Group Abstract Group Abstract

Message Boards Message Boards

Stationary dynamics in DNA: a nonlinear Klein-Gordon approach

11 Replies
Posted 1 year ago

Just out of curiosity, do we need some kind of precision control on numerical computation because I see the x[n] values are very close to zero (e.g., between 2.0x10^-18 and -1.5x10^-18)?

POSTED BY: Sangdon Lee

In numerical computations, especially when dealing with differential equations and their solutions, precision control is important to ensure the accuracy and stability of the results. When you observe that the computed values are very close to zero, like in the range of 2.0x10^-18 and -1.5x10^-18) it might indicate that the solutions are essentially zero within the numerical precision of the computation.

Yes, they are effectively zero. Which means the solution is trivial. To check this, change the parameters to exact values and rerun like so.

(*Solve the system with an initial guess for each variable*)
initialGuess = 
  Table[{x[n], 1/100}, {n, 1, 
    numBases}]; (*or any small value close to expected solutions*)

solution = 
  FindRoot[fullSystem, initialGuess, AccuracyGoal -> 8, 
   PrecisionGoal -> 30, WorkingPrecision -> 50];

You'll get a nontrivial solution if you set boundary values to unity.

POSTED BY: Daniel Lichtblau
initialGuess = 
  Table[{x[n], 5}, {n, 1, 
    numBases}]; (*or any small value close to expected solutions*)

also with this, I got nontrivial solutions

What are the exact values for those parameters? I used the following values but I did not receive realistic results

omegaD = 1.0*10^9; (* Frequency in Hz *)
kappa = 1.0*10^-20; (* Stiffness in N m^2 *)
beta = 0.1; (* Nonlinearity coefficient *)
numBases = 100;  (*Number of base pairs,representing a segment of DNA*)
kappa = 1/
   10;    (*Elasticity constant,chosen to reflect the \
stiffness;arbitrary unit*)
omegaD = 
  2/10;   (*Frequency term,speculative and low to reflect slow \
dynamics*)
beta = 5/
   100;    (*Nonlinearity coefficient small to introduce mild \
nonlinearity*)
POSTED BY: Daniel Lichtblau

Based on your suggestions, I have created the following notebook. I hope I have correctly understood and implemented your recommendations.

I think this now makes much more sense. This probably should be incorporated in the original top post, not only in the comment. Thanks for looking into this.

POSTED BY: Sam Carrettie

@Athanasios, I think what @Sangdon is asking: why your solutions values are so small? I am wondering the same thing. Parameters of your equations are many many times larger and in such cases magnitudes of solutions expected to be of the same order if they are not divergent. Is there any explanations why your solutions have such values -- order of magnitudes less than equations -- maybe even pushing machine numeric precision?

POSTED BY: Sam Carrettie

enter image description here -- you have earned Featured Contributor Badge enter image description here Your exceptional post has been selected for our editorial column Staff Picks http://wolfr.am/StaffPicks and Your Profile is now distinguished by a Featured Contributor Badge and is displayed on the Featured Contributor Board. Thank you!

POSTED BY: EDITORIAL BOARD
Reply to this discussion
Community posts can be styled and formatted using the Markdown syntax.
Reply Preview
Attachments
Remove
or Discard