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Copyright © 2005 American Scientiﬁc Publishers

All rights reserved

Printed in the United States of America

Journal of

Computational and Theoretical Nanoscience

Vol. 2, 1–9, 2005

Peyrard-Bishop-Dauxois Model of

DNA Dynamics and Impact of Viscosity

S. Zdravkovi´ c,

1 ∗

J. A. Tuszy´ nski,

2

and M. V. Satari´ c

3

1

Faculty of Technical Sciences, University of Pritina, Kosovska Mitrovica, Yugoslavia

2

Department of Physics, University of Alberta, T6G 2J1, Canada

3

Faculty of Technical Sciences, 21000 Novi Sad, Yugoslavia

In this paper we try to elucidate the physical signiﬁcance of the analytical solutions in the Peyrard-

Bishop-Dauxois (extended Peyrard-Bishop) model of DNA dynamics. We discuss the impact of

some parameters of the model, especially the harmonic constant of the helicoidal springs. We study

both the case of DNA dynamics when viscosity is ignored and when it is taken into consideration.

Keywords: DNA, PBD Model, Solitons, Viscosity.

1. INTRODUCTION

Deoxyribonucleic acid (DNA) is doubtlessly one of the

most important biomolecules. Its double standard heli-

cal structure undergoes a very complex dynamics and the

knowledge of that dynamics provides insights into var-

ious related biological phenomena such as transcription,

translation and mutation. The key problem in DNA bio-

physics is how to relate functional properties of DNA with

its structural and physical dynamical characteristics. The

possibility that nonlinear effects might focus the vibration

energy of DNA into localized soliton-like excitations was

ﬁrst contemplated by Englander et al.

1

Although several

authors

2–9

have suggested that either topological kink soli-

tons or bell-shaped breathers would be good candidates to

play a basic role in DNA nonlinear dynamics, there are

still several unresolved questions in this regard. A hier-

archy of the most important models for nonlinear DNA

dynamics was presented by Yakushevich.

10

The local openings can be analytically described as

breather-like objects of small amplitude, which have nev-

ertheless interesting properties; as long as their amplitude

is small enough they can move along the chain. This is

unidimensional, which allows local openings of the hydro-

gen bonds and formation of denaturation bubbles.

In the present paper we deal with the extended model for

DNA dynamics, ﬁrst proposed by Peyrard and Bishop

7

and

∗

Author to whom correspondence should be addressed.

further developed by Dauxois.

11, 12

This Peyrard-Bishop-

Dauxois model will be henceforth referred to as the PBD-

model for short.

The paper is organized in the following way. In Sec-

tion 2 we outline the PBD model primarily intended to

describe the process of local opening of base pairs (or

local melting of the double helix). Then we attempt to shed

new light on the still somewhat vague parameter values of

the PBD model, especially discussing the harmonic con-

stant of helicoidal springs. This section represents a certain

extension of two of our previous papers.

13, 14

However, we

introduce a new procedure which yields qualitatively new

results and solves a couple of problems.

In Section 3 we present our consideration of DNA

breather dynamics in the context of the PBD model when

viscosity is taken into consideration. Section 4 puts for-

ward our discussion and concluding remarks.

2. THE PBD MODEL OF DNA

The B-form DNA in the Watson-Crick model is a double

helix, which consists of two strands s

1

and s

2

(Fig. 1),

linked by the nearest-neighbour harmonic interactions

along the chains. The strands are coupled to each other

through hydrogen bonds, which are supposed to be respon-

sible for transversal displacements of nucleotides.

It was argued

7, 11, 12

that we could safely assume a com-

mon mass m for all the nucleotides and the same coupling

constant k along each strand. We will get back to this

J. Comput. Theor. Nanosci. 2005, Vol. 2, No. 2 1546-198X/2005/2/001/009/$17.00+.25 doi:10.1166/jctn.2005.110 1

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Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity Zdravkovi´ c et al.

s

1

s

2

k

k

m

m

v

n–1

v

n+1

v

n

u

n–1

u

n+1

u

n

Morse

Potential

Fig. 1. Graphical representation of the simple model for DNA strands.

point later. As was pointed out, we rely on the PBD model,

which takes into account the fact that the DNA molecule

is twisted. This helicoidal structure of the DNA chain

implies that nucleotides from different strands become

close enough so that they interact through water ﬁlaments.

This means that a nucleotide at the site n of one strand

interacts with both (n+h)th and (n−h)th nucleotides of

the other strand. In Refs. [13, 14] we used h = 4

11, 12

for all calculations. However, h = 5 might be better.

15, 16

This comes from the fact that there are approximately ten

nucleotides per one turn. Introducing the transversal dis-

placements u

n

, v

n

of the nucleotides from their equilibrium

positions along the direction of the hydrogen bonds, the

Hamiltonian for the DNA chain becomes

11, 12

H =

_

_

m

2

( ˙ u

2

n

+ ˙ v

2

n

) +

k

2

_

(u

n

−u

n−1

)

2

+(v

n

−v

n−1

)

2

_

+

K

2

_

(u

n

−v

n+h

)

2

+(u

n

−v

n−h

)

2

_

+D|e

−o(u

n

−v

n

)

−1]

2

_

(1)

Here k (respectively K) is the harmonic constant of the

longitudinal (respectively helicoidal) spring. The last term

in the Hamiltonian represents a Morse potential approxi-

mating the potential of the hydrogen bonds while D and o

are the depth and the inverse width of the Morse potential

well, respectively.

It is more convenient to describe the motion of two

strands by making a transformation to the centre-of-mass

coordinates representing the in-phase and out-of-phase

transversal motions, namely

x

n

=(u

n

+v

n

),

√

2, ,

n

=(u

n

−v

n

),

√

2 (2)

From relations (1) and (2) one can obtain the follow-

ing dynamical equations describing linear waves (phonons)

and nonlinear waves (breathers):

m¨ x

n

=k(x

n+1

+x

n−1

−2x

n

) +K(x

n+h

+x

n−h

−2x

n

) (3)

and

m¨ ,

n

= k(,

n+1

+,

n−1

−2,

n

) −K(,

n+h

+,

n−h

+2,

n

)

+2

√

2oD

_

e

−o

√

2,

n

−1

_

e

−o

√

2,

n

(4)

As was explained in a couple of articles

11–13, 17

, we can

apply the transformation

, =a4; (a 1) (5)

This means that we assume that oscillations of nucleo-

tides are large enough to be anharmonic but still small

enough so that the particles oscillate around the bottom of

the Morse potential. Equations (4) and (5), and the expan-

sion of exponential terms in Eq. (4), yield

¨

4

n

=

k

m

(4

n+1

+4

n−1

−24

n

) −

K

m

(4

n+h

+4

n−h

+24

n

)

−w

2

g

(4

n

+ao4

2

n

+a

2

p4

3

n

) (6)

where

w

2

g

=

4o

2

D

m

, o =

−3o

√

2

and p =

7o

2

3

(7)

To solve Eq. (6) we use the semi-discrete approxi-

mation.

17

This means that we look for wave solutions of

the form

4

n

(t) = E

1

(anI, at)e

i0

n

+a|E

0

(anI, at) +E

2

(anI, at)e

i20

n

]

+cc +O(a

2

) (8)

and

0 ≡0

n

=nqI −wt (9)

Here, I is the distance between two neighbouring nucleo-

tides in the same strand, w is the optical frequency of

the linear approximation of their vibrations, q is the

wave number whose role will be discussed later, cc are

conjugate-complex terms and the function E

0

is real.

Before we proceed with solving Eq. (6) we give some

explanations for Eq. (8). If there were not the last term in

Eq. (6), the one with w

2

g

, which comes from the nonlinear

term in Eq. (4), we would expect the solution in the form

E

1

e

i0

n

+cc instead of Eq. (8). This would be a modulated

wave with a carrier component e

i0

n

and an envelope E

1

. We

will see later that the modulation factor E

1

will be treated

in a continuum limit while the carrier wave will not. In

other words, the carrier component of the modulated wave

includes the discreteness and the procedure is called semi-

discrete approximation. As if there are terms with 4

2

n

and

4

3

n

in Eq. (6) we can not expect solution of this equation in

the simple form E

1

e

i0

n

and nonexponential term as well as

terms with e

i20

n

should be incorporated into the expression

for the solution. A whole method is explained in much

more details in Ref. [18], while its mathematical basis is

given in Refs. [19, 20].

Now, we are ready for solving Eq. (6). It was already

pointed out that the functions E

i

would be treated in the

continuum limit. So, taking this limit (nI →z) and apply-

ing the transformations

Z =az; T =at (10)

2 J. Comput. Theor. Nanosci. 2, 1–9, 2005

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Zdravkovi´ c et al. Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity

yields the following continuum approximation

E (a(n±h)I, at) →E (Z, T ) ±E

Z

(Z, T )aIh

+

1

2

E

ZZ

(Z, T )a

2

I

2

h

2

(11)

where E

Z

and E

ZZ

mean corresponding derivatives with

respect to Z. This allows us to obtain a new expression

for the function 4

n

(t):

4

n

(t) →E

1

(Z, T )e

i0

+a|E

0

(Z, T ) +E

2

(Z, T )e

i20

] +cc

=E

1

e

i0

+a|E

0

+E

2

e

i20

] +E

∗

1

e

−i0

+aE

∗

2

e

−i20

(12)

where ∗ stands for complex conjugate and E

i

≡E

i

(Z, T ).

From Eqs. (9)–(12) one can straightforwardly obtain

expressions for all the terms in Eq. (6).

18

From the con-

tinuum version of Eq. (6), equating the coefﬁcients for

the various harmonics, we can get a set of important

relations.

11–13

For example, equating the coefﬁcients for e

i0

one obtains a dispersion relation

w

2

=w

2

g

+

2k

m

(1−cos(qI)) +

2K

m

(cos(qhI) +1) (13)

This can be used to ﬁnd the corresponding group velocity

Jw,Jq as

V

g

=

I

mw

|k sin(qI) −Khsin(qhI)] (14)

In the same way, equating the coefﬁcients for e

i0

= 1,

we can easily obtain

E

0

=jE

1

2

(15)

where

j =−2o

_

1+

4K

mw

2

g

_

−1

(16)

However, for the next three harmonics (e

i20

, e

i30

and

e

i40

) the matter becomes more complicated. All of these

harmonics give a relation

E

2

=oE

2

1

(17)

but with different values for the parameter o. For example,

equating the coefﬁcients for e

i20

one can get

_

4w

2

+

2k

m

(cos(2qI) −1)

−

2K

m

(cos(2hqI) +1) −w

2

g

_

E

2

=w

2

g

oE

2

1

(18)

which means that o is not constant but a function of qI.

However, coefﬁcients for e

i30

and e

i40

give constant values

o, −

p

2o

and −

3p

o

respectively. We will return to this point

later.

As if we can express functions E

0

and E

2

through the

function E

1

we can derive an equation for E

1

. Using new

coordinates again:

S =Z−V

g

T , t =aT (19)

we can ﬁnally obtain the nonlinear Schrödinger equation

(NSE) for the function E

11–14

1

iE

1t

+PE

1SS

+QE

1

2

E

1

=0 (20)

where the dispersion coefﬁcient P and the coefﬁcient of

nonlinearity Q are given by

P =

1

2w

_

I

2

m

|k cos(qI) −Kh

2

cos(qhI)] −V

2

g

_

(21)

and

Q =−

w

2

g

2w

|2o(j+o) +3p] (22)

Those derivations can be found in some more details in

Ref. [18].

For PQ > 0 the solution of the NSE (20) is

11, 12, 21

E

1

(S, t) =A sech

_

S −u

e

t

L

e

_

exp

iu

e

(S −u

c

t)

2P

(23)

where the envelope amplitude A and its width L

e

have the

forms

A =

_

u

2

e

−2u

e

u

c

2PQ

(24)

and

L

e

=

2P

_

u

2

e

−2u

e

u

c

(25)

and u

e

and u

c

being the velocities of the envelope and the

carrier waves, respectively. Using Eqs. (23), (8), (9), (15),

(17), (10), and (19) we obtain

11–14

4

n

(t) = 2Asech

_

a

L

e

(nI −V

e

t)

_

×

_

cos(OnI −Dt)+aAsech

_

a

L

e

(nI −V

e

t)

_

×

_

j

2

+ocos|2(OnI−Dt)]

__

+O(a

2

) (26)

where

V

e

=V

g

+au

e

(27)

O =q +

au

e

2P

(28)

and

D=w+

au

e

2P

(V

g

+au

c

) (29)

In Ref. [13] we suggested discrete values for a wave

number q. For h =4 we obtained the following four values

for the wave length \: 6I, 7I, 8I, and 9I or, as if q =2r,\,

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Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity Zdravkovi´ c et al.

the following values for qI: 1.05 rad, 0.90 rad, 0.78 rad =

r,4 and 0.70 rad. We gave an argument to reject the ﬁrst

value (\ =6I). For h =5, using the same procedure,

13

one

obtains the following values for \: 7I, 8I, 9I, 10I, and 11I

and the following values for qI: 0.90 rad, 0.78 rad, 0.70 rad,

0.63 rad =r,5 and 0.57 rad. For the most favourable mode

we suggested the one for which qI = r,4 for h = 4. For

h =5 that would be qI =r,5.

For all the calculations we chose the following set of

values characterizing the DNA molecule:

k =3K =24 N/m (30a)

I =3.4· 10

−10

m (30b)

m=5.1· 10

−25

kg (30c)

o =2· 10

10

m

−1

(30d)

D =0.1 eV (30e)

The value for the mass is an average value for all four

nucleotides. Namely, molecular masses of nucleotides are

from 340 g/mol (Cytosine) to 380 g/mol (Guanine). There-

fore, for the average value, after subtraction the masses of

three water molecules, one obtains 305.75 g/mol, which

gives the above value for the mass of the single nucleotide.

All other constants were taken from the papers.

11, 12

It was pointed out that there were two possibilities for

the parameter o, constant and nonconstant. In Ref. [13] we

accepted the constant o coming from e

i30

. Therefore, we

did not use the lowest possible harmonic e

i20

! In Ref. [14],

however, we made a choice having more physical sence.

This is nonconstant o given by Eqs. (17) and (18). In that

article we suggested that the value of the parameter K

was overestimated. It was shown that there should be K ≤

4.6 N/m for qI = 0.78 rad and h = 4 and all the other

constants given by (30). For h =5 and qI =0.63 rad one

obtains K ≤4.4 N/m.

Of course, one can argue that those values for qI,

0.78 rad and 0.63 rad, were obtained for K = 8 N/m in

Ref. [13]. This is correct. However, using the same proce-

dure for the possible qI values, explained in Ref. [13], we

obtain, for h =4, \ =6I, 7I, 8I, and 9I, i.e., qI =1.05 rad,

0.9 rad, 0.78 rad and 0.7 rad for both K =8 N/m and K =

6 N/m. The value K = 4 N/m gives the same four values

for qI and two more (\=10I and 11I, or qI =0.63 rad and

qI =0.57 rad) in addition. For K =3 N/m we obtain \ =

6I, 7I, . . . , 13I while K =2 N/m gives \ =6I, 7I, . . . , 19I.

Hence, the value qI = 0.78 rad, as well as qI = 0.63 rad

for h = 5, corresponds to both large and small values of

the parameter K. This means that qI = 0.78 rad can be

suitable choice for all acceptable values of K, but does not

mean that this is the optional value for our calculations.

Thus, we need one more criterion for qI to be determined

and we show in the following that this exists.

The breather-type solution in Eq. (26) represents a sort

of a modulated solitonic wave. From hyperbolic and cosine

terms in Eq. (26) we can recognize wave numbers of both

the envelope and the carrier wave. In other words, we can

see that the length of the envelope, A, and the wavelength

of the carrier wave, \

c

, are

A=

2rL

e

a

(31)

and

\

c

=

2r

q +

au

e

2P

(32)

This allows us to calculate the number of wavelengths

of the carrier wave contained within the length of the enve-

lope as

D

o

≡

A

\

c

(33)

In what follows, we call D

o

a density of internal oscilla-

tions (density of carrier wave oscillations) for short even

though, strictly speaking, this is not density, i.e., the num-

ber of wavelengths per unit length. From Eqs. (31)–(33)

and (25) we can easily obtain

D

o

=

u

e

_

u

2

e

−2u

e

u

c

_

1+

2qIP

aIu

e

_

(34)

We should keep in mind that the dispersion coefﬁcient P

is deﬁned by Eq. (21) and is a function of qI.

If we choose the following set of values for parameters

characterizing a traveling wave solution

11, 12

u

e

=10

5

m/s (35a)

u

c

=0 (35b)

a =0.007 (35c)

we can plot the function D

o

vs. qI and this is done in

Figure 2 for h = 5 and three values for the parameter K.

From this ﬁgure we see that the density of the inter-

nal oscillations of the soliton D

o

reaches a maximum for

10

8

6

4

0.4 0.5 0.6 0.7 0.8 0.9

ql (rad)

a

b

c

D

0

Fig. 2. Density of the carrier wave oscillations D

o

as a function of qI.

(a: K =4.5 N/m, b: K =4 N/m, c: K =3.5 N/m).

4 J. Comput. Theor. Nanosci. 2, 1–9, 2005

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Zdravkovi´ c et al. Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity

qI = 0.636 rad, which is extremely close to the value of

0.628 rad = r,5 that was earlier selected as the most

favourable one. For h = 4 the highest value of the func-

tion occurs at about qI =0.77 rad, which is very close to

0.78 rad =r,4. Should we accept this value, correspond-

ing to the highest D

o

, for our calculations? Certainly yes,

since a higher D

o

probably means a more efﬁcient modu-

lation. It is required for modulation, when both signals are

cosine functions, that the frequency of the carrier compo-

nent be much higher then the frequency of the envelope.

In our case, however, there are no two frequencies, but

we introduced D

o

instead. Our intuition strongly suggests

that nature wants modulation with D

o

as high as possi-

ble, which one might call the most efﬁcient modulation.

According to Figure 2, the maximum value of the function

D

o

is around 8 to 10. We should emphasize that this does

not have too profound meaning since this value simply

depends on the choice of the somewhat arbitrary parame-

ters a and u

e

. In fact, we are looking for the maximum of

the product function qI · P(qI).

So, we can make two important conclusions based on

the analysis of how D

o

depends on qI. One can see from

Figure 2 that the highest values of the density of the internal

oscillations D

o

increases when the parameter K increases.

What is also important is the fact that an optimal qI, for any

reasonable K, does not differ signiﬁcantly from our previ-

ously accepted values of qI =0.63 rad and qI =0.78 rad for

h =5 and h =4. Otherwise, for K =0 one obtains D

om

≈2

for qI = 0.53 rad for both values of h. This means that,

from the criterion of modulation, the PBD model

11, 12

is bet-

ter then the original PB model,

7

which could be obtained

from the former one by letting K =0.

Now, we can plot our solitonic function 4

n

(t) given by

Eq. (26), or the function , deﬁned by Eq. (5). Before we

do this, however, we want to study how the amplitude A

depends on qI for various K. We should keep in mind that

the value A is the amplitude of the function E

1

(S, t) but

is not the amplitude of the soliton 4

n

(t). From Figure 3

0.3 0.4

0.6

0.9

1.2

1.5

1.8

0.5 0.6 0.7 0.8 0.9

ql (rad)

A

(

n

m

)

Fig. 3. Amplitude A as a function of qI for o =const (K =4 N/m).

0.4 0.5 0.6 0.7 0.8

ql (rad)

A

(

n

m

)

a

b

c

1

2

3

4

5

Fig. 4. Amplitude A as a function of qI for o =o(qI). (a: K =4.5 N/m,

b: K =4.3 N/m, c: K =3.8 N/m).

we can see how A depends on qI for constant o, i.e., for

o = −o,2p, the value that was previously accepted for

our calculations,

13

and for h =5. We selected K =4 N/m,

but for different K, both larger and smaller, the curves are

almost the same.

However, for o given by Eqs. (17) and (18) the situation

looks completely different. Figure 4 shows how the ampli-

tude A depends on qI for the three values of K and for

h =5. Instead of minimum (Fig. 3) the function A(qI) now

has a maximum. The highest values are 4.75 nm at qI ≈

0.62 rad for K = 4.3 N/m, 2.31 nm at qI ≈ 0.62 rad for

K =4 N/m and 1.78 nm at qI ≈0.64 rad for K =3.7 N/m.

One can see that those maxima decrease with smaller K.

For K = 4.58 N/m the maximum of the amplitude A is

even 16 nm, which probably does not make physical sense,

while for K = 3.4 N/m the function A(qI) does not have

any maximum at all.

Therefore, we can state three facts concerning the

parameter K. First, there is a maximum value K

m

=

4.39 N/m for qI =0.63 rad. Second, higher K means larger

D

0

, i.e., a better transmission of a signal through the DNA

chain, as was explained above. Third, K should be small

enough to ensure that the amplitude A be small enough so

that the oscillating nucleotide does not exceed the depth

of Morse potential well.

Finally, we can plot our soliton 4

n

(t) given by Eq. (26).

In Figures 5–7 we show the elongation 4

n

(t) vs. time

for K = 4.3 N/m, 4 N/m and 2.5 N/m, respectively. We

chose h = 5 for all of them. According to the shape of

the curve in Figure 5, and the maximum of the function

4

n

(t), we can conclude that this value for K, i.e., K =

4.3 N/m, would not be acceptable. For K = 4.39 N/m,

4

n

(t) has only positive values with the maximum reach-

ing up to 360 nm which is totally unacceptable because

the expansion of the Morse potential, Eq. (6), presumes

that the amplitude may not reach the Morse plateau! For

4

n

= 360 nm, from Eq. (5) it follows that ,

n

= 2.5 nm

which is far beyond the plateau. However, Figures 6 and 7

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15

10

5

0

–5

48 52 56 60 64

t (ps)

Φ

(

n

m

)

Fig. 5. Elongation of the out-of-phase motion as a function of time

(n =300, qI =0.628 rad, h =5, K =4.5 N/m, o =o(qI)).

–4

–2

0

2

4

6

48 52 56 60 64

t (ps)

Φ

(

n

m

)

Fig. 6. Elongation of the out-of-phase motion as a function of time

(n =300, qI =0.628 rad, h =5, K =4 N/m, o =o(qI)).

–2

–1

0

1

2

3

52 56 54 50 58 60 62

t (ps)

Φ

(

n

m

)

Fig. 7. Elongation of the out-of-phase motion as a function of time

(n =300, qI =0.628 rad, h =5, K =2.5 N/m, o =o(qI)).

suggest that the values K =4 N/m and K =2.5 N/m might

be acceptable. Of course, we should keep in mind that

a higher K means more oscillations of the carrier wave

in one envelope, i.e., a higher D

0

. For K = 0 only three

internal oscillations can hardly be discerned which shows,

as we stated above, the superiority of the PBD model

11, 12

over the original PB version.

7

At this point we can speak of a certain range for

accepted values for the parameter K. Also, as was pointed

out earlier, K should be big enough to ensure a large D

0

,

but still not too large to bring about a very large amplitude.

Finally it might be interesting to compare solitonic solu-

tions 4

n

(t) given in Figures 5–7 with the same function

obtained for constant o.

13

In Figure 8 we show the soli-

tonic wave 4

n

(t) for K =4 N/m and constant o, i.e., o =

−

p

2o

. Comparing Figures 6 and 8, both plotted with the

same K, we see that the amplitude for the non-constant

o (Fig. 6) is about three times larger than that for the

constant o (Fig. 8). In both cases positive amplitudes are

higher than negative, which is a result of the term with

the parameter o in Eq. (26). One can see that the shapes

of both curves are almost the same. This is not surprising

since D

0

, the density of the carrier wave oscillations of the

breather, does not depend on o.

Finally, we need to point out a couple of advantageous-

ness of this procedure (nonconstant o) over the one when o

was constant. First, the amplitude A(qI) has the maximum

having very big values in a limit when the parameter K

approaches its critical value, which suggests a certain res-

onance behaviour. This procedure solves the problem of a

small amplitude discussed in Ref. [13].

Also, the existence of the upper limit of the parame-

ter K, which we explained in this chapter and in Ref. [14],

solves one more problem. Namely, in Ref. [11] optical

and acoustical frequencies were compared. There are four

crossing points in the ﬁrst Brillouin zone for h =4. How-

ever, for K - K

m

those crossing points do not exist and

w

o

>w

o

in the whole zone.

22

In that article,

22

a resonance

48 52 56 60 64

t (ps)

Φ

(

n

m

)

1.5

1.0

–1.0

0.5

–0.5

0.0

Fig. 8. Elongation of the out-of-phase motion as a function of time

(n =300, qI =0.628 rad, h =5, K =4 N/m, o =const).

6 J. Comput. Theor. Nanosci. 2, 1–9, 2005

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Zdravkovi´ c et al. Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity

mode was deﬁned. It might be interested to point out

that the resonance mode occurs at qI = 0.785 rad/s and

0.628 rad for h =4 and h =5 respectively. Those are well

known values ﬁrst obtained in Ref. [13] and conﬁrmed in

this section by maximization of the function D

0

(qI).

3. THE INFLUENCE OF VISCOSITY

In the previous paper on this topic

13

we attempted to deal

with a more realistic description of DNA dynamics, which

takes into account the impact of the medium, surround-

ing a DNA molecule. It is well known the importance of

hydrating water for the biochemical activities of proteins

and especially DNA. Since water molecules are highly

polar they form an ordered network on the surface of a

protein along which protons can be transferred. The forma-

tion of this network with long-range connectivity has been

detected as a percolation transition when the water con-

tent approaches 0.5 g per 1 g of protein.

23

We suggest that

the helicoidal spring parameter K in the model considered

here may reﬂect the mediating role of the water molecules.

Moreover, the helicoidal structure itself arises as the result

of optimization of the interplay between hydrogen bond-

ing, hydrophobicity and long-range connectivity. On the

other hand, we must take into consideration the fact that

the solvating water does act as a viscous medium that

damps out DNA dynamics, favouring energy expenditure.

We took this effect in Ref. [13] by adding the viscous

force on the nucleotide pairs, i.e., in Eq. (4) of this paper.

In that treatment

13, 24

viscous force was considered as com-

petitive with other forces arising from Hamiltonian (1).

The consequence of that approach was the outcome which

showed the impact of viscosity being so strong that the

breather solution (26) decays almost instantaneously into

its asymptotic form which is localized bell-shaped mode

given by expression:

,

n

(t) =a

2

A

2

¡

j sech

2

_

a

L

¡

(nI −V

e¡

t)

_

(36)

where A

¡

, L

¡

, V

e¡

are parameters deﬁned by Eqs. (24),

(25), and (14), respectively, renormalized by viscosity

impact. This procedure was shown in Refs. [13, 24] where

we deﬁned so called “big” and “small” viscosities. So, the

ﬁrst one, big viscosity, was explained in Refs. [13, 24],

while the second one will be in what follows.

Here we start from probably more realistic and favour-

able approach that viscous force has features of small per-

turbation. The viscous forces exerted on the bases within

a pair n are −a¡ ˙ u

n

and −a¡ ˙ v

n

. The small a, the same as

in Eq. (5), indicates that viscous force has the character of

small perturbation. It leads to the effective damping force

acting on the out of phase base pair motion as follows:

E

v

=−a¡ ˙ ,

n

(37)

Now starting from the perturbed equation of motion

m¨ ,

n

= k(,

n+1

+,

n−1

−2,

n

) −K(,

n+h

+,

n−h

+2,

n

)

+2

√

2oD(e

−o

√

2,

n

−1)e

−o

√

2,

n

−a¡ ˙ ,

n

(38)

and performing the expansion according to Eqs. (5), (8),

(10) and (19) one ﬁnds

iE

1t

+PE

1SS

+QE

1

2

E

1

=−a

¡

2mw

E

1t

(39)

This equation could be solved by the method of “slowly

varying parameters” developed in Ref. [25]. The essence

of the method is that the carrier wave number O=q +a

u

e

2P

slowly changes with time through change of u

e

.

The breather solution, Eq. (23), can be written in more

suitable form:

E

1

(S,;)=Asech

_

1

L

e

(S−;)

_

exp

_

i

_

«

_

S−

u

c

u

e

;

_

+ç

__

(40)

where « =

u

e

2P

is the carrier wave number shift, which is

expected to depend of viscosity, ; =u

e

t is the position of

centre of the breather, and ç is time phase.

According to Ref. [25], the above parameters should

slightly depend on time on the following ways:

«(t) =«

0

+] («)t (41)

;(t) =;

0

+

u

e0

«

0

«t (42)

ç(t) =

u

e0

2«

0

_

1

L

2

e

+«

2

_

t

=

u

e0

2«

0

_

1

L

2

e

+«

2

0

_

t +

_

u

e0

] («)t +u(«)

_

t (43)

where «

0

, ;

0

, and u

e0

are corresponding unperturbed

values, while u(«) denotes possible phase shift of the

breather caused by viscosity.

The wave function of the breather perturbed by viscosity

E

1v

could be expressed by expansion with respect to small

parameter a:

E

1v

=E

1

(S, ;) +a

__

oE

1

oç

_

+L

e

_

oE

1

o;

___

u

e0

2«

0

_

] («)t

2

(44)

The above approximation holds for time t smaller than

characteristic time scale t

0

=

«

0

a] («

0

)

. It can be shown on

the basis of Eqs. (41)–(43) that this expansion diverges

when a →0 except if the secular sum in square brackets

vanishes. If we use deﬁnitions, Eqs. (41)–(43), and take

into account that the derivative E

1t

on the right hand side

of Eq. (39) could be transformed as follows

oE

1

ot

=

_

oE

1

o«

_

J«

Jt

+

_

oE

1

o;

_

J;

Jt

=

oE

1

o;

_

oE

1

o«

oE

1

o;

J«

Jt

+

J;

Jt

_

(45)

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Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity Zdravkovi´ c et al.

the effective perturbation caused by viscosity could be

written as

(«, ;, S) = −i

_

oE

1

o«

] («) +

oE

1

oç

u(«)

_

−

u

e0

w«

0

_

¡

m

«+] («)

_

oE

1

o;

(46)

The unknown functions from Eqs. (41), (43) ] («) and

u(«) now play the role of Lagrange multipliers, which

could be determined by orthogonality conditions:

_

−

JS(«, ;, S)

_

oE

1

o;

_

∗

=0 (47a)

_

−

JS(«, ;, S)

_

oE

1

oç

_

∗

=0 (47b)

where ∗ stands for complex conjugates. This removes the

mentioned divergence of Eq. (44). Taking into account the

derivatives

oE

1

o«

=iSE

1

, for u

c

=0, and

oE

1

oç

=iE

1

, contained

in Eq. (46), the second condition, Eq. (47b), gives that the

phase shift u(«) is zero in this approximation, while the

ﬁrst condition yields the rate of change of carrier wave

number in the form:

J«

Jt

=] («) =−

¡

m

_

D

1+D

_

« (48)

where

D =

1

3

u

e0

wL

e

=

1

6

u

2

e0

Pw

(49)

From Eq. (48) easily follows

« =«

0

exp

_

−

¡

m

D

1+D

t

_

(50)

Having in mind the deﬁnition « =

u

e

2P

we get

u

e

=u

e0

exp

_

−

¡

m

D

1+D

t

_

(51a)

u

e0

=2P«

0

(51b)

If we estimate P and w from Eqs. (21) and (13) taking

K = 4 N/m and qI = 0.78 rad, we readily get P = 0.89 ·

10

−6

m

2

/s and w =8.6· 10

12

rad/s.

If we choose, as before, u

e0

= 10

5

m/s, dimensionless

parameter D, Eq. (49), becomes

D =217 1 (52)

Under such circumstances of high launching breather’s

velocity, the envelope velocity, Eq. (27), by using Eqs. (10)

and (19), becomes

V

e

=V

g

+au

e0

exp

_

−

¡

m

a

2

t

_

(53)

From the absolute viscosity of water (T ≈ 300 K), q =

7· 10

−4

kg/ms, and considering a base as thin rigid rode, it

could be roughly estimated ¡ ∼10

−12

kg/s. With a =0.007

the breather’s decay time is t

J

=

m

¡a

2

≈10

−8

s. Starting with

V

e

≈1.9· 10

3

m/s the path passed by the breather for t

J

=

10

−8

s reaches approximately 20 · 10

−6

m or 6 · 10

4

base

pairs along DNA chain. This is quite favourable regarding

expected role of breathers as long-range effects mediators

in DNA.

Finally, on the basis of Eqs. (24) and (25) it follows

that the breather’s amplitude decays with the same rate as

envelope velocity, and the width of the breather spreads

exponentially.

4. CONCLUSION AND DISCUSSION

In this paper we have dealt with the PBD model applied

to an idealized DNA chain. The hydrogen bonds in this

DNA chain are represented by the Morse potential, which

results in the nonlinear Schrödinger equation describing

the breather excitations.

In Section 2, we brieﬂy described the model proposed.

The nonlinear dynamics in the context of this model

depends on several parameters and the values of some of

them are still rather vague and uncertain. We ﬁrst consid-

ered our attention on the issue of choosing the parameter

o, which relates the amplitudes of the ﬁrst and second har-

monics in the expansion in Eq. (8). Usually, this parameter

has been taken to be a constant, but a richer physical situ-

ation arises if we take the condition in Eqs. (17) and (18),

which seems more signiﬁcant emerging from a lower har-

monic in the perturbation procedure. This brought about

the qualitatively different dependence of the amplitude A

from qI (Figs. 3 and 4). Our second concern was the dis-

cussion of the helicoidal spring constant K.

In Section 3 we introduced viscosity term, i.e., the inter-

action of DNA nucleotides with the surrounding water

molecules. Here, we have expanded our earlier approach

to this problem

13

by considering viscous term as small per-

turbation, Eq. (43). We found that the envelope velocity

of breather exponentially decays eventually reaching the

group velocity, Eq. (14). We estimated that the decay time

for breather with parameters used in this paper is of the

order of t

J

≈10

−8

s. This leads to the path of about 20 jm.

If the electric ﬁeld of appropriate frequency is applied on

DNA

26

the energy loss due to viscous dissipation should

be balanced by the parametric resonance effect preventing

breather’s decay.

It should be stressed that a great deal of attention

was given earlier to the numerical analysis of the PBD

model but this was done without viscous perturbation.

27–30

The so-called discrete breathers arising in these numerical

treatment exhibit a number of very interesting properties,

especially regarding their mutual interactions.

For example, the modulation instability of the wave put

in the discrete PBD Hamiltonian splits it into wave pack-

ets, which are small breathers. Subsequently, the interaction

8 J. Comput. Theor. Nanosci. 2, 1–9, 2005

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Zdravkovi´ c et al. Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity

of these breathers tends to favour the largest excitations,

which grow at the expense of others. This process satu-

rates when the breathers, that get narrower as they grow

in amplitude, are so narrow that they are trapped by lattice

discreteness and no longer propagate in the lattice. It still

remains to be demonstrated numerically how the helicos-

ity and viscosity affect the dynamics behaviour of discrete

breathers. It is expectable that the viscosity which shows

opposite tendency of above described growing of ampli-

tude and narrowing of discrete breather could establish

subtle balance which enables breather to self sustain sta-

bility and maintain capability of reaching long way along

DNA chain.

Acknowledgments: This project was supported by

funds from NSERC, MITACS, the Institute of Theoreti-

cal Physics at the University of Alberta and from Serbian

Ministry of Sciences, project No H1822.

References and Notes

1. S. W. Englander, N. R. Kalenbach, A. J. Heeger, J. A. Krumhansl,

and S. Litwin, Proc. Natl. Acad. Sci. USA 77, 7222 (1980).

2. S. Yomosa, Phys. Rev. A 30, 474 (1984).

3. S. Homma and S. Takeno, Prog. Theor. Phys. 72, 679 (1984).

4. Ch. T. Zhang, Phys. Rev. A 35, 886 (1987).

5. V. Muto, A. C. Scott, and P. L. Christiansen, Phys. Lett. A 13, (1989).

6. S. N. Volkov, J. Theor. Biol. 143, 485 (1989).

7. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. 62, 2755 (1989).

8. Ch. T. Zhang, Phys. Rev. A 40, 2148 (1989).

9. L. V. Yakushevich, Phys. Lett. A 136, 413 (1989).

10. L. V. Yakushevich, Nonlinear Physics of DNA, Wiley Series in Non-

linear Science, John Wiley, Chichester (1998).

11. T. Dauxois, Phys. Lett. A 159, 390 (1991).

12. T. Dauxois and M. Peyrard, Dynamics of Breather Modes in a Non-

linear Helicoidal Model of DNA, Lecture Notes in Physics 393,

Dijon (1991), p. 79.

13. S. Zdravkovi´ c and M. V. Satari´ c, Phys. Scripta 64, 612 (2001).

14. S. Zdravkovi´ c, J. A. Tuszy´ nski, and M. V. Satari´ c, J. Comput. Theor.

Nanosci. 1, 171 (2004).

15. Peyrard, private communication.

16. G. Gaeta, Phys. Lett. A 172, 365 (1993).

17. M. Remoissenet, Phys. Rev. B 33, 2386 (1986).

18. S. Zdravkovi´ c, Nonlinear Dynamics of DNA Chain, will be pub-

lished in Finely Dispersed Particles: Micro-, Nano-, and Atto-

Engineering, Edited by A. Spasi´ c and Jyh-Ping Hsu, Marcel Dekker,

Inc., New York (2005).

19. T. Kawahara, J. Phys. Soc. Japan 35, 1537 (1973).

20. R. K. Dodd, J. C. Eilbeck, J. D. Gibbon, and H. C. Morris, Soli-

tons and Nonlinear Wave Equations, Academic Press, Inc., London

(1982).

21. A. C. Scot, F. Y. F. Chu, and D. W. McLaughlin, Proc. IEEE 61,

1443 (1973).

22. S. Zdravkovi´ c and M. V. Satari´ c, About optical and acoustical fre-

quencies in a nonlinear helicoidal model of DNA molecule, submit-

ted to Chin. Phys. Lett.

23. G. Carreri, M. Geraci, A. Ginansanti, and J. A. Ruply, Proc. Natl.

Acad. Sci. USA 82, 5342 (1985).

24. S. Zdravkovi´ c and M. V. Satari´ c, Int. J. Mod. Phys. B 17, 5911

(2003).

25. N. N. Bogoliubov and Y. A. Mitropolskii, The Asymptotic Method

in the Theory of Nonlinear Vibrations, Nauka, Moscow (1974), (in

Russian).

26. M. V. Satari´ c, Physica D 126, 60 (1999).

27. T. Dauxois, M. Peyrard, and C. R. Willis, Phys. Rev. E 48, 4768

(1993).

28. O. Bang and M. Peyrard, Phys. Rev. E 53, 4143 (1996).

29. K. Forinach, T. Cretegny, and M. Peyrard, Phys. Rev. E 55, 4740

(1997).

30. M. Peyrard, Physica D 119, 184 (1998).

Received: 7 December 2004. Accepted: 5 January 2005.

J. Comput. Theor. Nanosci. 2, 1–9, 2005 9

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