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Abstract
Internal oscillations of an alpha-helix soliton are studied numerically on a
modified version of Davydov’s equations and analytically on an approxi-
mating system of coupled nonlinear Schrodinger equations. The numerical
results are used to interpret lines in recently measured laser-Raman spectra
of metabolically active E. coli. Agreement between measured and calcu-
lated lines appears to be within the uncertainties of computation and
measurement.
1. Introduction
The idea that bond energy could be transported along one-
dimensional molecular chains (such as alpha-helix protein
molecules) by solitary waves (or “solitons”) was first pro-
posed by Davydov and Kislukha in 1973 [ 11. Since that time
Davydov and his co-workers have published a number of papers
that discuss various soliton parameters including lifetime,
damping, energy, and wave structure [ 11. The physical notion
of Davydov’s alpha-helix soliton can be understood rather
easily with reference to Fig. 1. The energy to be transported
is stored as “stretching” quanta of the amide4 bond (i.e.,
C = 0) which has an absorption peak at 1653 cm-’ correspond-
ing to a quantum unit of 0.205eV. Naively one would expect
such energy to disperse rapidly (- IO-’* s) via dipole-dipole
interactions throughout all the amide-I bonds. But if certain
“ 9I
J 0.145
L 0.231
N 0.073
P 0.034
Q 0.019
R 0.012
S 0.0089
T 0.0073
U 0.0037
V 0.0030
X 0.0022
Z 0.0017
10"
2. Alpha-helix models k3 = -xl
W
In this section the several numerical and analytical models to be
considered are listed in order of decreasing complexity. 10"
k4 = -x2
W
2.1, Modified Davydov (MO) equations
The following equations were developed in [5] to describe the where M is one third of the mass of a unit cell, w is the linear
coupled propagation of bond energy probability density, A,,, force constant of a hydrogen bond, x1 (as previously noted) is
and longitudinal displacement of an amide-I bond, E,,,. the change in amide-I bond energy per unit extension of an
adjacent hydrogen bond, and x2 is the change in the longitudinal
(nearest neighbor) dipole-dipole coupling term, J , per unit of
differential displacement.
The time scale, 7,measures laboratory time in units of
Physica Scripta 25
The VibrationalStructure of Davydov Solitons 653
2L
z= E
i. ol 0
E
f .
P a , * t - P a , x x A (lAa12)xx
where
e = JL
2.3. Coupled nonlinear Schrodinger (CNLS) equations at w + kZ = - 2e, and two linearly independent unsymmetric
For the solitary wave solutions that arise in this study, the eigenvectors at w + k2 = E which can be written as
velocities observed are small compared with unity (longitudinal
sound speed). Thus the first term in (CZ2’) can be neglected, Au1
leading to the coupled system of nonlinear Schrodinger
equations.
i A 1 , t +AL..+
iAz,t +-42,xx+ A general solution of CLS is then
iA3,t +’43,xx+
-
* From here on a subscript notation is used t o indicate partial differenti-
ation.
2
[:I-
= A, I F(k)expi[kx-(k2+2e)t]dk
Physica Scripta 25
654 Alwyn C.Scott
+
[ ]
A e-2ni/3
AU 2 e2ni/3 -m
H(k)expi[kx-(k’-~)t]dk
1
1 e-3iet
i#t+hx+1612$ = 0 (14) Manakov [9] has shown that eq. (23) is completely integrable,
Equation (1 2) also has a double root at w = E which correspond Thus the “mixed solitary wave” given by eqs. (16) and (19) [or
to two unsymmetric solitary waves from eq. (23) by taking $ = col (aGm, 0, Gm)] is a true soliton
of CNLSNB. The squared amplitudes (i.e., bond energies) of its
three components are:
Ao(x - s t )
[1+ a’ + 2a cos 3et]
42
aeiet+2ni/3 + e-2iet
16. (16)
Following Gibbons et al. [lo] it is straightforward to show
that the Hamiltonian associated with CNLSNB is
3
leads to the requirements that Gm must satisfy the three pde’s: -00
Physica Scripta 25
The Vibrational Structure of Davydov Solitons 655
0.09
0.08
physical significance is readily assigned to the terms in eq. (29): >
the first term is kinetic energy, the second is binding energy, 50 0.07
and the third is interspine interaction energy. It is energetically z
favorable for the mixed mode to add more of the unsymmetric 0.06
z
mode by increasing a. 0
m 0.05
Table I1
~
45 2E,
52 3E1
63 3E1
85 5E 1
0.02I I 90 E, -2E,
I50 170 190 210 230 250
T 108 E, -E1
123 E,
Rg. 3. Peak bond energy on each spine as a function of computer time 152 E, + 2E,
with the nonlinear parameter x, = 0.3 X lo-"' newtons which is below 182 E, + 3E,
threshold for soliton formation.
Physica Scripta 25
Alwyn C.Scott
I E, = 125.7(1 k 0.0506)cm-'
0 175 -
150 -
./A -h
'E 125 -
s
n
W
3 100 -
v)
3 m
= 75-
/
I
t
0
2525 50 75 100 125 150 175 200
CALCULATED (cm-9
R g . 6. Spatial waveform on spine No. 2 above threshold (xl = 0.4 x Rg. 7. Comparison laser-Raman lines measured in Fig. 2 with calcu-
newtons). (a) Maximum amplitude at 7 = 246. (b) Minimum lations according to the assignments in Table I1 from E , in eq. (33) and
amplitude'at 7 = 234. E, in eq. (34).
Physica Scripta 25
The VibrationalStructure of Davydov Solitons 657
15.4* 3.7%
150
/ (1) Calculation of component
frequencies from MD.
125.7 r 5.1%
25 50 75 100 125 150 175 200 Figure 8 shows the agreement between the lines measured
CALCULATED: LEAST SQUARES FIT (cm-') from the spectrum of Fig. 2 and those calculated from the
energies listed in the second row of Table 111. Figure 9 shows
Fig. 8. Same as Fig. 7 but E , and E , are the "least-squares-fit" given in
eq. (35).
the agreement between data from 125 lines measured during ten
separate experiments and those calculated from the energies
listed in the third row of Table 111. The differences between
measured and calculated lines shown in Figs. 8 and 9 must be
7. Concluding discussion attributed either to measurement errors or theoretical miscon-
The central question in this paper is to decide whether the laser- ceptions [ 151. Noting that [ 11,161: (i) The spectral band width
Raman spectrum displayed in Fig. 2 can be assigned to internal of the measurements is 5 cm-'; (ii) The lines often move several
oscillations of alpha-helix solitons. According to Webb [6] these cm-' during the time of measurement (- 100 minutes); and (iii)
spectra are characterized by the following facts: (i) At 300K a Low frequency lines are difficult to resolve because of Rayleigh
Raman spectrum is observed only when the cells are metabolic- scattering (see Fig. 2), I conclude that Figs. 8 and 9 show
ally active, (ii) The intensity ratios of Stokes to anti-Stokes lines reasonable agreement between measurements and calculations.
indicate that the Raman active states are produced in vivo by The reader may not agree, but certainly the evidence is
non-thermal means, and (iii) Spectral lines below 300cm" strong enough to encourage a vigorous search for corroborative
shift to lower wave numbers as the cells progress through their experiments.
life cycles. Although broad laser-Raman spectra have been
observed on the alpha-helix proteins in aqueous solution and in
Appendix
crystalline form [ 12-14], such an explanation is unlikely for
the lines in Fig. 2. Here we consider a generalization of CNLSNB from three to n
A convenient summary of the foregoing results is provided interacting channels. Thus
by Table 111.
Since there was n o adjustment of parameters in MD prior to the i A, + A , + -n1( A- *--A-) A = ZA
calculations of row (l), the agreement displayed in this table is
quite remarkable. There is little difficulty in supposing the MD .
where A = col (Al, . . , A n ) . If the channels are spaced close
together compared with the decay constant for lateral inter-
action, it is reasonable to assume
e e ...
0 e ...
z=[ (A-2)
FREQUENCY (cm-')
reduces (A-1) to
Fig. 9. Histogram of lines from ten laser-Raman experiments on meta- -* - -
bolically active E. coli. Calculated lines are from the least squares fit i&+$,,+(@ = 0
values of E , and E , given in eq. (36). Data from Webb, S. J. (private
communication). where 8 = col (@',. . . ,&).
658 Alwyn C.Scott
Physica Scripta 25