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Manuscript Number: CNSNS-D-09-00004

Title: THERMODYNAMICS AND DYNAMICS OF DNA WITH POTENTIALS OF MORSE

MODIFIED

Article Type: Research Paper

Section/Category:

Keywords: Hill equations, breather stability, center of energy, ground state wave
function,pseudoSchrodinger equation,hybrid potential

Corresponding Author: professor HERNAN CORTEZ GUTIERREZ, MASTER

Corresponding Author's Institution: UNIVERSIDAD NACIONAL DEL CALLAO

First Author: HERNAN C GUTIERREZ, DOCTOR

Order of Authors: HERNAN C GUTIERREZ, DOCTOR; HERNAN CORTEZ GUTIERREZ,

MASTER

Manuscript Region of Origin:

Abstract: Abstract: In this paper we solve the "pseudoSchrodinger" equation using the finite
difference related with the study of the thermodynamic properties of the DNA denaturation.Also we
study stationary breathers using Fourier's series in the Klein Gordon equations for the Peyrard-
Bishop model with the original Morse potential and a symmetric version of this potential. The
stability is analyzed in the context of the Aubry's band theory and the Floquet theory in Hill
linearized equations corresponding to perturbations in the periodic solution of the model. The
mobile breather is also studied by the analysis close to an instability threshold. The mobile breather
can be constructed using the profile of the stationary breather and the initial velocity associated to
the center of energy calculated by the gradient method. In addition, we use the concept of center of
energy to study the breather interaction with impurity on the lattice. The results obtained for the
Symmetric Peyrard-Bishop (SPB) model is compared with the original Peyrard-Bishop (PB) model
for DNA.
Cover Letter

SR. EDITOR DR. LOU:

THIS PAPER HAVE SOME RESULTS ABOUT DNA WITH A NEW MODEL.
* Manuscript
Click here to view linked References

THERMODYNAMICS AND DYNAMICS OF DNA WITH POTENTIALS OF

MORSE MODIFIED

Hernán Cortez Gutiérrez 1,2, Elso Drigo Filho 1 , José Roberto Ruggiero 1 Jesus Cuevas Maraver 3
1
UNESP, Universidade Estadual Paulista, Departamento de Física, Rua Cristovão Colombo, 2265, 15054-000, São

José Rio Preto, Brasil.

2
UNAC, Universidad Nacional Del Callao, Facultad de Ciências de la Salud,Av. Juan Pablo II s/n, Bellavista,

Callao, Perú.
3
Universidad de Sevilla, Departamento de Fisica, Av. Reina Mercedes II s/n, 41012, Sevilla, España.

Abstract: In this paper we solve the “ pseudoSchrodinger ” equation using the finite difference related

with the study of the thermodynamic properties of the DNA denaturation. We study stationary breathers

by using Fourier’s series in the Klein Gordon equations for the Peyrard-Bishop model with the original

Morse potential and a symmetric version of this potential. The stability is analyzed in the context of the

Aubry’s band theory and the Floquet theory in Hill linearized equations corresponding to perturbations in

the periodic solution of the model. The mobile breather is also studied by the analysis close to an

instability threshold. The mobile breather can be constructed using the profile of the stationary breather

and the initial velocity associated to the center of energy calculated by the gradient method. In addition,

we use the concept of center of energy to study the breather interaction with impurity on the lattice. The

results obtained for the Symmetric Peyrard-Bishop model is compared with the original Peyrard-Bishop

model for DNA. Finally, we use Finite-difference methods for determine the mean value of the

displacement for the “Hump Morse” .

Keywords: Hill equation, breather stability, center of energy, Finite-difference methods, ground state

wave function, “pseudoSchrödinger” equation , hybrid potential.

1. INTRODUCTION

Phase transition have been characterized in many different ways, for instance, by topological change

[1, 2], by discontinuity on the curve of the mean strength of the basis pair in the DNA analysis [3] and by

using a domain wall approach [1, 4]. The phase transition is an important effect in order to understand the

physics aspects of the model and it is related with the stability of the lattice.
 Dynamics properties of the PB model are extensively studied on the literature (see, for instance, ref.

[5, 6, 7] and references therein). These studies are concerning localization of energy [8, 9], breather

trapping [10, 11], breather collision [12] and other ones. Different mathematical tools have been used to

study the dynamics of this kind of models as the Floquet Theorem [13] and the Band Theory of

Aubry[14].

The study on effect of impurity on the breathers is a fundamental aspect in real systems, for instance,

it can be an important ingredient by the energy localization and breathes trapping. A common treatment

of impurity in PB model use semi-discrete approximation to obtain solutions on the lattice [11]. In a

discrete lattice it is possible to introduce impurity by a local deformation of the potential or mass. Then,

one way to introduce impurity is by change the deep of the potential in just one site of the lattice [2, 10].

On the other hand, the impurity can be introduced by a local variation on the mass as it is made in ref.

[15].

In contrast with the great number of papers dedicated to the PB model, the dynamic of symmetric

version of this model is not studied until the moment. The main contribution of this work is complete this

lacuna and explore the thermodynamic properties solving the pseudoSchrodinger equation of the transfer

integral [7] for the “Hump Morse” . The results for the symmetric Peyrard-Bishop model (SPB) obtained

in this work are comparative with the original PB model.

The mathematical tools used in the theoretical study of the problem are the anticontinuum Theorem,

Floquet Theorem (FT) and Aubry’s Band Theory. The numerical tools used in the present work are

Newton’s Method (NM), vector gradient method, Fourier series , Runge-Kutta method (RKM) and Finite

Difference Method (FDM).

This paper is organized as follows. In the section 2, the models studied are present. In section 3 the

breather stability are discussed. In the section 4, the results for stability and mobility in the PB and SPB

model are presented. The breather trapping for both models is analyzed in section 5. The section 6 will be

devoted to the average stretching of the base pairs in DNA model with the Morse original and the

modified potential. Finally, we pose the conclusions in the section 7.

2. THE MODELS

In the models adopts here [3, 7], DNA molecule is mimicked by two parallel strands composed each

one of a chain of masses (the nucleotides) coupled elastically one to another and coupled to a parallel
mass on the other strand by a Morse potential simulating the H-bond between the bases in the

macromolecule. The Hamiltonian for the BP model is given by

N
m 2 N
 N
 N
H  ( xn  y n2 )    xn  xn 1     yn  yn 1   V  yn  xn 
2 2
(1)
n 1 2 n 1 2 n 1 2 n 1

or in the general form :

N N N N
m 2
H  ( xn  y n2 )  W  xn  xn 1   W  yn  yn 1   V  yn  xn 
2 2
(1.1)
n 1 2 n 1 n 1 n 1

where W is given by :

 (1  e  ( y n  y n 1 )
)
W (1.2)
2
where xn and yn denote the relative displacements of the nth nucleotide bases at each strand and N

denotes the number of nucleotides. This expression can be viewed as a non-harmonic interaction with the

parameter ρ≠0. For simplicity, the masses of the nucleotides have a common value m as well as are

elastically coupled along each strand by a common constant μ. The potential V(yn – xn) in the original

(PB) model is taken as a Morse potential. We can also considered a hybrid Potential formed by Morse

Potential, a quártic potential and an exponential potential [28].

Using a suitable change of coordinates in equation (1), defined by

xn  yn xn  y n
un  and vn  , (2)
2 2

the Hamiltonian (1) is divided in two parts, the acoustic (Hac) and optical (Hop) parts. They are given by:

N
m 2 N 
H ac   vn   vn  vn1 
2
(3)
n 1 2 n 1 2

and

N
m 2 N  N
H op   un   un  un 1   V ( 2un ) , (4)
2

n 1 2 n 1 2 n 1
respectively.

The general form is:

N
m 2 N N
H op   un  W un  un 1   V ( 2un )
2
(4.1)
n 1 2 n 1 n 1

The main interest here is in the optical Hamiltonian (4), because it contains the non linearity of the

problem. The equations of motion for equation (4) are a system of discrete nonlinear Klein-Gordon (KG)

equations (n=1, 2... N):

..
u n  V ´(un )   (2un  un 1  un 1 )  0 , (5)

with V (un ) being the derivative of the potential with respect the coordinate un .

The evaluation of the configurational partition of equation (4.1) using the transfer integral operator

method in the thermodynamic limit reduces to solving the “ pseudoSchrodinger equation:

{1 /( 2. 2 . .h(u n ))d 2 / d u n  U eff (u n ,  )} (u n )   *  (un )

2
(5.1)

U eff (un ,  )  V ( 2un )  (1 / 2 ) ln( / 2 )  (1 / 2 ) ln h(u n ) (5.2)

Where

h(un )  1  e 2u n (5.3)

In this work, we use two different potential in equation (4). The first one is the Morse Potential (PB

model),

D
V (u )  exp(au )  12 , (6)
2
and the other one is a symmetric Morse potential (SPB model) given by

V (u ) 
D
2
exp( a u )  1 .
2
(7)

The potential (6) is the usual in the model used to describe the DNA lattice [1-12]. The potential (7) is a

symmetric form of the Morse potential, suggested here.

3. BREATHER STABILITY

Our study is concentrated in the equation of motion (5) for the two potentials describe in equation (6)

and (7). For simplicity we adopt m = 1, a=1, and D=1.

 Discrete breather with a given frequency wb and period T=2π/wb, can be obtained from nonlinear

discrete systems of the form (5). MacKay and Aubry proved analytically their existence [16]. Numerical

methods have been used to obtain breathers using truncated Fourier series for the coordinates un(t) [17]:

km
u n  z n0   2 z nk cos(k b t ) , n= 1, 2…N. (8)
k 1

The integer number km is the number of coefficient to be used in the series. This parameter is used to

truncate the Fourier series in order to realize the numerical calculations.

Substituting the expression (8) in equation (5) we obtain a system of algebraic equations given by

k 2b2 zn2  Vn' k   (2 znk  znk1  znk1 )  0 . (9)

In this expression, V'nk is the kth Fourier coefficient for the periodic function V'(un(t)) and we observe that

it depends on a control parameter µ.

The equation (9) can be analyzed by using the anti-continuous limit [16, 17] method. In this way, the

first step is to solve numerically the system of equations (5) in the uncoupled limit, i.e., µ = 0. In this

work, we use the truncated Fourier series (8) with b = 0.8 and km = 17. Then, the eighteen coefficients,

including z0n, were obtained by usual numerical calculation using Newton Method. The next step to create

the breather is to introduce the coupling between the neighbor oscillators. In other words, we solve the

dynamical equations for   0, using the previous isolated oscillator solution as a trial function in the

central site, and maintained the other oscillators in rest. In this calculation, if the time evolution of the

solution leaves to amplitude localization in a few sites then we get a breather. It is important to emphasize

that the mathematical solution must satisfy the Mackay-Aubry conditions [16].

In our calculation, we start from a trial solution determined, by using  = 0, wb =0.8, for a lattice with

the number of oscillators N = 21 in (8). Then, we increase the parameter  by small steps. Each solution

obtained for a value of  is used as the trial solution for the new value of this parameter, replaced by ( +

δ) in a modified Newton process, typically we use δ = 0.01.

The linear stability of the breather solution can be performed numerically. The goal is to get the

behavior of the system around the periodic solutions un(t). Let us introduce a new function ũn(t) = un(t) +

n(t), where un(t) is the periodic breather solution obtained by equations (5) and εn(t) is a perturbation.
Imposing that ũn(t) also satisfy the equations (5) and expanding around un(t) to first order (linearization)

we obtain the following system of equations for εn(t)

n  V " (un (t ))  n   (2 n   n 1   n 1 )  0 . (10)

The Floquet theory [13] applied to equation (10) can be used to study the stability of the solution. We

observe that in the cases under considerations, symmetric and non-symmetric Morse potential, V(un(t))

are periodic functions in time, since the variable un(t) is periodic (equation (8)). Then, the system (10) can

be transformed in Hill equations with periodic coefficients, since V ' ' (un (t )) is also a continuous

periodic function.

The linear stability of these solutions can be obtained from the eigenvalues of the Floquet matrix F0 ,

called Floquet multipliers. The Floquet matrix F0 is given by the fundamental matrix Φ(t) associated to

the system (10) at the period T.

The equations (10) can be transformed in a system of first order equations as

   , (11)

  [V ' ' (u (t ))]  J ,

 (12)

where ξ and П are N dimensional vectors, represented by column matrix of dimension N x 1. [V''(un(t))]

and [J] are NxN matrix with elements given by [V’’(un(t))]i,j = V’’(un(t)) i,j and [J]i,j = 2i,j - i,j-1 - i,j+1,

respectively, i,j being the Kronecker delta symbol. To account for the appropriate periodic boundary

conditions, that is,

u 0  u N and u1  u N 1 , (13)

we must have [J]1,N = [J]N,1 = -1.

In short, we can construct a vector Ω(t)=( ξ(t), π(t) ) and a periodic matrix [A] (2N x 2N) composed by

four blocks with dimension N x N so that Ω(t) satisfies the equation

  A(t ) .
 (14)
 The fundamental matrix [Φ (t)] can be construct from the 2N linearly independent solution of (14)

corresponding to different initial conditions, defined as a column vector with 2N-1 zeros and 1 in the ith

position (i =1, ... , 2N) such that, for any instant t, [Φ] satisfy

.
  [ A(t )] . (15)

This equation is a Floquet type equation. The matrix [A] is periodic one, i.e., [A (t + T)] = [A (t)]. Then, it

is easy to show that [Φ(t+T)] is also solution of (14) with each element of [Φ(t+T)] being a linear

combination of all elements of [Φ(t)]. In general, it can be written

[Φ (t+T)]= [Φ (t)]. [M], (16)

where M is a matrix of constant elements. Obviously, by construction Φ(0) is the identity matrix and

Φ(T) = M is known as the monodromy matrix. In this case, M is the Floquet matrix F0 and the

eigenvalues of monodromy matrix are the Floquet multipliers.

As discussed in reference [13] the solution is stable (bounded) if the modules of Floquet multipliers

are one, and unstable if at least one multiplier has modulus different from one. In this case, the

perturbation solution εn(t) will increase in time because after p periods of time, the equation (16) leaves

us to

p
(t  pT )  (t ) M (17)

that will blow up if any multiplier have modulus greater than 1.

To ensure linear stability, all eigenvalues fν =exp (iθν) of the Floquet matrix M have to lie on the unit

circle, i.e., the Floquet arguments θ = {θ} must be real-valued.

It has been shown in references [6] and [14] that the following N equations are useful for study the

stability

n  V " (un (t ))  n   (2 n   n1   n1 )  E n (18)

In this equation it is introduced the parameter E, when E =0 we recover the original Hill equation (10).

The set of points (θ, E) leave to a band structure. For a stable breather there are N-1 band intersecting the
axis E=0 and one corresponding to the phase mode which is tangent to the axis at θ = 0 [14]. The

parameter E(θ) permits to study bifurcations of the breathers.

Other way to study bifurcations is by analyzes of the Floquet multipliers. In general, the solution can

lose stability in just three ways [6,14]:

1) The Tangent or Harmonic bifurcation occurs when a pair of eigenvalues merges at λ=1 and splits off

S1 (unitary circle) onto the positive real axis.

2) The Period-doubling or Sub-harmonic bifurcation occurs when a pair of eigenvalues merges at λ=-1

and splits off S1 (unitary circle) onto the negative real axis.

3) The bifurcation of the Krein collision appears when two pair of eigenvalues merges at λ , λ*, with

λ2≠1, and splits off the unitary circle .

We can construct a breather mobile following the methodology of the references [18-20] using a

harmonic bifurcation. In this way, it is necessary to define the center of energy XE as

N
X E   nH n / H op , (19)
n 1

where Hop is given by equation (4) and the density energy Hn for each site n is given by

1 2  
u n  un  u n1   un1  un   V ( 2un ) (20)
2 2
Hn 
2 4 4

The evolution of XE determines the mobile breather, for example, if it is constant the breather is static.

Our interest is when the breather velocity is constant [20]. We can use the profiles of the stationary

breather for these parameters and the velocities { vn(0) } given by [2]

vn(0)= [un+1(0)- un-1(0)]/2 , (21-a)

For our calculation, the initial velocity of the breather (V) is introduced by the relation, following ref.

[18]:

Vn = λ.vn(0)/|v| , (21-b)

where Vn is the nth component of the vector V(0), |v| is the norm of the vector {vn(0)} and λ = |V(0)| is

the modulus of the initial velocity. The mobile breather is obtained by perturbing its velocity components
through an appropriated parameter λ. Then, the motion equations (5) is solved using Runge-Kutta

method and considering the initial conditions given by u(0) = {un(0)} (profile of the stationary breather)

and V(0) given by (21-b).

4. STABILITY AND MOBILITY FOR THE BREATHERS

The two studied systems of interests are described by the equation (4) with different potentials, the

original Morse potential (6) and the symmetric one (7). We first present the SPB model results which

correspond to new ones. The results for the PB model are showed in the end of this section and are used

present to compare the dynamic behavior. Our results for the PB model is in concordance with the other

ones find in the literature (see, for example, the references [2,10].

4.1 Breather stability and mobility on SPB model

The Fourier coefficients were obtained by the Newton’s method [17]. The solutions for a short period

of time are presented in Figure 1(a). In this figure, the oscillators are numbered from -10 to +10 with the

central one labeled with n = 0.

For the SPB model, the equation of motion (10) can be written as

 
n  2 exp(2 un )  exp( un )  n   (2 n   n 1   n 1 )  0 (22) .

The analysis of the Floquet multiplier from equation (22) using the formalism discussed in previous

section can be represented in the unit circle. The results, for = 0.28, are indicated in figure 1(b). For the

solution displayed, we have found that two eigenvalues are out of the unit circle, and then the breather is

linearly unstable in this case.

The band analysis can also be used to characterize the stability of the solutions of equation (18).

Figure 2(a) indicates the Aubry´s bands for the breather in the SPB model (=0.28). We observe that the

band lose the intersection with the axis E=0 at θ =0. Thus, the solution can be considerate unstable in the

temporal variable.
 (a) (b)

Figure 1: Numerically bright breather obtained from equation (5) (KG equation) using the symmetric

potential (7), with μ = 0.305, wb = 0.8 (a) and Distribution on the unit circle of the extended Floquet matrix

in the SPB model for =0.28 and wb=0.8. Two eigenvalues are out of the unit circle and this exact solution is

linearly unstable (b).

(a) (b)

Figure 2. Bands E(θ), defined by eqations (18), calculated for the bright breather at frequency wb=0.8 for

the SPB model with =0.280 (a) and Distribution on the unit circle of the extended Floquet matrix in the SPB

model for = 0.305 and wb= 0.8. Two eigenvalues are out of the unit circle and this exact solution is linearly

unstable (b).

In order to make the instability more evident than the results showed in figure 1(b), we present the

results for the parameter =0.305 in figure 2(b). In this case, the pair of eigenvalues which are out of the

unit circle, characterizing the breather linear unstable, are clearly observed. The Aubry´s bands for this

case are indicated in figure 3(a). We observe the band lose the intersection with the axis E = 0 at θ = 0, in

a similar way with the precedent case (=0.280). Then, it confirms the instability of the breather for

=0.305.
 (a) (b)

Figure 3. Aubry´s Bands, E(θ), defined by equations (18). The calculation is made for the breather at

frequency wb=0.8 with =0.305 (a) and the Evolution of the Floquet multipliers with SPB model for 0<<0.35

and wb= 0.8 (b) .

An inspection on the parameter  shows the range where the breathers are stable. We obtain the

breathers stability for a relative large range comparative with the PB model discussed in the next section.

It can be saw in figure 6 that in the interval 0 < µ < 0.28, for frequency wb =0.8, the breather is stable.

The velocity of the center of energy can be analyzed thought the evolution of the center of energy. In

this way, it is necessary to attribute an initial velocity for the stationary breather from an initial input in

the parameter λ = v(0) in equation (21-b). The numerical results obtained for the SPB model are

presented in figure 4(a). These results are evaluated for the parameters  = 0.28 and wb= 0.8, however it

is used different values for v(0). We observe that for v(0) = 0.01 the center of energy remains static

which implies that the breather is stationary. For v(0) = 0.1 the center of energy is displaced, i.e., we get

a mobile breather with approximately constant velocity. Finally, for v(0) = 1.0 there is a velocity of the

center of energy, however this velocity are not constant.

Figure 4. Evolution of the center of energy of a breather with three different values for initial velocities (v(0) =

0.01, 0.1, 1.0) obtained for the SPB model at μ=0.28, wb=0.8 (a) and the Center of energy evolution of a

breather in PB model for =0.13 and wb=0.8 (b).

4.2 Breather stability and mobility in PB Model

The PB original model has been extensively studied in the literature (see, for example, ref. [7, 18, 21,

22]).

The equation of motion of the perturbation (10) for the Morse Potential (6) can be written as:

n  2 exp(2u )  exp(u )  n   (2 n   n1   n1 )  0 , (23)

The range of the coupling parameter  where the model admits stability of the breather is 0 < µ ≤

0.1297 from frequency wb = 0.8. For the coupling parameter  = 0.13 and wb = 0.8 the breather is already

unstable and there is a harmonic bifurcation for these parameters. These results re-obtained by us are the

same presented in literature [18,22]. The Floquet multipliers and the band analysis for this model can also

be finding, for example, in ref. [18].

The breather mobile can be analyzed following the methodology describe for the SPB model. In figure

4(b) the evolution of the center of energy for v(0) = 0.1 is showed. This result is obtained for = 0.13

and wb = 0.8. Similar results for different values of the parameters are discussed in ref. [18].

5. BREATHER TRAPPING

In real systems the non homogeneity is an important aspect. In theoretical approach one way to introduce

these properties is by change the potential in one site of the lattice [2, 23]. This approach is used by ref.
[23] by the PB model and we extend the treatment for the SPB model. In order to introduce the impurity

in the studied models, it is considered the on site potentials of the form:

Vn u n   D0 (1   n ,n 0 )[V (u n )] , (24)

where V(un) is the potential given by (6) for the PB model and (7) for the SPB model. D0 is the deep of

the potential and it is adopt to be equal to 1 in our calculations. The term contain the δ Kronecker (δn,n0)

represents the discontinuity of the lattice on the n0 site. The parameter α is the non-homogeneity and

considered in the interval [-1, ∞). The initial velocity of the breather is introduced choosing the parameter

v(0) = 0.1 (equation 21-b).

The dynamical equations used in this section are the same as indicated in section 3. The unique

difference is the potential on the n0 site.

5.1 Breather trapping in SPB model

For the calculation, the impurity of the lattice is localized in the site 9 and we use  = 0.305 and wb =

0.8. For the numerical simulations the center of energy stars from the site 11 (central position of the

lattices). In this condition, we obtain two different behaviors for the breathers depending on the value of

for α. The breather trapping is observed for α = - 0.30 and the breather rebooted is obtained for α = 0.10.

The figure 5(a) shows the time evolution of the center of energy for the breather trapping. The

trapping is characterized by the oscillation in the neighbor the site 9. However, the breather localization is

difficult in this case once the center of energy gets a large vibration. We interpret this effect as result of

the breather amplitude is very small. This behavior is in concordance with the results indicates in ref. [24]

for big breather.

 Figure 9. Trapping regime of the breather observed in the center of energy time evolution in SPB model

for α = - 0.30,= 0.305 and wb = 0.8. The impurity is localized in the site 9( a) and the Center of energy time

evolution of a breather for the PB model for =0.13 , wb=0.8 and λ=0.10. The upper curve is for the case α =

0.10 (reflection regime) and the lower one is for α = - 0.30 (trapping regime) (b).

5.2 Breather trapping in PB model

As we made in the SPB model, the impurity for the PB model is localized in the site 9. In the PB

model, we fix the parameters  = 0.13 and wb=0.8. The results for this case are similar to that ones

obtained in ref. [18, 23]. The trapping regime of the breather is obtained for α = - 0.30, indicated by the

lower curve in the figure 5(b). On the other hand, the reflection regime of the breather is obtained for α =

0.10 and is indicated for the upper curve in figure 5(b).

6. THERMODYNAMICS: THE MEAN VALUE OF THE DISPLACEMENTS

The thermodynamics provides the average stretching of the base pairs in DNA model [7]. In our case we

can use the Finite difference methods for obtain the ground state wave function and the mean value of the

displacement using the formulas of the reference [7]. We use the model (1) with the Morse Potential and

the parameters μ =0.06, a= 4.45 and D=0.04. The Figure 6(b) shows that the mean of the amplitude is

approximately 2.0 ºA.

 (a) (b)

Figure 6. The ground state wave function  0 for the Schrodinger equation (5.3) (a) and the mean of the


displacements (b) using the formula:  u    2 0 udu [7]. We solve the equation 5.3 using the Finite-


difference methods with the parameter ρ=0.

Also we can use the Finite difference methods for obtain the ground state wave function and the mean

value of the displacement for the Hybrid potential (“hump Morse”) [28] when the temperature is low and

high. The electronic transport and the tunneling currents in DNA are described by the hump Morse.

(a) (b)

Figure 7. The “Morse hump” [28](a) and the mean of the displacements (b) using the formula:


 u    2 0 udu [7]. We solve the equation 5.3 using the Finite-difference methods with the parameter


ρ=3, μ=0.01 and δ=0.08.

7. CONCLUSION

The main contribution of this work is the results for the SPB model. The numerical results for this

model indicates that the existence of the breather and its stability for a large range of the coupling

parameter (μ). This result suggests the inexistence of phase transition for this model. The results obtained

using the Floquet theory (figures (2) and (4)) are complemented by the Aubry`s bands analysis (figures

(3) and (5)).

Our results show that the breather existent in the SPB model is much more stable in terms of the

coupling parameter (μ) than that one in PB model. We observe that increasing the value of μ implies in to

increase the potential energy of the system. In the case of the SPB model, the increment of the potential

energy occurs in a large range, 0 < μ < 0.305 (figure 6). For the PB model the range is small as indicate in

the literature [18,25], 0 < μ < 0.13. This observation is in agreement with the ref. [2] argument. In that

work, the authors analyze the increment of the potential energy in terms of the temperature and they find

a large range of temperature where the potential is smooth for the SPB model. In contrast, for the PB

model the potential change drastically in a small range of the temperature. These two approaches are

different in the form of changing the energy, but the conclusions are similar.

The mobile breather in homogeny SPB model is obtained for v(0) = 0.10, as indicate in figure 7. For

small values of this parameter (0.01, for example) the breather remain static and for large values (1.0, for

example) the velocity is not uniform. Similar behavior occurs for the PB model [18, 23], in figure 8 the

uniform velocity is observed for this model.

In more realistic model impurity is an important ingredient for the models. In this way, we observe

that the trapping and the reflection regime occurs in the two studied models. In the SPB model the two

regimes are characterized in the figures 9 and 10, respectively. The same regimes are showed in figure 11

for the PB model and can be confirmed in ref. [23].

As a final remark we emphasize that the procedure adopts here permits to analyze the relation between

phase transitions and breather stability, as indicated in ref. [26, 27]. For the SPB model, the large range of

the breather stability, in terms of the coupling parameter (μ), and its small amplitude suggest that the

phase transition does not occur in this case. For the PB model we solve the “ pseudoSchrodinger”

equation using the finite difference to determine eigenfunctions , the mean value of the displacements
with a threshold value of 2.0 ºA for the denaturation temperature of 350 K. The ¨Hump Morse” allow the

model to describe the tunneling currents and the sharp thermal denaturation of DNA.

ACKNOWLEDGMENTS

This work was supported by Universidad Nacional del Callao-Facultad Ciencias de la Salud- Escuela

Profesional de Enfermeria of Lima-Perú. The authors would like to thank FAPESP and CNPq (Brazilian

Agencies) by partial support.

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