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S. Zdravkovic, J.A. Tuszynski and M.V. Sataric: Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity

S. Zdravkovic, J.A. Tuszynski and M.V. Sataric: Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity

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R S AR C HARI     C 
Copyright © 2005 American Scientific PublishersAll rights reservedPrinted in the United States of America
Journal of Computational and Theoretical Nanoscience 
Vol. 2, 1–9, 2005
Peyrard-Bishop-Dauxois Model ofDNA 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 ofsome parameters of the model, especially the harmonic constant of the helicoidal springs. We studyboth 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 themost important biomolecules. Its double standard heli-cal structure undergoes a very complex dynamics and theknowledge 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 withits structural and physical dynamical characteristics. Thepossibility that nonlinear effects might focus the vibrationenergy of DNA into localized soliton-like excitations wasfirst contemplated by Englander et al.
1
Although severalauthors
2–9
have suggested that either topological kink soli-tons or bell-shaped breathers would be good candidates toplay a basic role in DNA nonlinear dynamics, there arestill several unresolved questions in this regard. A hier-archy of the most important models for nonlinear DNAdynamics was presented by Yakushevich.
10
The local openings can be analytically described asbreather-like objects of small amplitude, which have nev-ertheless interesting properties; as long as their amplitudeis small enough they can move along the chain. This isunidimensional, which allows local openings of the hydro-gen bonds and formation of denaturation bubbles.In the present paper we deal with the extended model forDNA 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 todescribe the process of local opening of base pairs (orlocal melting of the double helix). Then we attempt to shednew 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 certainextension of two of our previous papers.
13
14
However, weintroduce a new procedure which yields qualitatively newresults and solves a couple of problems.In Section 3 we present our consideration of DNAbreather dynamics in the context of the PBD model whenviscosity 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 doublehelix, which consists of two strands
s
1
and
s
2
(Fig. 1),linked by the nearest-neighbour harmonic interactionsalong the chains. The strands are coupled to each otherthrough 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 couplingconstant
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
 
      R      E      S      E      A      R      C      H      A      R      T      I      C      L      E
Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity
Zdravkovi´ c et al.
s
1
s
2
mmv
n
–1
v
n
+1
v
n
u
n
–1
u
n
+1
u
n
MorsePotential
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 moleculeis twisted. This helicoidal structure of the DNA chainimplies that nucleotides from different strands becomeclose enough so that they interact through water filaments.This means that a nucleotide at the site
n
of one strandinteracts 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 tennucleotides per one turn. Introducing the transversal dis-placements
u
n
,
v
n
of the nucleotides from their equilibriumpositions along the direction of the hydrogen bonds, theHamiltonian for the DNA chain becomes
11
12
=
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
au
n
v
n
1
2
(1)Here
k
(respectively
K
) is the harmonic constant of thelongitudinal (respectively helicoidal) spring. The last termin the Hamiltonian represents a Morse potential approxi-mating the potential of the hydrogen bonds while
D
and
a
are the depth and the inverse width of the Morse potentialwell, respectively.It is more convenient to describe the motion of twostrands by making a transformation to the centre-of-masscoordinates representing the in-phase and out-of-phasetransversal motions, namely
x
n
=
u
n
+
v
n
/
√ 
2
y
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
2
x
n
+
Kx
n
+
h
+
x
n
h
2
x
n
(3)and
m
¨
y
n
=
ky
n
+
1
+
y
n
1
2
y
n
Ky
n
+
h
+
y
n
h
+
2
y
n
+
2
√ 
2
aD
e
a
√ 
2
y
n
1
e
a
√ 
2
y
n
(4)As was explained in a couple of articles
11–13
17
, we canapply the transformation
y
=
1
(5)This means that we assume that oscillations of nucleo-tides are large enough to be anharmonic but still smallenough 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
¨
n
=
km
n
+
1
+
n
1
2
n
Km
n
+
h
+
n
h
+
2
n
2
g

n
+

2
n
+
2

3
n
(6)where
2
g
=
4
a
2
Dm
=
3
a
√ 
2and
=
7
a
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
n
t
=
1
nlte
i
n
+
F 
0
nlt
+
2
nlte
i
2
n
+
cc
+
O(
2
(8)and
n
=
nql
t
(9)Here,
l
is the distance between two neighbouring nucleo-tides in the same strand,
is the optical frequency of the linear approximation of their vibrations,
q
is thewave number whose role will be discussed later, cc areconjugate-complex terms and the function
0
is real.Before we proceed with solving Eq. (6) we give someexplanations for Eq. (8). If there were not the last term inEq. (6), the one with
2
g
, which comes from the nonlinearterm in Eq. (4), we would expect the solution in the form
1
e
i
n
+
cc instead of Eq. (8). This would be a modulatedwave with a carrier component
e
i
n
and an envelope
1
. Wewill see later that the modulation factor
1
will be treatedin a continuum limit while the carrier wave will not. Inother words, the carrier component of the modulated waveincludes the discreteness and the procedure is called semi-discrete approximation. As if there are terms with
2
n
and
3
n
in Eq. (6) we can not expect solution of this equation inthe simple form
1
e
i
n
and nonexponential term as well asterms with
e
i
2
n
should be incorporated into the expressionfor the solution. A whole method is explained in muchmore details in Ref. [18], while its mathematical basis isgiven in Refs. [19, 20].Now, we are ready for solving Eq. (6). It was alreadypointed out that the functions
i
would be treated in thecontinuum limit. So, taking this limit (
nl
z
) and apply-ing the transformations
Z
=
z
=
t
(10)
2
J. Comput. Theor. Nanosci. 2, 1–9,
2005 
 
R S AR C HARI     C 
 Zdravkovi´ c et al.
Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity
yields the following continuum approximation
Fn
±
hlt
FZT
±
Z
ZTlh
+
12
ZZ
ZT
2
l
2
h
2
(11)where
Z
and
ZZ
mean corresponding derivatives withrespect to
Z
. This allows us to obtain a new expressionfor the function
n
t
:
n
t
1
ZTe
i
+
F 
0
ZT
+
2
ZTe
i
2
+
cc
=
1
e
i
+
F 
0
+
2
e
i
2
+
1
e
i
+
F 
2
e
i
2
(12)where
stands for complex conjugate and
i
i
ZT
.From Eqs. (9)–(12) one can straightforwardly obtainexpressions for all the terms in Eq. (6).
18
From the con-tinuum version of Eq. (6), equating the coefficients forthe various harmonics, we can get a set of importantrelations.
11–13
For example, equating the coefficients for
e
i
one obtains a dispersion relation
2
=
2
g
+
2
km
1
cos
ql
+
2
Km
cos
qhl
+
1
(13)This can be used to find the corresponding group velocity
d/dq
as
g
=
lmk
sin
ql
Kh
sin
qhl
(14)In the same way, equating the coefficients for
e
i
0
=
1,we can easily obtain
0
=
1
2
(15)where
=
2
1
+
4
Km
2
g
1
(16)However, for the next three harmonics (
e
i
2
,
e
i
3
and
e
i
4
) the matter becomes more complicated. All of theseharmonics give a relation
2
=
F 
21
(17)but with different values for the parameter
. For example,equating the coefficients for
e
i
2
one can get
4
2
+
2
km
cos
2
ql
1
2
Km
cos
2
hql
+
1
2
g
2
=
2
g
F 
21
(18)which means that
is not constant but a function of 
ql
.However, coefficients for
e
i
3
and
e
i
4
give constant values
,
2
and
3
respectively. We will return to this pointlater.As if we can express functions
0
and
2
through thefunction
1
we can derive an equation for
1
. Using newcoordinates again:
S
=
Z
g
T 
=
T 
(19)we can finally obtain the nonlinear Schrödinger equation(NSE) for the function
11–141
iF 
1
 
+
P
1
SS
+
Q
1
2
1
=
0 (20)where the dispersion coefficient
and the coefficient of nonlinearity
Q
are given by
=
12
l
2
mk
cos
ql
Kh
2
cos
qhl
2
g
(21)and
Q
=
2
g
2
2

+

+
3

(22)Those derivations can be found in some more details inRef. [18].For
PQ >
0 the solution of the NSE (20) is
11
12
21
1
S
=
A
sech
S
u
e
 L
e
exp
iu
e
S
u
c

2
(23)where the envelope amplitude
A
and its width
L
e
have theforms
A
=
 
u
2
e
2
u
e
u
c
2
PQ
(24)and
L
e
=
2
 
u
2
e
2
u
e
u
c
(25)and
u
e
and
u
c
being the velocities of the envelope and thecarrier waves, respectively. Using Eqs. (23), (8), (9), (15),(17), (10), and (19) we obtain
11–14
n
t
=
2
A
sech
L
e
nl
e
t
×
cos
nl
t
+
A
sech
L
e
nl
e
t
×
2
+
cos
2
nl
t

+
O

2
(26)where
e
=
g
+
u
e
(27)
=
q
+
u
e
2
(28)and
=
+
u
e
2
V 
g
+
u
c
(29)In Ref. [13] we suggested discrete values for a wavenumber
q
. For
h
=
4 we obtained the following four valuesfor the wave length
: 6
l
, 7
l
, 8
l
, and 9
l
or, as if 
q
=
2
/
,
J. Comput. Theor. Nanosci. 2, 1–9,
2005 
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