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Many times when ploting, we not only need to set the color of the plot, but also its
transparency, Then how we set the alphaData of colorbar at the same time ?
It seems easy to do so :
data = rand(12,12);
% Transparency range 0-1, .3-1 for better appearance here
AData = rescale(- data, .3, 1);
% Draw an imagesc with numerical control over colormap and transparency
imagesc(data, 'AlphaData',AData);
colormap(jet);
ax = gca;
ax.DataAspectRatio = [1,1,1];
ax.TickDir = 'out';
ax.Box = 'off';
% get colorbar object
CBarHdl = colorbar;
pause(1e-16)
% Modify the transparency of the colorbar
CData = CBarHdl.Face.Texture.CData;
ALim = [min(min(AData)), max(max(AData))];
CData(4,:) = uint8(255.*rescale(1:size(CData, 2), ALim(1), ALim(2)));
CBarHdl.Face.Texture.ColorType = 'TrueColorAlpha';
CBarHdl.Face.Texture.CData = CData;
But !!!!!!!!!!!!!!! We cannot preserve the changes when saving them as images ：
It seems that when saving plots, the `Texture` will be refresh, but the `Face` will not :
however, object Face only have 4 colors to change(The four corners of a quadrilateral), how
can we set more colors ??
`Face` is a quadrilateral object, and we can change the `VertexData` to draw more than one little quadrilaterals:
data = rand(12,12);
% Transparency range 0-1, .3-1 for better appearance here
AData = rescale(- data, .3, 1);
%Draw an imagesc with numerical control over colormap and transparency
imagesc(data, 'AlphaData',AData);
colormap(jet);
ax = gca;
ax.DataAspectRatio = [1,1,1];
ax.TickDir = 'out';
ax.Box = 'off';
% get colorbar object
CBarHdl = colorbar;
pause(1e-16)
% Modify the transparency of the colorbar
CData = CBarHdl.Face.Texture.CData;
ALim = [min(min(AData)), max(max(AData))];
CData(4,:) = uint8(255.*rescale(1:size(CData, 2), ALim(1), ALim(2)));
warning off
CBarHdl.Face.ColorType = 'TrueColorAlpha';
VertexData = CBarHdl.Face.VertexData;
tY = repmat((1:size(CData,2))./size(CData,2), [4,1]);
tY1 = tY(:).'; tY2 = tY - tY(1,1); tY2(3:4,:) = 0; tY2 = tY2(:).';
tM1 = [tY1.*0 + 1; tY1; tY1.*0 + 1];
tM2 = [tY1.*0; tY2; tY1.*0];
CBarHdl.Face.VertexData = repmat(VertexData, [1,size(CData,2)]).*tM1 + tM2;
CBarHdl.Face.ColorData = reshape(repmat(CData, [4,1]), 4, []);
The higher the value, the more transparent it becomes
data = rand(12,12);
AData = rescale(- data, .3, 1);
imagesc(data, 'AlphaData',AData);
colormap(jet);
ax = gca;
ax.DataAspectRatio = [1,1,1];
ax.TickDir = 'out';
ax.Box = 'off';
CBarHdl = colorbar;
pause(1e-16)
CData = CBarHdl.Face.Texture.CData;
ALim = [min(min(AData)), max(max(AData))];
CData(4,:) = uint8(255.*rescale(size(CData, 2):-1:1, ALim(1), ALim(2)));
warning off
CBarHdl.Face.ColorType = 'TrueColorAlpha';
VertexData = CBarHdl.Face.VertexData;
tY = repmat((1:size(CData,2))./size(CData,2), [4,1]);
tY1 = tY(:).'; tY2 = tY - tY(1,1); tY2(3:4,:) = 0; tY2 = tY2(:).';
tM1 = [tY1.*0 + 1; tY1; tY1.*0 + 1];
tM2 = [tY1.*0; tY2; tY1.*0];
CBarHdl.Face.VertexData = repmat(VertexData, [1,size(CData,2)]).*tM1 + tM2;
CBarHdl.Face.ColorData = reshape(repmat(CData, [4,1]), 4, []);
More transparent in the middle
data = rand(12,12) - .5;
AData = rescale(abs(data), .1, .9);
imagesc(data, 'AlphaData',AData);
colormap(jet);
ax = gca;
ax.DataAspectRatio = [1,1,1];
ax.TickDir = 'out';
ax.Box = 'off';
CBarHdl = colorbar;
pause(1e-16)
CData = CBarHdl.Face.Texture.CData;
ALim = [min(min(AData)), max(max(AData))];
CData(4,:) = uint8(255.*rescale(abs((1:size(CData, 2)) - (1 + size(CData, 2))/2), ALim(1), ALim(2)));
warning off
CBarHdl.Face.ColorType = 'TrueColorAlpha';
VertexData = CBarHdl.Face.VertexData;
tY = repmat((1:size(CData,2))./size(CData,2), [4,1]);
tY1 = tY(:).'; tY2 = tY - tY(1,1); tY2(3:4,:) = 0; tY2 = tY2(:).';
tM1 = [tY1.*0 + 1; tY1; tY1.*0 + 1];
tM2 = [tY1.*0; tY2; tY1.*0];
CBarHdl.Face.VertexData = repmat(VertexData, [1,size(CData,2)]).*tM1 + tM2;
CBarHdl.Face.ColorData = reshape(repmat(CData, [4,1]), 4, []);
The code will work if the plot have AlphaData property
data = peaks(30);
AData = rescale(data, .2, 1);
surface(data, 'FaceAlpha','flat','AlphaData',AData);
colormap(jet(100));
ax = gca;
ax.DataAspectRatio = [1,1,1];
ax.TickDir = 'out';
ax.Box = 'off';
view(3)
CBarHdl = colorbar;
pause(1e-16)
CData = CBarHdl.Face.Texture.CData;
ALim = [min(min(AData)), max(max(AData))];
CData(4,:) = uint8(255.*rescale(1:size(CData, 2), ALim(1), ALim(2)));
warning off
CBarHdl.Face.ColorType = 'TrueColorAlpha';
VertexData = CBarHdl.Face.VertexData;
tY = repmat((1:size(CData,2))./size(CData,2), [4,1]);
tY1 = tY(:).'; tY2 = tY - tY(1,1); tY2(3:4,:) = 0; tY2 = tY2(:).';
tM1 = [tY1.*0 + 1; tY1; tY1.*0 + 1];
tM2 = [tY1.*0; tY2; tY1.*0];
CBarHdl.Face.VertexData = repmat(VertexData, [1,size(CData,2)]).*tM1 + tM2;
CBarHdl.Face.ColorData = reshape(repmat(CData, [4,1]), 4, []);
While searching the internet for some books on ordinary differential equations, I came across a link that I believe is very useful for all math students and not only. If you are interested in ODEs, it's worth taking the time to study it.
A First Look at Ordinary Differential Equations by Timothy S. Judson is an excellent resource for anyone looking to understand ODEs better. Here's a brief overview of the main topics covered:
  1. Introduction to ODEs: Basic concepts, definitions, and initial differential equations.
  2. Methods of Solution:
  • Separable equations
  • First-order linear equations
  • Exact equations
  • Transcendental functions
  1. Applications of ODEs: Practical examples and applications in various scientific fields.
  2. Systems of ODEs: Analysis and solutions of systems of differential equations.
  3. Series and Numerical Methods: Use of series and numerical methods for solving ODEs.
This book provides a clear and comprehensive introduction to ODEs, making it suitable for students and new researchers in mathematics. If you're interested, you can explore the book in more detail here: A First Look at Ordinary Differential Equations.
The study of the dynamics of the discrete Klein - Gordon equation (DKG) with friction is given by the equation :
In the above equation, W describes the potential function:
to which every coupled unit adheres. In Eq. (1), the variable $$ is the unknown displacement of the oscillator occupying the n-th position of the lattice, and is the discretization parameter. We denote by h the distance between the oscillators of the lattice. The chain (DKG) contains linear damping with a damping coefficient , whileis the coefficient of the nonlinear cubic term.
For the DKG chain (1), we will consider the problem of initial-boundary values, with initial conditions
and Dirichlet boundary conditions at the boundary points and , that is,
Therefore, when necessary, we will use the short notation for the one-dimensional discrete Laplacian
Now we want to investigate numerically the dynamics of the system (1)-(2)-(3). Our first aim is to conduct a numerical study of the property of Dynamic Stability of the system, which directly depends on the existence and linear stability of the branches of equilibrium points.
For the discussion of numerical results, it is also important to emphasize the role of the parameter . By changing the time variable , we rewrite Eq. (1) in the form
. We consider spatially extended initial conditions of the form: where is the distance of the grid and is the amplitude of the initial condition
We also assume zero initial velocity:
the following graphs for and
% Parameters
L = 200; % Length of the system
K = 99; % Number of spatial points
j = 2; % Mode number
omega_d = 1; % Characteristic frequency
beta = 1; % Nonlinearity parameter
delta = 0.05; % Damping coefficient
% Spatial grid
h = L / (K + 1);
n = linspace(-L/2, L/2, K+2); % Spatial points
N = length(n);
omegaDScaled = h * omega_d;
deltaScaled = h * delta;
% Time parameters
dt = 1; % Time step
tmax = 3000; % Maximum time
tspan = 0:dt:tmax; % Time vector
% Values of amplitude 'a' to iterate over
a_values = [2, 1.95, 1.9, 1.85, 1.82]; % Modify this array as needed
% Differential equation solver function
function dYdt = odefun(~, Y, N, h, omegaDScaled, deltaScaled, beta)
U = Y(1:N);
Udot = Y(N+1:end);
Uddot = zeros(size(U));
% Laplacian (discrete second derivative)
for k = 2:N-1
Uddot(k) = (U(k+1) - 2 * U(k) + U(k-1)) ;
end
% System of equations
dUdt = Udot;
dUdotdt = Uddot - deltaScaled * Udot + omegaDScaled^2 * (U - beta * U.^3);
% Pack derivatives
dYdt = [dUdt; dUdotdt];
end
% Create a figure for subplots
figure;
% Initial plot
a_init = 2; % Example initial amplitude for the initial condition plot
U0_init = a_init * sin((j * pi * h * n) / L); % Initial displacement
U0_init(1) = 0; % Boundary condition at n = 0
U0_init(end) = 0; % Boundary condition at n = K+1
subplot(3, 2, 1);
plot(n, U0_init, 'r.-', 'LineWidth', 1.5, 'MarkerSize', 10); % Line and marker plot
xlabel('$x_n$', 'Interpreter', 'latex');
ylabel('$U_n$', 'Interpreter', 'latex');
title('$t=0$', 'Interpreter', 'latex');
set(gca, 'FontSize', 12, 'FontName', 'Times');
xlim([-L/2 L/2]);
ylim([-3 3]);
grid on;
% Loop through each value of 'a' and generate the plot
for i = 1:length(a_values)
a = a_values(i);
% Initial conditions
U0 = a * sin((j * pi * h * n) / L); % Initial displacement
U0(1) = 0; % Boundary condition at n = 0
U0(end) = 0; % Boundary condition at n = K+1
Udot0 = zeros(size(U0)); % Initial velocity
% Pack initial conditions
Y0 = [U0, Udot0];
% Solve ODE
opts = odeset('RelTol', 1e-5, 'AbsTol', 1e-6);
[t, Y] = ode45(@(t, Y) odefun(t, Y, N, h, omegaDScaled, deltaScaled, beta), tspan, Y0, opts);
% Extract solutions
U = Y(:, 1:N);
Udot = Y(:, N+1:end);
% Plot final displacement profile
subplot(3, 2, i+1);
plot(n, U(end,:), 'b.-', 'LineWidth', 1.5, 'MarkerSize', 10); % Line and marker plot
xlabel('$x_n$', 'Interpreter', 'latex');
ylabel('$U_n$', 'Interpreter', 'latex');
title(['$t=3000$, $a=', num2str(a), '$'], 'Interpreter', 'latex');
set(gca, 'FontSize', 12, 'FontName', 'Times');
xlim([-L/2 L/2]);
ylim([-2 2]);
grid on;
end
% Adjust layout
set(gcf, 'Position', [100, 100, 1200, 900]); % Adjust figure size as needed
Dynamics for the initial condition , , for , for different amplitude values. By reducing the amplitude values, we observe the convergence to equilibrium points of different branches from and the appearance of values for which the solution converges to a non-linear equilibrium point Parameters:
Detection of a stability threshold : For , the initial condition , , converges to a non-linear equilibrium point.
Characteristics for , with corresponding norm where the dynamics appear in the first image of the third row, we observe convergence to a non-linear equilibrium point of branch This has the same norm and the same energy as the previous case but the final state has a completely different profile. This result suggests secondary bifurcations have occurred in branch
By further reducing the amplitude, distinct values of are discerned: 1.9, 1.85, 1.81 for which the initial condition with norms respectively, converges to a non-linear equilibrium point of branch This equilibrium point has norm and energy . The behavior of this equilibrium is illustrated in the third row and in the first image of the third row of Figure 1, and also in the first image of the third row of Figure 2. For all the values between the aforementioned a, the initial condition converges to geometrically different non-linear states of branch as shown in the second image of the first row and the first image of the second row of Figure 2, for amplitudes and respectively.
Refference:
  1. Dynamics of nonlinear lattices: asymptotic behavior and study of the existence and stability of tracked oscillations-Vetas Konstantinos (2018)
Check out this episode about PIVLab: https://www.buzzsprout.com/2107763/15106425
Join the conversation with William Thielicke, the developer of PIVlab, as he shares insights into the world of particle image velocimetery (PIV) and its applications. Discover how PIV accurately measures fluid velocities, non invasively revolutionising research across the industries. Delve into the development journey of PI lab, including collaborations, key features and future advancements for aerodynamic studies, explore the advanced hardware setups camera technologies, and educational prospects offered by PIVlab, for enhanced fluid velocity measurements. If you are interested in the hardware he speaks of check out the company: Optolution.
One of the starter prompts is about rolling two six-sided dice and plot the results. As a hobby, I create my own board games. I was able to use the dice rolling prompt to show how a simple roll and move game would work. That was a great surprise!
How to leave feedback on a doc page
Leaving feedback is a two-step process. At the bottom of most pages in the MATLAB documentation is a star rating.
Start by selecting a star that best answers the question. After selecting a star rating, an edit box appears where you can offer specific feedback.
When you press "Submit" you'll see the confirmation dialog below. You cannot go back and edit your content, although you can refresh the page to go through that process again.
Tips on leaving feedback
  • Be productive. The reader should clearly understand what action you'd like to see, what was unclear, what you think needs work, or what areas were really helpful.
  • Positive feedback is also helpful. By nature, feedback often focuses on suggestions for changes but it also helps to know what was clear and what worked well.
  • Point to specific areas of the page. This helps the reader to narrow the focus of the page to the area described by your feedback.
What happens to that feedback?
Before working at MathWorks I often left feedback on documentation pages but I never knew what happens after that. One day in 2021 I shared my speculation on the process:
> That feedback is received by MathWorks Gnomes which are never seen nor heard but visit the MathWorks documentation team at night while they are sleeping and whisper selected suggestions into their ears to manipulate their dreams. Occassionally this causes them to wake up with a Eureka moment that leads to changes in the documentation.
I'd like to let you in on the secret which is much less fanciful. Feedback left in the star rating and edit box are collected and periodically reviewed by the doc writers who look for trends on highly trafficked pages and finer grain feedback on less visited pages. Your feedback is important and often results in improvements.
Oleksandr
Oleksandr
Last activity 2024-5-28

Pricing and Licensing

Let's talk about probability theory in Matlab.
Conditions of the problem - how many more letters do I need to write to the sales department to get an answer?
To get closer to the problem, I need to buy a license under a contract. Maybe sometimes there are responsible employees sitting here who will give me an answer.
Thank you
In the MATLAB description of the algorithm for Lyapunov exponents, I believe there is ambiguity and misuse.
https://www.mathworks.com/help/predmaint/ref/lyapunovexponent.html
The lambda(i) in the reference literature signifies the Lyapunov exponent of the entire phase space data after expanding by i time steps, but in the calculation formula provided in the MATLAB help documentation, Y_(i+K) represents the data point at the i-th point in the reconstructed data Y after K steps, and this calculation formula also does not match the calculation code given by MATLAB. I believe there should be some misguidance and misunderstanding here.
According to the symbol regulations in the algorithm description and the MATLAB code, I think the correct formula might be y(i) = 1/dt * 1/N * sum_j( log( ||Y_(j+i) - Y_(j*+i)|| ) )
📚 New Book Announcement: "Image Processing Recipes in MATLAB" 📚
I am delighted to share the release of my latest book, "Image Processing Recipes in MATLAB," co-authored by my dear friend and colleague Gustavo Benvenutti Borba.
This 'cookbook' contains 30 practical recipes for image processing, ranging from foundational techniques to recently published algorithms. It serves as a concise and readable reference for quickly and efficiently deploying image processing pipelines in MATLAB.
Gustavo and I are immensely grateful to the MathWorks Book Program for their support. We also want to thank Randi Slack and her fantastic team at CRC Press for their patience, expertise, and professionalism throughout the process.
___________
David
David
Last activity 2024-5-23

Introduced in...

A colleague said that you can search the Help Center using the phrase 'Introduced in' followed by a release version. Such as, 'Introduced in R2022a'. Doing this yeilds search results specific for that release.
Seems pretty handy so I thought I'd share.
Jonny Pats
Jonny Pats
Last activity 2024-5-24

UX Night at MathWorks

Are you local to Boston?
Shape the Future of MATLAB: Join MathWorks' UX Night In-Person!
When: June 25th, 6 to 8 PM
Where: MathWorks Campus in Natick, MA
🌟 Calling All MATLAB Users! Here's your unique chance to influence the next wave of innovations in MATLAB and engineering software. MathWorks invites you to participate in our special after-hours usability studies. Dive deep into the latest MATLAB features, share your valuable feedback, and help us refine our solutions to better meet your needs.
🚀 This Opportunity Is Not to Be Missed:
  • Exclusive Hands-On Experience: Be among the first to explore new MATLAB features and capabilities.
  • Voice Your Expertise: Share your insights and suggestions directly with MathWorks developers.
  • Learn, Discover, and Grow: Expand your MATLAB knowledge and skills through firsthand experience with unreleased features.
  • Network Over Dinner: Enjoy a complimentary dinner with fellow MATLAB enthusiasts and the MathWorks team. It's a perfect opportunity to connect, share experiences, and network after work.
  • Earn Rewards: Participants will not only contribute to the advancement of MATLAB but will also be compensated for their time. Plus, enjoy special MathWorks swag as a token of our appreciation!
👉 Reserve Your Spot Now: Space is limited for these after-hours sessions. If you're passionate about MATLAB and eager to contribute to its development, we'd love to hear from you.
Sign up today to shape the future of MATLAB with MathWorks
Chen Lin
Chen Lin
Last activity 2024-5-22

Celebrating Spring: MATLAB Tulip

Bringing the beauty of MathWorks Natick's tulips to life through code!
Get the code from @Eric Ludlam.
Remix challenge: create and share with us your new breeds of MATLAB tulips!
Mathew
Mathew
Last activity 2024-5-16

Any helpful link

is there any sites available online free ai course learning except: coursera.org
Are you a Simulink user eager to learn how to create apps with App Designer? Or an App Designer enthusiast looking to dive into Simulink?
Don't miss today's article on the Graphics and App Building Blog by @Robert Philbrick! Discover how to build Simulink Apps with App Designer, streamlining control of your simulations!
Build Simulink Apps with App Designer
Chen Lin
Chen Lin
Last activity 2024-7-3

Northern Lights

Northern lights captured from this weekend at MathWorks campus ✨
Did you get a chance to see lights and take some photos?
From Alpha Vantage's website: API Documentation | Alpha Vantage
Try using the built-in Matlab function webread(URL)... for example:
% copy a URL from the examples on the site
URL = 'https://www.alphavantage.co/query?function=TIME_SERIES_DAILY&symbol=IBM&apikey=demo'
% or use the pattern to create one
tickers = [{'IBM'} {'SPY'} {'DJI'} {'QQQ'}]; i = 1;
URL = ...
['https://www.alphavantage.co/query?function=TIME_SERIES_DAILY_ADJUSTED&outputsize=full&symbol=', ...
+ tickers{i}, ...
+ '&apikey=***Put Your API Key here***'];
X = webread(URL);
You can access any of the data available on the site as per the Alpha Vantage documentation using these two lines of code but with different designations for the requested data as per the documentation.
It's fun!
Hi to all.
I'm trying to learn a bit about trading with cryptovalues. At the moment I'm using Freqtrade (in dry-run mode of course) for automatic trading. The tool is written in python and it allows to create custom strategies in python classes and then run them.
I've written some strategy just to learn how to do, but now I'd like to create some interesting algorithm. I've a matlab license, and I'd like to know what are suggested tollboxes for following work:
  • Create a criptocurrency strategy algorythm (for buying and selling some crypto like BTC, ETH etc).
  • Backtesting the strategy with historical data (I've a bunch of json files with different timeframes, downloaded with freqtrade from binance).
  • Optimize the strategy given some parameters (they can be numeric, like ROI, some kind of enumeration, like "selltype" and so on).
  • Convert the strategy algorithm in python, so I can use it with Freqtrade without worrying of manually copying formulas and parameters that's error prone.
  • I'd like to write both classic algorithm and some deep neural one, that try to find best strategy with little neural network (they should run on my pc with 32gb of ram and a 3080RTX if it can be gpu accelerated).
What do you suggest?
Dear MATLAB contest enthusiasts,
I believe many of you have been captivated by the innovative entries from Zhaoxu Liu / slanderer, in the 2023 MATLAB Flipbook Mini Hack contest.
Ever wondered about the person behind these creative entries? What drives a MATLAB user to such levels of skill? And what inspired his participation in the contest? We were just as curious as you are!
We were delighted to catch up with him and learn more about his use of MATLAB. The interview has recently been published in MathWorks Blogs. For an in-depth look into his insights and experiences, be sure to read our latest blog post: Community Q&A – Zhaoxu Liu.
But the conversation doesn't end here! Who would you like to see featured in our next interview? Drop their name in the comments section below and let us know who we should reach out to next!
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