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Keywords: Hill equations, breather stability, center of energy, ground state wave
function,pseudoSchrodinger equation,hybrid potential
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
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
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
Keywords: Hill equation, breather stability, center of energy, Finite-difference methods, ground state
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
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
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
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
N
m 2 N
N
N
H ( xn 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
N N N N
m 2
H ( xn 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
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 vn vn vn1
2
(3)
n 1 2 n 1 2
and
N
m 2 N N
H op un un un 1 V ( 2un ) , (4)
2
n 1 2 n 1 2 n 1
respectively.
N
m 2 N N
H op un 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)
..
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
Where
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 ) 12 , (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
3. BREATHER STABILITY
Our study is concentrated in the equation of motion (5) for the two potentials describe in equation (6)
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
Substituting the expression (8) in equation (5) we obtain a system of algebraic equations given by
In this expression, V'nk is the kth Fourier coefficient for the periodic function V'(un(t)) and we observe that
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 ( +
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)
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
, (11)
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 = 2i,j - i,j-1 - i,j+1,
respectively, i,j being the Kronecker delta symbol. To account for the appropriate periodic boundary
u 0 u N and u1 u N 1 , (13)
In short, we can construct a vector Ω(t)=( ξ(t), π(t) ) and a periodic matrix [A] (2N x 2N) composed by
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
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
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)
To ensure linear stability, all eigenvalues fν =exp (iθν) of the Floquet matrix M have to lie on the unit
It has been shown in references [6] and [14] that the following N equations are useful for study the
stability
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
Other way to study bifurcations is by analyzes of the Floquet multipliers. In general, the solution can
1) The Tangent or Harmonic bifurcation occurs when a pair of eigenvalues merges at λ=1 and splits off
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
We can construct a breather mobile following the methodology of the references [18-20] using a
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 n1 un1 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]
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)
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].
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
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
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
(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
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
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
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:
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
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
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
The dynamical equations used in this section are the same as indicated in section 3. The unique
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 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).
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 =
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
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-
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
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
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
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
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
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