) = 0
% Time span with more points for better resolution
tspan = linspace(0, 200,2000); % Increase the number of points
% Solve the system
[t, y] = ode45(odeSystem, tspan, y0);
% Plot the results
figure;
plot(t, y(:, 1));
xlabel('Time');
ylabel('x(t)');
title('Solution of the nonlinear system');
grid on;
% Plot the phase portrait
figure;
plot(y(:, 1), y(:, 2));
xlabel('x(t)');
ylabel('v(t)');
title('Phase Portrait');
grid on;
% Define the tail (e.g., last 10% of the time interval)
tail_start = floor(0.9 * length(t)); % Starting index for the tail
tail_end = length(t); % Ending index for the tail
% Plot the tail of the solution
figure;
plot(y(tail_start:tail_end, 1), y(tail_start:tail_end, 2), 'r', 'LineWidth', 1.5);
xlabel('x(t)');
ylabel('v(t)');
title('Phase Portrait - Tail of the Solution');
grid on;
ax = gca;
chart = ax.Children(1);
datatip(chart,0.5581,-0.1126);
% Define parameters
gamma = 0.35;
alpha = -1;
beta = 1;
delta = 0.1;
omega = 1.4;
% Define the system of equations
odeSystem = @(t, y) [y(2);
-delta*y(2) - alpha*y(1) - beta*y(1)^3 + gamma*cos(omega*t)];
% Initial conditions
y0 = [0; 0]; % x(0) = 0, v(0) = 0
% Time span with more points for better resolution
tspan = linspace(0, 400,3000); % Increase the number of points
% Solve the system
[t, y] = ode45(odeSystem, tspan, y0);
% Plot the results
figure;
plot(t, y(:, 1));
xlabel('Time');
ylabel('x(t)');
title('Solution of the nonlinear system');
grid on;
% Plot the phase portrait
figure;
plot(y(:, 1), y(:, 2));
xlabel('x(t)');
ylabel('v(t)');
title('Phase Portrait');
grid on;
% Define the tail (e.g., last 10% of the time interval)
tail_start = floor(0.9 * length(t)); % Starting index for the tail
tail_end = length(t); % Ending index for the tail
% Plot the tail of the solution
figure;
plot(y(tail_start:tail_end, 1), y(tail_start:tail_end, 2), 'r', 'LineWidth', 1.5);
xlabel('x(t)');
ylabel('v(t)');
title('Phase Portrait - Tail of the Solution');
grid on;
Studying the attached document Duffing Equation from the University of Colorado, I noticed that there is an analysis of The Non-Chaotic Duffing Equation and all the graphs were created with Matlab. And since the code is not given I took the initiative to try to create the same graphs with the following code.
- Plotting the Potential Energy and Identifying Extrema
% Define the range of x values
x = linspace(-2, 2, 1000);
% Define the potential function V(x)
V = -x.^2 / 2 + x.^4 / 4;
% Plot the potential function
figure;
plot(x, V, 'LineWidth', 2);
hold on;
% Mark the minima at x = ±1
plot([-1, 1], [-1/4, -1/4], 'ro', 'MarkerSize', 5, 'MarkerFaceColor', 'g');
% Add LaTeX title and labels
title('Duffing Potential Energy: $$V(x) = -\frac{x^2}{2} + \frac{x^4}{4}$$', 'Interpreter', 'latex');
xlabel('$$x$$', 'Interpreter', 'latex');
ylabel('$$V(x)$$','Interpreter', 'latex');
grid on;
hold off;
- Solving and Plotting the Duffing Equation
% Define the system of ODEs for the non-chaotic Duffing equation
duffing_ode = @(t, X) [X(2);
X(1) - X(1).^3];
% Time span for the simulation
tspan = [0 10];
% Initial conditions [x(0), v(0)]
initial_conditions = [1; 1];
% Solve the ODE using ode45
[t, X] = ode45(duffing_ode, tspan, initial_conditions);
% Extract displacement (x) and velocity (v)
x = X(:, 1);
v = X(:, 2);
% Plot both x(t) and v(t) in the same figure
figure;
plot(t, x, 'b-', 'LineWidth', 2); % Plot x(t) with blue line
hold on;
plot(t, v, 'r--', 'LineWidth', 2); % Plot v(t) with red dashed line
% Add title, labels, and legend
title(' Component curve solutions to $$\ddot{x}-x+x^3=0$$','Interpreter', 'latex');
xlabel('t','Interpreter', 'latex');
ylabel('$$x(t) $$ and $$v(t) $$','Interpreter', 'latex');
legend('$$x(t)$$', ' $$v(t)$$','Interpreter', 'latex');
grid on;
hold off;
% Phase portrait with nullclines, equilibria, and vector field
figure;
hold on;
% Plot phase portrait
plot(x, v,'r', 'LineWidth', 2);
% Plot equilibrium points
plot([0 1 -1], [0 0 0], 'ro', 'MarkerSize', 5, 'MarkerFaceColor', 'g');
% Create a grid of points for the vector field
[x_vals, v_vals] = meshgrid(linspace(-2, 2, 20), linspace(-1, 1, 20));
% Compute the vector field components
dxdt = v_vals;
dvdt = x_vals - x_vals.^3;
% Plot the vector field
quiver(x_vals, v_vals, dxdt, dvdt, 'b');
% Set axis limits to [-1, 1]
xlim([-1.7 1.7]);
ylim([-1 1]);
% Labels and title
title('Phase-Plane solutions to $$\ddot{x}-x+x^3=0$$','Interpreter', 'latex');
xlabel('$$ (x)$$','Interpreter', 'latex');
ylabel('$$v(v)$$','Interpreter', 'latex');
grid on;
hold off;
The study of the dynamics of the discrete Klein - Gordon equation (DKG) with friction is given by the equation :
above equation, W describes the potential function :
The objective of this simulation is to model the dynamics of a segment of DNA under thermal fluctuations with fixed boundaries using a modified discrete Klein-Gordon equation. The model incorporates elasticity, nonlinearity, and damping to provide insights into the mechanical behavior of DNA under various conditions.
% Parameters
numBases = 200; % Number of base pairs, representing a segment of DNA
kappa = 0.1; % Elasticity constant
omegaD = 0.2; % Frequency term
beta = 0.05; % Nonlinearity coefficient
delta = 0.01; % Damping coefficient
- Position: Random initial perturbations between 0.01 and 0.02 to simulate the thermal fluctuations at the start.
- Velocity: All bases start from rest, assuming no initial movement except for the thermal perturbations.
% Random initial perturbations to simulate thermal fluctuations
initialPositions = 0.01 + (0.02-0.01).*rand(numBases,1);
initialVelocities = zeros(numBases,1); % Assuming initial rest state
The simulation uses fixed ends to model the DNA segment being anchored at both ends, which is typical in experimental setups for studying DNA mechanics. The equations of motion for each base are derived from a modified discrete Klein-Gordon equation with the inclusion of damping:
% Define the differential equations
dt = 0.05; % Time step
tmax = 50; % Maximum time
tspan = 0:dt:tmax; % Time vector
x = zeros(numBases, length(tspan)); % Displacement matrix
x(:,1) = initialPositions; % Initial positions
% Velocity-Verlet algorithm for numerical integration
for i = 2:length(tspan)
% Compute acceleration for internal bases
acceleration = zeros(numBases,1);
for n = 2:numBases-1
acceleration(n) = kappa * (x(n+1, i-1) - 2 * x(n, i-1) + x(n-1, i-1)) ...
- delta * initialVelocities(n) - omegaD^2 * (x(n, i-1) - beta * x(n, i-1)^3);
end
% positions for internal bases
x(2:numBases-1, i) = x(2:numBases-1, i-1) + dt * initialVelocities(2:numBases-1) ...
+ 0.5 * dt^2 * acceleration(2:numBases-1);
% velocities using new accelerations
newAcceleration = zeros(numBases,1);
for n = 2:numBases-1
newAcceleration(n) = kappa * (x(n+1, i) - 2 * x(n, i) + x(n-1, i)) ...
- delta * initialVelocities(n) - omegaD^2 * (x(n, i) - beta * x(n, i)^3);
end
initialVelocities(2:numBases-1) = initialVelocities(2:numBases-1) + 0.5 * dt * (acceleration(2:numBases-1) + newAcceleration(2:numBases-1));
end
% Visualization of displacement over time for each base pair
figure;
hold on;
for n = 2:numBases-1
plot(tspan, x(n, :));
end
xlabel('Time');
ylabel('Displacement');
legend(arrayfun(@(n) ['Base ' num2str(n)], 2:numBases-1, 'UniformOutput', false));
title('Displacement of DNA Bases Over Time');
hold off;
The results are visualized using a plot that shows the displacements of each base over time . Key observations from the simulation include :
- Wave Propagation: The initial perturbations lead to wave-like dynamics along the segment, with visible propagation and reflection at the boundaries.
- Damping Effects: The inclusion of damping leads to a gradual reduction in the amplitude of the oscillations, indicating energy dissipation over time.
- Nonlinear Behavior: The nonlinear term influences the response, potentially stabilizing the system against large displacements or leading to complex dynamic patterns.
% 3D plot for displacement
figure;
[X, T] = meshgrid(1:numBases, tspan);
surf(X', T', x);
xlabel('Base Pair');
ylabel('Time');
zlabel('Displacement');
title('3D View of DNA Base Displacements');
colormap('jet');
shading interp;
colorbar; % Adds a color bar to indicate displacement magnitude
% Snapshot visualization at a specific time
snapshotTime = 40; % Desired time for the snapshot
[~, snapshotIndex] = min(abs(tspan - snapshotTime)); % Find closest index
snapshotSolution = x(:, snapshotIndex); % Extract displacement at the snapshot time
% Plotting the snapshot
figure;
stem(1:numBases, snapshotSolution, 'filled'); % Discrete plot using stem
title(sprintf('DNA Model Displacement at t = %d seconds', snapshotTime));
xlabel('Base Pair Index');
ylabel('Displacement');
% Time vector for detailed sampling
tDetailed = 0:0.5:50; % Detailed time steps
% Initialize an empty array to hold the data
data = [];
% Generate the data for 3D plotting
for i = 1:numBases
% Interpolate to get detailed solution data for each base pair
detailedSolution = interp1(tspan, x(i, :), tDetailed);
% Concatenate the current base pair's data to the main data array
data = [data; repmat(i, length(tDetailed), 1), tDetailed', detailedSolution'];
end
% 3D Plot
figure;
scatter3(data(:,1), data(:,2), data(:,3), 10, data(:,3), 'filled');
xlabel('Base Pair');
ylabel('Time');
zlabel('Displacement');
title('3D Plot of DNA Base Pair Displacements Over Time');
colorbar; % Adds a color bar to indicate displacement magnitude
