Scattering Functions and Correlation Functions of

Random Knots
Tetsuo Deguchi and Akihisa Yao
Abstract
For random knots, we discuss correlation functions and scattering functions, which
are fundamental in the statistical mechanics of ring polymers. Random knots gives a
theoretical model for a ring polymer with xed knot in solution at the temperature.
We introduce a model function for the probability distribution of distance between
two nodes in random polygon with xed knot. We then perform numerical simulation
of random knots, and conrm that the model function gives good tting curves to
the simulation data. From the model function we obtain an analytic formula for the
correlation functions of random knots. It also gives an analytic formula for the scat-
tering functions of random knots. We thus obtain an exact description of topological
correlations, which show nontrivial topological entropic eects. The result should be
important in future applications to polymer physics.
1 Introduction
1.1 Polymers in solution
Polymers are very large molecules consisting of a long chain of the same chemical units or
groups, called monomers. We consider a polymer made of N monomers. Many soft materials
such as rubbers, gels and plastics are constructed from polymers. DNAs and proteins are
typical polymers in nature.
Figure 1: A random walk. Random walks gives a model of linear polymers in solution.
1
1.2 Random knots and ring polymers
Let us introduce random knots. We call such random polygons that have a xed knot type
random knots. They give a model of ideal ring polymers in solution. We note that ideal
polymers in solution have no excluded volume (no thickness) eectively, and are modeled
by random walks. A random polygon is given by such a random walk whose two ends are
connected.
Ring polymers have attracted much interest in polymer physics, and various proper-
ties have been studied not only theoretically but also experimentally such as using circular
DNAs. [1, 2, 3, 4, 5, 6] For the Gaussian random polygon the analytic expression of the
static structure factor was obtained. [1] The scattering function is compared with that of
star polymers with four or ve arms. [1, 5] The scattering data of cyclic polystyrene in deu-
teriated cyclohexane at the temperature was obtained by the SANS (Small Angle Neutron
Scattering) experiment. [6]
Figure 2: A random polygon. Random polygons give a model of ring polymers in solution.
Relative position vector R
m
R
n
.
Recently, statistical properties of ring polymers under topological constraints have been
investigated extensively through numerical simulation and theoretical analysis. [7, 8, 9, 10,
11, 12, 13, 14, 15, 16] (For a review, see Refs. [17, 18].) It is rst conjectured by des Cloizeaux
that a topological constraint should lead to an eective repulsion among segments of ring
polymers [7]. It is indeed observed that a ring polymer with xed knot can be much larger
in size than that of no topological constraint. Moreover, the scattering functions of random
polygons with some dierent knots are evaluated through simulation. [19]
1.3 Radial distribution function
Let us consider a polygon of N nodes and denote by R
m
the position vector of the mth node
for m = 1, 2, . . . , N. We rst introduce the following:
g
n
(r) =
N

m=1
(r (R
m
R
n
)) . (1)
2
Here the average is taken over all possible congurations of the polygon of N nodes.
The quantity: g
n
(r) d
3
r/N describes the probability of nding another vertex in the volume
element d
3
r = dxdydz located at position vector r relative to the position of the nth vertex,
R
n
. Here g
n
(r) does not depend on n due to the cyclic symmetry with respect to n.
Formally, however, we dene the pair correlation function for an N-noded random poly-
gon, taking the average of g
n
(r), as follows: [20]
g(r) =
1
N
N

n=1
g
n
(r) =
1
N
N

m,n=1
(r (R
m
R
n
)) . (2)
Due to the rotational symmetry, the pair correlation function g(r) depends only on the
distance r = |r|. We denote it by g(r), and call it the radial distribution function.
For an N-noded random polygon with xed knot K we dene the pair correlation function
by
g
K
(r) =
1
N
N

m,n=1
(r (R
m
R
n
))
K
. (3)
Here the average
K
is taken over all possible congurations of the random polygon with
knot K.
1.4 Distribution function of distance between two nodes of a ran-
dom polygon
Let us formulate the distribution function of distance between two selected nodes of random
polygon with xed knot. We recall that we consider a polygon of N nodes where R
m
denotes
the position vector of the mth node for m = 1, 2, . . . , N. We select a pair of nodes, say, j
and k, out of the N nodes. If the two arcs of the polygon between them have segments n
and N n, respectively, where n N n, we dene arclength by fraction n/N:
= n/N . (4)
Here we recall that n is given by min(|j k|, N |j k|). We denote by f(r; , N) the
probability distribution of distance r between the two nodes. Here r denotes the dierence
of the position vectors: r = R
j
R
k
, and r = |r|.
For random polygons that have a xed knot type K, we denote by f
K
(r; , N) the
distribution function of distance between two nodes with arclength = n/N . In a recent
simulation it was shown that the distribution function f
K
(r; , N) is roughly approximated
by the Gaussian one, although there exists some deviation from it. [21]
1.5 Correlation functions expressed in terms of distance distribu-
tions
We now show that the pair correlation function of a knotted random polygon is related to
the distribution function of distance between two nodes.
The quantity 4r
2
g(r)r/N gives the probability of nding another segment in a spheri-
cal shell from radius r to r+r centered at a given segment. In short, it gives the probability
3
Figure 3: Distance r between two nodes with arclength = n/N. Here r = R
n
R
0
.
distribution of distance r between two nodes for all pairs of the nodes of the polygon. The
distribution f(r; , N) is therefore related to the radial distribution function g(r) by
4r
2
g(r) = 2N
_
1/2
0
f(r; , N) d. (5)
Similarly, the distribution f
K
(r; , N) is related to the radial distribution function g
K
(r) by
4r
2
g
K
(r) = 2N
_
1/2
0
f
K
(r; , N) d. (6)
1.6 Scattering functions
We dene the (single-chain) static structure factor g(q) of the ring polymer by [20]
g(q) =
_
dre
iqr
g(r) =
1
N
N

m,n=1
exp(iq (R
m
R
n
)) . (7)
We also call it the scattering function. In terms of the spherical coordinate system (r, , )
with dr = r
2
dr d sin d, we calculate
_
e
iqr
dr as follows:
_
e
iqr
g(r)dr =
_

0
g(r)r
2
dr
_

0
sin d
_
2
0
de
iqr cos
=
_

0
g(r)
sin qr
qr
dr . (8)
Here q = |q| and we set the z-axis such that we have q = qe
z
= (0, 0, q) and q r = qr cos .
In terms of the distribution f
K
(r; , N), the scattering function of a ring polymer with
knot K is expressed as follows:
g
K
(q) =
_
dre
iqr
g
K
(r) = 2N
_

0
_
1/2
0
f
K
(r; , N)d
sin qr
qr
dr . (9)
1.7 The purpose of the paper
In the paper we review some recent result on correlation functions of random knots. [22]
We introduce a tting formula which describes the r- and -dependence of the distribution
4
function f
K
(r; , N) for random polygon with N nodes, completely. Through computer sim-
ulation we conrm that it is perfectly tted to the data as a function of r and for some
knots. The nontrivial correlation eects due to topological constraints should be character-
ized by the formula. In fact, we obtain an analytic expression for the scattering function of
random polygon with xed knot, and derive its large q and small q behaviors, analytically.
They are consistent with the previous simulation result.
2 Algorithms of simulation
We have constructed 10
6
random polygons with unit bond length by a kind of pivot method.
We take randomly two nodes of a polygon and rotate one arc around the line between the
two nodes with randomly chosen angle. We perform this process 500 times, and then employ
the conguration as a random polygon.
The algorithm for constructing random polygons is illustrated as follows:
(0) Take an initial 3D conguration of a polygon of N vertices with unit bond length
(1) Take two vertices A and B, arbitrarily
(2) Around the line AB, rotate one of the two subchains with a random angle
(3) Repeat the process (1) and (2) many times, and we have a random polygon
After constructing 10
6
random congurations of random polygons, we then calculate the
second order Vassiliev invariant and the determinant of knots for the 10
6
polygons. [23] We
eectively classify their knot types by the set of the values of the topological invariants. [24]
We numerically evaluated knotting probabilities for several knots. [25]
Let us now dene the mean square radius of gyration of an N-noded random polygon
with knot K by
R
2
g,K
=
1
2N
2
N

j=1
N

k=1
(R
j
R
k
)
2

K
. (10)
For N = 800, numerical estimates of R
2
g,K
are given in Table I. The mean square average
of gyration radius for the trivial knot, 81.9459, is larger than that of all, 66.7255. We thus
observe topological swelling.
K R
2
g,K
errors fractions
0 81.9459 0.4074 0.040456
3
1
79.3937 0.2883 0.075828
3
1
#3
1
76.7232 0.2889 0.070522
other 63.9200 0.0709 0.813194
all 66.7255 0.0667 1.0
Table 1: Mean square radius of gyration R
2
g,K
of an equilateral random polygon with a
topological condition K, and fractions (probabilities) of knot species. Here N = 800.
5
0
0.002
0.004
0.006
0.008
0.01
0 0.5 1 1.5 2 2.5 3
f
K
(
x
;

,
N
)

x
x
=1/20, N=300
All
Trivial
Trefoil
3
1
#3
1
Others
Figure 4: Probability distribution

f
K
(x; , N) for = 1/20 and N = 300. For topological
conditions, 0, 3
1
, 3
1
#3
1
, others and all, the
2
per datum are given by 7.70, 4.27, 1.09,
4.19 and 16.6, respectively; the estimates of
K
are given by 0.17 0.006, 0.10 0.005,
0.04 0.004, 0.007 0.004 and 0.07 0.005, respectively.
3 Simulation results on distance distributions
3.1 Exact result in the case of no topological constraint
Let us now derive probability distribution f(r; , N) of distance r between two nodes sep-
arated by N bonds in a random polygon of N segments with no topological constraint.
Here we recall that r denotes the dierence of the position vectors of the two nodes, and
r = |r|. With arclength parameter , the polygon consists of two linear chains of n = N
and N n = N(1 ) bonds, respectively, which have the same end-to-end vector r in
common. Thus, the probability distribution (r; n, N n) of the vector r is proportional to
the product of the Gaussian distributions such as (r; n, N n) p(r; n)p(r; N n). Here
p(r; N) denotes the probability distribution of the end-to-end vector r of random walk of N
steps. For very large N, it is given by the Gaussian distribution: p(r, N) exp(3r
2
/2Nb
2
).
Considering the rotational symmetry, we therefore have
f(r; , N) 4r
2
exp
_

3r
2
2(1 )Nb
2
_
(11)
Hereafter we write the distribution function under no topological constraint, f(r; , N), as
f
all
(r; , N), and we set b = 1.
6
3.2 Model function for the distance distribution
Generalizing distribution (11) we propose the following formula for the distance distribution
under a topological constraint K, f
K
(r; , N):
f
K
(r; , N) = C
K
(, N) r
2+
K
()
exp
_
3r
2
2N
K
()
2
_
, (12)
where the normalization C
K
(, N) is given by
C
K
(, N) =
_
3
2N
K
2
_
3+
K
2
2

_
3+
K
2
_
.
The constants
K
and
K
are functions of variable z = (1 ) as

K
(z; N) = z
1
2
exp(
K
z) ,
K
(z; N) = b
K
z

K
. (13)
The parameters
K
,
K
and b
K
depend on the knot K and the number of nodes, N.
Formulas (13) show that
K
vanishes when = 0. Here we note that function (12)
becomes Gaussian if
K
= 0. In fact, the distribution f
K
(r; , N) should become close to
the Gaussian one when is very small. Let us assume probability distributions p
K
(r; n)
and p
K
(r; N n) of the end-to-end vector r of the sub-chains of length n and N n in
the N-noded polygon with knot K, respectively. For small n, p
K
(r; n) should be given
by a Gaussian distribution. If the length of chain is very small, the probability of making
nontrivial knots is very small. Furthermore, the value of p
K
(r; N n) should be almost
constant with respect to r for such r that has |r| as large as n, if N is very large and n
is much smaller than N. Thus, p
K
(r; n) should be dominant in the r-dependence of the
product, p
K
(r; n)p
K
(r; N n), and hence f
K
(r; , N) for 1 should be given by the
Gaussian distribution.
The average distance between two nodes with parameter , r
K
(, N), is given by
r
K
(, N) :=
_

0
r f(r; , N)dr =

2
3
N
1
2
D(
K
)
K
. (14)
Here D(
K
) is given by D(
K
) = ((4 +
K
)/2) /((3 +
K
)/2). In terms of the ratio of
distance r to the average distance, x = r/r
K
(, N), we express the distribution function
f
K
(r; , N) as

f
K
(x; , N) =
2D
3+
K
(
K
)x
2+
K

_
3+
K
2
_
exp
_
D
2
(
K
) x
2
_
. (15)
Here we note that

f
K
(x; , N)dx = f
K
(r; , N)dr. We also remark that

f
K
(x; , N) has only
one tting parameter
K
.
3.3 Good tting curves to the data
We nd through the simulation data that formula (12) together with (13) gives good tting
curves not only as a function of r but also as a function of . First, we evaluate numerically
the distribution function f
K
(r; , N) of the random polygon of unit bond length for N = 100,
7
0
0.002
0.004
0.006
0.008
0.01
0 0.5 1 1.5 2 2.5 3
f
K
(
x
;

,
N
)

x
x
=1/2, N=300
All
Trivial
Trefoil
3
1
#3
1
Others
Figure 5: Probability distribution

f
K
(x; , N) for = 1/2 and N = 300. For topological
conditions, 0, 3
1
, 3
1
#3
1
, others and all, the
2
per datum are given by 3.19, 1.30, 0.31,
2.85 and 0.17, respectively; the estimates of
K
are given by 0.300 0.004, 0.225 0.003,
0.169 0.003, 0.164 0.003 and 0.0007 0.0005, respectively.
N = 800 N = 300 N = 100

K

2

K

2

K

2
Trivial 0.194 0.002 0.03 0.097 0.006 0.77 0.035 0.006 1.37
Trefoil 0.147 0.003 0.07 0.014 0.005 0.54 0.180 0.004 0.60
3
1
#3
1
0.086 0.003 0.06 0.125 0.004 0.32 0.412 0.005 0.09
Others 0.080 0.002 0.76 0.233 0.005 0.92 0.427 0.008 0.62
Table 2:
K
is estimated from z
K
curves. Values of
2
per datum are shown.
300 and 800 with 12 dierent values of . In each case of and N, we numerically evaluate
the average distance, r
K
(, N), through the distribution function f
K
(r; , N). We then
derive the normalized distribution

f
K
(x; , N), and apply formula (15) to the graphs. It
indeed gives good tting curves in all cases we have investigated, such as shown in Figures
4 and 5 for N = 300 and = 1/20, 1/2. Secondly, we apply the rst formula of (13) to the
best estimates of
K
as a function of z. We also apply the second formula of (13) to the the
best estimates of
K
as a function of z. Then, we nd that both of them give good tting
curves except for the case of other knots as shown in Figures 6 and 7, respectively, where
the best estimates are listed in Tables 2 and 3, respectively.
8
-0.06
-0.04
-0.02
0
0.02
0.04
0 0.1 0.2
l
n
(

K
/

z
)
z
z
K
Curves N=300
Trivial
Trefoil
3
1
#3
1
Others
Figure 6:
K
versus z = (1 ) for N = 300
N = 800 N = 300

K
b
K

2
/datum
K
b
K

2
/datum
Trivial 0.440 0.007 0.847 0.011 0.86 0.412 0.019 0.528 0.017 2.20
Trefoil 0.491 0.006 0.819 0.010 0.58 0.69 0.04 0.57 0.04 6.16
3
1
#3
1
0.61 0.01 0.90 0.02 2.72 1.54 0.07 1.38 0.14 5.64
Others 0.27 0.10 0.051 0.009 67.2 0.68 0.08 0.45 0.07 49.7
Table 3:
K
and b
K
are estimated from z
K
curves.
3.4 Consistency check with respect to the mean square radius of
gyration
Formulas (12) and (13) for the distribution function f
K
(r; , N) are also consistent with the
numerical values of the mean square radius of gyration directly evaluated from the 3-dim.
coordinate data of random polygons.
In terms of the distribution function f
K
(r; , N), we express the mean square radius of
gyration of random polygons with knot K, R
2
g,K
, as follows:
R
2
g,K
:=
1
2
_
1
0
d
_

0
r
2
f
K
(r; , N) dr
= N
_
1/2
0

2
K
_
1 +

K
3
_
d. (16)
Here
K
and
K
are functions of through formula (13). In Tables 4 and 5, we nd that the
estimates of mean-squared gyration radius directly evaluated by (10) agree well with those
9
-0.1
0
0.1
0.2
0.3
0.4
0 0.1 0.2

K
z
z-
K
Curves N=300
Trivial
Trefoil
3
1
#3
1
Others
Figure 7:
K
versus z = (1 ) for N = 300
evaluated by integral (16) through the best estimates of the tting parameters
K
,
K
and
b
K
which are listed in Tables 2 and 3.
K R
2
g,K
/R
2
g,all
errors estimates of the integral
0 1.2281 0.0061 1.2298
3
1
1.1899 0.0043 1.1908
3
1
#3
1
1.1498 0.0043 1.1503
other 0.9580 0.0011 0.9580
Table 4: Ratio R
2
g,K
/R
2
g,all
and its estimates evaluated by using formulas (13) for equi-
lateral random polygon with a topological condition K. Here N = 800.
4 Analytic expression of the scattering functions
4.1 Integral expression
The scattering function of an N-noded random polygon with xed knot K is given by
g
K
(q) = 2N
_
1/2
0
d
2
a()((3 +
K
())/2)

_

0
y
1+
K
()
exp(y
2
) sin(a()y)dy . (17)
where a() is given by a() = r
K
(, N)q/D(
K
). Here we recall that the scattering function
is given by the Fourier transform of the correlation function (See, eqs. (7) and (9)).
10
K R
2
g,K
/R
2
g,all
errors estimates
0 1.1313 0.0020 1.1329
3
1
1.0551 0.0022 1.0560
3
1
#3
1
0.9885 0.0036 0.9890
other 0.8670 0.0014 0.8662
Table 5: Ratio R
2
g,K
/R
2
g,all
and its estimates evaluated by using formulas (13) for equi-
lateral random polygons with a topological condition K. Here N = 300.
4.2 Asymptotic behaviors
In the small q limit, we show from (17) that the scattering function does not depend on the
knot type, if it is expressed as a function of qR
g,K
, as follows:
g
K
(q)/N = 1
q
2
3
R
2
g,K
+ . (q 1) . (18)
The result is consistent with the previous numerical simulation. [19]
In the large q case, however, the behavior might be nontrivial. Through the saddle point
approximation, we have
g
K
(q)/N 2
_
1/2
0

2 sin(
K
() + /4)
((3 +
K
())/2)/(

/2)
_
Nq
2
6

2
K
()
_

K
()/2
exp(
Nq
2
6

2
K
()) d.
(19)
Furthermore, with respect to a large parameter A = Nq
2
/12 = R
2
g,all
q
2
, we can show
g
K
(q)/N
1
A
_
1 + O(A

K
)
_
(q 1) . (20)
For the trivial, trefoil and composite knots, we have
K
0.5 and we may have a very slow
asymptotic expansion with respect to A = Nq
2
/12.
5 Conclusion: an exact description of topological cor-
relation
(i) The exact expression (12) and (13) of distance distribution f
K
(r; n/N, N) as a function
of distance r and arclength n/N should be valid for any knot K.
(ii) The formula (12) and (13) is consistent with several numerical data such as the mean
square radius of gyration.
(iii) It is suggested that the scattering function might have a nontrivial large q behavior.
11
6 Open question
Characterize the scaling behavior of random knots
As shown in Table 1, the average size of random knots becomes large under a topological
constraint. This suggests that topological entropic repulsion should play a similar role as
the excluded volume. However, as far as the correlation functions concerns, the behavior of
random knots is almost given by the Gaussian one. Thus, the scaling behavior of random
knots should be nontrivial.
Acknowledgment
One of the authors (T.D.) is thankful for useful discussions on random knots to many par-
ticipants of the International Workshop on Knot Theory for Scientic Objects, Osaka City
University, Osaka, Japan, March 810, 2006.
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Tetsuo Deguchi
Department of Physics, Ochanomizu University,
2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
deguchi@phys.ocha.ac.jp
Akihisa Yao
Internal Audit Division,
Mizuho Corporate Bank, Ltd.,
1-2-16 Yaesu, Chuo-ku, Tokyo 103-0028, Japan
yao@degway.phys.ocha.ac.jp
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