ArticlePDF Available

The Schr dinger equation for a Kirchhoff elastic rod with noncircular cross section

Authors:

Abstract

The extended Schrödinger equation for the Kirchhoff elastic rod with noncircular cross section is derived using the concept of complex rigidity. As a mathematical model of supercoiled DNA, the Schrödinger equation for the rod with circular cross section is a special case of the equation derived in this paper. In the twistless case of the rod when the principal axes of the cross section are coincident with the Frenet coordinates of the centreline, the Schrödinger equation is transformed to the Duffing equation. The equilibrium and stability of the twistless rod are discussed and a bifurcation phenomenon is presented.
     K if 
      
  ̄ 纭) , 延柱) ,a  陈立群)  
  Ap M a  M eha Unha 2, 
Depam e  M ean Enneng ns  Te,S 00,Ch 
D epa of Enne M eSh  ning ,Chna 
         
Th  ScSd uaon   f   wi nar os on  ve us 
 on   .A s  m ahem a m o   D NA. ScSd     
      pe s e    de   pe.I  wi   he od  
 pa xe   os on  nc    Fr cdina o  e,t Sdi 
auon  m e o  D ui n uaon.The qum  an    w i   di,and 
 bi heno  nt 
ds   DNA   
PA CC :0D 
ntod 
Th    m    
            
      Eu.Th  
    mp    
          
   NA.  Ki  
         
   mo         
       
        I    
  Ki   He   
      wi 
  wn  As  w   
mo   DNA     
    wi     
      mp  
  we       
mo li  wh      
  . Th    
   He wa       
 n.As      
  ,t    
wi    wh     
     wi    
 
   ,a    
     i n n. A 
          
  m       
    
  ne  
ng  
   s t  wi   
.L P        
wi  . E    
 e(    
mi        P  
.A   e( 
    .wh  —a  i lo 
        we  
 d(   
    d( 
ws  
en ‘e1    S) 
  e   
De         
    ,     
n(  mi    , 
维普资讯 http://www.cqvip.com
  T hr quon   Kihh   wi  95 
 _  (a  
  s  
  COS) 
  + ) 
wh t     w   
      
  
    
         
n+  e      
n(    
   2 
  0 
wh  =  .De      
      P , F  nd 
    a尬 (n( 
 m e    ha   wing 
   ,t  wi  
   
M 1= A 1 
M 2= B 2 
M3=c   )   
wh A ,B ,C     wi  
     ,Y 
   qu  = M l+ iM 2,a  
m p  D  
D = D1+  
1= A  )+ B   
—A 
        
   
= J 
  
mp   R +      ,we 
      s( 
d(    m, 
  F-  一i  F 
M +iMa+i=0 
Th   f  
n     wr  
+I:0 
c 3+ D2  = 0 
 
d( 
 
 
   wi    F。= 0.t 
  pem i     
    ( 
wh         f ̄ 
nd   ni  rcdi  
We      
=iM 一     
       
    M     
bt   dint   
      F 
wh  d  r e   
    )  
 __  
+D+i一(C—  
 
 
 
n(       
  w n  s. Th  o 
d(     
  ri  
    ∈i 
 n(     
nd m ar y ,w  
    =  
托+ #2   3  =   
Th Ki       or   . 
W nre 
+    + F。 = 0 
M +  x M +     
 
 
 wh  d wi rpe t the a 
      
 
 
+D  +(  +2—2 
Dl  一C  
  一_+2 _ 2 
一D+D+D一c+戈.( 
= 乏 
,● 
  一 
矸 
维普资讯 http://www.cqvip.com
  Xue ’  n  al  V0 
    
+戈+D  = 
     d( 
     . an  
ng 
pe  
A od   ul   
   wi   n, A = B 
     
ir nt  
  C  )  0一T   
 mens   wi     d 
 .Th i c  ng  
d( 
一C 
= 一日 
 
 
 
u u3+ 
  
 
  u 
 一u+2 
 
   
   d( 
he di on     
   wi   n.  
o r 
 
bt 
 
   一   
  T
_+  3 
T -   ,  
 A ( =F  
 
 
  Q 
B  4   
 
  =      
Tw  
 
 
      wi ul   
   
  B)  C   
As A ≠ B wi  33    
n)(三 j   
       nc wi  
 na   .W i   
(三 丌 1=  ,2= 0  
l= A2= 0.S    wi   
   me戈= 0   
 33  ui   on .L 
3 3  33 
  oei c    mpl  
    (C一 
 
 
     = 
}w   Du     
一        
  + 一    
     de  
C  +      
 
 
    
 
 ic   in n(  
wr  
C      ( 
wh    m e m e,d  
  di  he  
g 忍    an    ur 
  s a 
  )    
  > 2       
   s = on    
quum  he . W   ,a we   
 ut e wo novi  
= - 一2 一    
 m . Th ur       
    = 1    
   m    n   
     Po  
: s 
  ( 
 
+ 
 
 
2  
\、●/  
O 
+ 
维普资讯 http://www.cqvip.com
r 『 
N o.  The hrSd uaon   K ihh  od wi  97 
        s  
  0= Mo     
      
    1    
    
    wh C = 2   
       
Re 
 
he di 
he Grnh 
 
  ( 
  w n   bi  o r   
 wi       
  fe  a wi  od  
     di  he 
Ko nd C =  
 Ki   Re Anw.   
        Ma   
  n(  
         
   Ma      5( 
 
         .5 0( 
 
】R          6( 
 
】S          m. 
03 31 
】S He        
】G    Me 
维普资讯 http://www.cqvip.com
... Shi et al [7][8] derived a class of one-dimensional fixed-state nonlinear Schrödinger equation by introducing complex vectors and complex bending moments, and gave a closed solution of the DNA molecular centerline. Xue et al. [9] further extended the results to the general case of non-circular cross sections. Wang et al. [10][11][12] used symmetry to derive some conserved quantities of elastic thin rods. ...
... Since there is no friction, the contact torque is m = 0. The elastic rod equation (3) can be expressed as complex curvature equation [9]. ...
... class of nonlinear Schrödinger equation for elastic thin rod equation is given by Ref.[8,9] but there was no further discussion, and the Euler-Lagrangian equation expressed by curvature is given. Because it contains the derivative of curvature cubed, we can not use Schrödinger equation analogy method. ...
Article
Full-text available
Inspired by Kirchhoff dynamic analogy, we write the Kirchhoff equation of thin elastic rod in form of curvature expression. Compared it with nonlinear Schrödinger equation, we extend a Jacobi elliptic function analogy solution to elastic rod equation and give a new alternative way to solve the Kirchhoff equation.
... Shi and Hearst [15] derived a time-independent, one-dimensional nonlinear Schrödinger equation for the stationary state configurations of supercoiled DNA. Xue et al. [16] extended the Schrödinger equation to fit the noncircular Kirchhoff elastic rod by using the complex rigidity. Wang et al. [17,18] rebuilt the initial Kirchhoff equations in a complex style to suit the character of obvious asymmetry and the periodically varying bending coefficients, which is embodied on the cross-section by considering the mathematical background of DNA double helix, and introduced a complex form variable solution of the torque to obtain a simplified second ordinary differential equation 2 Mathematical Problems in Engineering with single variable. ...
... As a coarse-grained description, a DNA can be approximately regarded as a thin flexible and inextensible rod or string [12,15,16]. The classical theory of elasticity describes the geometry of an elastic rod in terms of its center line R = R( ) = ( ( ), ( ), ( )), three-dimensional curve parameterized by its arc-length . ...
... Phase space of(16). ...
Article
Full-text available
The mechanical deformation of DNA is very important in many biological processes. In this paper, we consider the reduced Kirchhoff equations of the noncircular cross-section elastic rod characterized by the inequality of the bending rigidities. One family of exact solutions is obtained in terms of rational expressions for classical Jacobi elliptic functions. The present solutions allow the investigation of the dynamical behavior of the system in response to changes in physical parameters that concern asymmetry. The effects of the factor on the DNA conformation are discussed. A qualitative analysis is also conducted to provide valuable insight into the topological configuration of DNA segments.
... [14,15] Liu and Xue [11,16] studied thin elastic rod nonlinear mechanics of the DNA model. Xue et al. [17,18] developed the analytical mechanic theory of elastic rods. Furrer et al. [19] studied the relationship between the intrinsic shape and the existence of multiple stable equilibria within the context of DNA rings based on the Kirchhoff elastic rod model. ...
Article
Full-text available
Biological growth is a common phenomenon in nature, and some organisms such as DNA molecules and bacterial filaments grow in viscous media. The growth induced instability of morphoelastic rod in a viscous medium is studied in this paper. Based on the Kirchhoff kinetic analogy method, the mechanical model for growing elastic thin rod in the viscous medium is established. A perturbation analysis is used to analyze the stability of the growing elastic rod in the viscous medium. We apply the results into planar growing ring and get its criterion of instability. Take the criterion into DNA ring to discuss the influence of viscous resistance on its instability.
Article
Full-text available
Many flexible settings characterized by long, thin, and twisted structures exist in the natural world. They consistently follow some inherent principles of configuration transition, which are implicitly embodied in their structures. To understand such basic principles, the elastic rod model plays a key role in the mathematical analysis of a structure’s generic instabilities. In this article, we present a novel effective bending rigidity of the noncircular cross-section elastic rod model and an analytical strategy to reveal those inherent conformation principles. First, a transformation parameter indicates the correlation between bending and twisting variables on the cross-section, which converts the original system into a lower order system. Second, the new effective rigidity reflects the conformation information and improves consistency with numerical results. Third, a reduced-form Kirchhoff equation is obtained, which is coherent with the original system but expressed in a more compact form. Finally, bifurcation and stability analyses reveal the trivial and buckling conformations of the rod. These results will benefit further study of conformation analysis for noncircular rod models using analytical methods and possible biological applications under generic instabilities.
Article
Conserved quantities of the Cosserat elastic rod dynamics are studied according to the general theorems of dynamics. The rod dynamical equation takes the cross section of the rod as its objective of study and is expressed by two independent variables, the arc coordinate of the rod and the time, so the conserved quantities are written in the integral forms and there exist the arc coordinate conservation and the time conservation. The existence conditions and the formulas of conservations of momentum and moment of momentum are derived from the theorem of momentum and the theorem of moment of momentum respectively, which contain two cases of conserved quanties, one is the time and the other is arc coordinate. Also existence conditions and formulas of conservations of energy about time and are coordinate, which contain mechanical energy conservation, are derived from energy equations about the time and arc coordinate of the rod respectively. All of conservative motions of the rod are explained by examples. The conserved quantities in the integral form are of practical significance in both theoretical and numerical analysis for the Cosserat elastic rod dynamics.
Article
The Kirchhoff thin elastic rod models and related systems are always the important basis to research the topology and stability of the flexible structures in not only the macroscopic but also microscopic scale. Firstly the initial Kirchhoff equations are rebuilt in a complex style to suit the character of obvious asymmetry embodied on the cross section by considering the mathematical background of DNA double helix. Then we introduce a complex form variable solution of the torque, and extend the knowledge of effective bending coefficients as well as its facility in the high dimensional system by using the complicated system. As the result, a simplified second order ordinary differential equation with single variable is obtained. Furthermore the periodically varying bending coefficients of the DNA molecular are considered as the appended components to the effective bending coefficients. The whole reduction process makes the numerical simulation become not solely the exclusively eligible approach, and produces adaptable channel to quantitative analysis.
Article
The external environment affects the structural form of biological system. Many biological systems are surrounded by cell solutions, such as DNA and bacteria. The solution will offer a viscous resistance as the biological system moves in the viscous fluid. How does the viscous resistance affect the stability of biological system and what mode will be selected after instability? In this paper, we establish a super-long elastic rod model which contains the viscous resistance to model this phenomenon. The stability and instability of the super-long elastic rod in the viscous fluid are studied. The dynamic equations of motion of the super-long elastic rod in viscous fluid are given based on the Kirchhoff dynamic analogy. Then a coordinate basis vector perturbation scheme is reviewed. According to the new perturbation method, we obtain the first order perturbation representation of super-long elastic rod dynamic equation in the viscous fluid, which is a group of the second order linear partial differential equations. The stability of the super-long elastic rod can be determined by analyzing the solutions of the second order linear partial differential equations. The results are applied to a twisted planar DNA ring. The stability criterion of the twisted planar DNA ring and its critical region are obtained. The results show that the viscous resistance has no effect on the stability of super-long elastic rod dynamics, but affects its instability. The mode selection and the influence of the viscous resistance on the instability of DNA ring are discussed. The amplitude of the elastic loop becomes smaller under the influence of the viscous resistance, and a bifurcation occurs. The mode number of instability of DNA loop becomes bigger with the increase of viscous resistance.
Article
Based on Kirchhoff's analogue, generalized Hamilton canonical equations for the dynamics of super-thin elastic rod are analyzed. The Mei symmetry transformations and the theorem are introduced. And the condition and theorem of Noether conserved quantity are deduced directly by Mei symmetry for the super-thin elastic rod system. An example is given to illustrate the application of the result.
Article
The Kirchhoff thin elastic rod models and related systems are always the important basis to research the topology and stability of the flexible structures in not only the macroscopic but also microscopic scale. Firstly the initial Kirchhoff equations are rebuilt in a complex style to suit the character of obvious asymmetry embodied on the cross section by considering the mathematical background of DNA double helix. Then we introduce a complex form variable solution of the torque, and extend the knowledge of effective bending coefficients as well as its facility in the high dimensional system by using the complicated system. As the result, a simplified second order ordinary differential equation with single variable is obtained. Furthermore the periodically varying bending coefficients of the DNA molecular are considered as the appended components to the effective bending coefficients. The whole reduction process makes the numerical simulation become not solely the exclusively eligible approach, and produces adaptable channel to quantitative analysis.
Article
Considering the forces and torques acted on the Kirchhoff thin elastic ring rod with asymmetric cross section, equivalent initial torque was introduced as a new concept to reveal the quantitative relationship between the state properties and parameters of torque dynamic model, which determines the configuration of the ring rod. As there exists formally a similarity between the potential energy density function and the Hamiltonian function, the quantitative relationship was obtained, which connects the equivalent initial torque, Hamiltonian function and initial link number. With DNA ring molecule as the physical background, this paper made the nonlinear dynamic analysis of torque model, and used undecided fundamental frequency method to obtain the asymptotic expressions for steady state periodic solutions around the practical equilibrium point. When the equivalent initial torque took different values, the graph of arc length-torque and phase portrait were drawn. The curvature could be expressed by the torque function with the equivalent bending stiffness considered, which provides a new methodological way to understand and describe the stable topological configuration of DNA ring under the influences of biological enzymes.
Article
Full-text available
We have derived a generalized one-dimensional time-independent nonlinear Schrödinger equation for the stationary state configurations of supercoiled DNA, based on an elastic rod model which includes deformations of bending, twisting, shear, and extension. Closed-form solutions for the axis of DNA have been obtained in terms of elliptic functions and elliptic integrals. These solutions describe the stationary state configurations of supercoiled DNA. © 1995 American Institute of Physics.
Article
Full-text available
We have derived a time‐independent, one‐dimensional nonlinear Schrödinger equation for the stationary state configurations of supercoiled DNA. The effect of DNA self‐contact has been included analytically. For the cases of non‐self‐contact and periodic boundary conditions, closed‐form solutions have been obtained which describe the stationary state configurations of supercoiled DNA.