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Article history: Energy transport and storage in α − helix proteins, in the presence of long-range intermolecular interac-
Received 25 July 2018 tions, is addressed. The modified discrete Davydov model is first reduced to a space-fractional nonlinear
Revised 19 September 2018
Schrödinger (NLS) equation, followed by the stability analysis of its plane wave solution. The phenomenon
Accepted 19 September 2018
is also known as modulational instability and relies on the appropriate balance between nonlinearity and
dispersion. The fractional-order parameter (σ ), related to the long-range coupling strength, is found to re-
Keywords: duce the instability domain, especially in the case 1 ≤ σ < 2. Beyond that interval, i.e., σ > 2, the fractional
α − helix NLS reduces to the classical cubic NLS equation, whose dispersion coefficient depends on σ . Rogue waves
Fractional dispersion solution for the later are proposed and the biological implications of the account of fractional effects are
Solitons
discussed in the context of energy transport and storage in α − helix proteins.
Energy
© 2018 Elsevier Ltd. All rights reserved.
https://doi.org/10.1016/j.chaos.2018.09.037
0960-0779/© 2018 Elsevier Ltd. All rights reserved.
C.B. Tabi / Chaos, Solitons and Fractals 116 (2018) 386–391 387
rameter. RW solutions are presented and discussed for this partic- where the parameter k is a wavenumber, d is the lattice spacing
ular case, including some biological implications. Some concluding and Jn is given by Eq. (2). Inversely, the function un (t) is related to
remarks end the paper. φ (k, t) through the formula
π
2. Model and dynamical equation un (t ) = eiknd φ (k , t )dk . (7)
−π
2.1. Model In the continuum approximation, i.e., un (t) → u(x, t), with x = nd,
when k → 0, relations (6) and (7) become
The generalized Hamiltonian for a linear chain of amide-I units +∞
that make an α − helix has been proposed by Davydov [1,2]. It con- φ (k, t ) = e−ikx u(x, t )dx and
−∞
siders the coupling between amide-I vibration, and displacements +∞
of amino-acid residues, and all the interactions are summarized in 1
u(x, t ) = eikx φ (k , t )dk . (8)
the following Hamiltonian [1,2,9,17]: 2π −∞
Applying all the above to Eq. (5) in the continuum approximation
H= h̄ω0 βn† βn − Jn−m (βn† βm + βn βm
†
) − Dβn βn† βn†+1 βn+1 , (1) leads to
n m =n
∂ u(x, t ) +∞
∂ u(x, t )
i = −J (0 )u(x, t ) − dydxK (x − y )
with the subscript n referring to the lattice index along a strand (or ∂t −∞ ∂x
chain). The expression of H suggests that an individual amino acid
− 2D|u(x, t )|2 u(x, t ), (9)
will be identified by the index pair n, such that β n (βn ) are bo-
†
son creation (annihilation) operators associated with intramolecu- where the Kernel K(x) is given by
lar vibrations of the nth peptide group. These operators satisfy the
1 +∞
G (k )
usual commutation relations for bosons, i.e., [βn , βm ] = δm,n and
†
K (x ) = eikx dk, (10)
π k2
[βn , βm ] = 0 . ω0 is the local amide-I vibrational energy, and the −∞
+ ∞
+ ∞ Riemann–Liouville fractional derivatives of order σ , that are re-
φ (k, t ) = e−iknd un (t ) and J (k ) = e−iknd Jn , (6) spectively given by [32,33]
m=−∞ m=−∞
388 C.B. Tabi / Chaos, Solitons and Fractals 116 (2018) 386–391
Fig. 1. The panels show plots of the MI growth rate versus the wavenumber λ and the fractional-order parameter σ . For a fixed value of the transfer strength J0 = 0.08,
the instability regions arise with changing the exciton-exciton coupling parameter D: (a) D = 0.1, (b) D = 0.2 and (c) D = 0.3.
σ u (x, t ) = 1 ∂n x
u ( ξ , t )d ξ Table 1
D+ , Instability regions with changing σ and D as in Fig. 2.
( n − σ ) ∂ xn −∞ (x − ξ )σ −x+1
Fractional-order(σ ) D = 0.1 D = 0.2 D = 0.3
σ u (x, t ) = (−1 )n ∂ n x
u ( ξ , t )d ξ
D− . (17)
( n − σ ) ∂ xn −∞ (ξ − x )σ −x+1 1.1 λ ∈ [0; 0.22π ] λ ∈ [0; 0.35π ] λ ∈ [0; 0.40π ]
1.4 λ ∈ [0; 0.48π ] λ ∈ [0; 0.65π ] λ ∈ [0; 0.78π ]
1.8 λ ∈ [0; 0.63π ] λ ∈ [0; 0.82π ] λ ∈ [0; 0.98π ]
3. Modulational instability analysis
The fractional NLS Eq. (16) admits the plane wave u(x, t ) =
(1 + χ (x, t ))eiQt as solution, where χ (x, t) is a small perturbation nonlinear effects that arise in the system are characterized by the
governed by the equation parameter D of the initial model. The above-described effect is also
well pictured by the panels of Fig. 2, where the growth rate of
∂ ∂σ
i χ (x, t ) = −Pσ χ (x, t ) − Q (χ (x, t ) + χ ∗ (x, t )). (18) MI is plotted versus the wavenumber λ, with changing σ and D.
∂t ∂|x|σ In general, the instability region enlarges with increasing D, and
Separating the real and imaginary parts of the solution χ = χ1 + get more larger when σ also increases. This can be observed by
iχ2 , Eq. (18) becomes comparing Fig 2(a), (b) and (c), where σ progressively increases.
The different regions of instability are summarized in Table 1. We
∂ ∂σ
χ (x, t ) = −Pσ χ (x, t ), should stress that the calculations made in this section are re-
∂t 1 ∂|x|σ 2 stricted to the case 2 ≤ s < 3, with σ = s − 1 . However, we can con-
∂ ∂σ sider some other cases, specifically when s > 3. The fractional-order
χ2 (x, t ) = Pσ χ (x, t ) + 2Q χ1 (x, t ). (19)
∂t ∂|x|σ 1 NLS Eq. (15) then becomes
Solutions for Eq. (19) can be considered in the form of the follow-
∂ u(x, t ) ∂2
ing Fourier transfroms: i = −Pσ 2 u(x, t ) − Q |u(x, t )|2 u(x, t ), (23)
∂t ∂x
+∞
χ˜ 1 (λ, ) = χ1 (x, t )ei(λx+t ) dxdt, with
−∞
+∞ J0 ξ (σ − 1 )
χ˜ 2 (λ, ) = χ2 (x, t )ei(λx+t ) dxdt. (20)
P= , with σ = s − 1. (24)
2
−∞
Q keeps the same expression. ζ (x) is the Riemann zeta function.
Replacing the above solutions into Eq. (19) leads to a homogeneous
This form of the NLS equation is due to the fact that the spectrum
system for χ˜ 1 and χ˜ 2 . The condition for such a system to admit
function G, when s > 3 (σ > 2), tends to the limit [18,19,31]
non-trivial solutions is obtained by setting its determinant to zero,
which leads to the nonlinear dispersion relation J0 ξ (σ − 1 ) 2
G (k ) = k . (25)
2Q 2
2 = Pσ2 |λ|σ |λ|σ + . (21)
Pσ This shows that for a certain critical value of the fractional-order
From the above, the growth rate of MI is given by parameter, the fractional derivative NLS equation behaves like the
classical cubic-NLS equation, except that in this case, the disper-
2Q sion coefficient still depends on s, i.e., σ .
G (σ , k ) = − 2 = |Pσ ||λ|σ /2 − |λ|σ + . (22)
Pσ
The corresponding growth rate of instability is computed in 4. Rogue wave solutions
Fig. 1 versus the wavenumber λ and the fractional-order parameter
σ . We should however stress that the fractional-order parameter The coefficients Pσ and Q of Eq. (23) are all positive, their prod-
also characterizes the effect of the LR dispersive coupling among uct Pσ × Q is consequently positive. This gives the possibility of
peptide groups. For instance, the regions of λ, where the plane finding the RW solutions for Eq. (23), and discuss their behav-
wave is expected to break-up into solitonic structures gets enlarged ior when nonlinear and dispersive effects are varied. We mainly
with increasing σ . Obviously, the fractional derivative brings about focus on solitons on finite background (SFB) consisting of a lo-
important changes in the dispersion of the system, and, when bal- calized nonlinear structure evolving upon a nonzero background
anced with the changes in D, trains of solitons can emerge from plane wave. A generalized SFB solution of the NLS equation is writ-
the studied system. The reader should however remember that the ten as [25]
C.B. Tabi / Chaos, Solitons and Fractals 116 (2018) 386–391 389
Fig. 2. The panels show plots of the MI growth rate (22) versus the wavenumber λ and q, with changing the fractional-order parameter σ and the exciton-exciton coupling
parameter D. Panel (a) corresponds to σ = 1.1, (b) to σ = 1.4 and (c) to σ = 1.8, with J0 = 0.08.
Fig. 3. The panels show the spatiotemporal plots of the Akhmediev RW with changing the fractional-order parameter σ ( > 2): (a) σ = 2.1, (b) σ = 2.4 and (c) σ = 3, with
J0 = 0.08 and D = 0.2. The Akhmediev RW is obtained for a < 1/2, and we have considered a = 0.1 in this case.
√
2Pσ (1 − 4a ) cosh(2bPσ t ) + 2a cos(cx ) + i sinh(2bPσ t )
u(x, t ) = √ exp(2iPσ t ). (26)
Q 2a cos(cx ) − cosh(2bPσ t )
Fig. 4. The panels show the spatiotemporal plots of the Kuznetsov-Ma RW with changing the fractional-order parameter σ > 2: (a) σ = 2.1, (b) σ = 2.4 and (c) σ = 3,
with J0 = 0.08 and D = 0.2. The Kuznetsov-Ma RW is obtained for a > 1/2, and we have considered a = 0.95 to plot these panels.
spine coupling, where different classes of RWs were found using References
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