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Athanasios Paraskevopoulos
Last activity on 10 Mar 2024

Exploring DNA oscillations with the discrete Klein-Gordon framework

The study of nonlinear dynamical systems in lattices is an area of research with continuously growing interest.The first systematic studies of these systems emerged in the late 1930 s,thanks to the work of Frenkel and Kontorova on crystal dislocations.These studies led to the formulation of the discrete Klein-Gordon equation (DKG).Specifically,in 1939,Frenkel and Kontorova proposed a model that describes the structure and dynamics of a crystal lattice in a dislocation core.The FK model has become one of the fundamental models in physics,as it has been proven to reliably describe significant phenomena observed in discrete media.The equation we will examine is a variation of the following form:

The process described involves approximating a nonlinear differential equation through the Taylor method and simplifying it into a linear model.Let's analyze step by step the process from the initial equation to its final form.For small angles,

can be approximated through the Taylor series as:

We substitute

in the original equation with the Taylor approximation:

To map this equation to a linear model,we consider the angles

to correspond to displacements

in a mass-spring system.Thus,the equation transforms into:

We recognize that the term

expresses the nonlinearity of the system,while β is a coefficient corresponding to this nonlinearity,simplifying the expression.The final form of the equation is:

The exact value of β depends on the mapping of coefficients in the Taylor approximation and its application to the specific physical problem.Our main goal is to derive results regarding stability and convergence in nonlinear lattices under nonlinear conditions.We will examine the basic characteristics of the discrete Klein-Gordon equation:

This model is often used to describe the opening of the DNA double helix during processes such as transcription.The model focuses on the transverse motion of the base pairs,which can be represented by a set of coupled nonlinear differential equations.

 % Parameters
numBases = 50; % Number of base pairs
kappa = 0.1; % Elasticity constant
omegaD = 0.2; % Frequency term
beta = 0.05; % Nonlinearity coefficient
% Initial conditions
initialPositions = 0.01 + (0.02 - 0.01) * rand(numBases, 1);
initialVelocities = zeros(numBases, 1);
Time span
tSpan = [0 50];
>> % Differential equations
odeFunc = @(t, y) [y(numBases+1:end); ... % velocities
                   kappa * ([y(2); y(3:numBases); 0] - 2 * y(1:numBases) + [0; y(1:numBases-1)]) + ...
                   omegaD^2 * (y(1:numBases) - beta * y(1:numBases).^3)]; % accelerations
 % Solve the system
[T, Y] = ode45(odeFunc, tSpan, [initialPositions; initialVelocities]);
% Visualization
plot(T, Y(:, 1:numBases))
legend(arrayfun(@(n) sprintf('Base %d', n), 1:numBases, 'UniformOutput', false))
xlabel('Time')
ylabel('Position')
title('Dynamics of DNA Base Pairs')

% Choose a specific time for the snapshot
snapshotTime = 10;
% Find the index in T that is closest to the snapshot time
[~, snapshotIndex] = min(abs(T - snapshotTime));
% Extract the solution at the snapshot time
snapshotSolution = Y(snapshotIndex, 1:numBases);
% Generate discrete plot for the DNA model at the snapshot time
figure;
stem(1:numBases, snapshotSolution, 'filled')
title(sprintf('DNA Model Displacement at t = %d', snapshotTime))
xlabel('Base Pair Index')
ylabel('Displacement')

% Time vector for detailed sampling
tDetailed = 0:0.5:50;
% 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(T, Y(:, 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')
colormap('rainbow')
colorbar