Supercoiling of Knotted and Unknotted DNA Plasmids Contact in Kirchhoff Rods With Applications To Theory of Self

doi: 10.1098/rsta.2004.
1393
, 1281-1299 362 2004 Phil. Trans. R. Soc. Lond. A
Bernard D. Coleman and David Swigon
supercoiling of knotted and unknotted DNA plasmids

contact in Kirchhoff rods with applications to Theory of self
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10.1098/rsta.2004.1393
Theory of self-contact in Kirchho rods with
applications to supercoiling of knotted and
unknotted DNA plasmids
By Bernard D. Coleman
1
and David Swi gon
2
1
Department of Mechanics and Materials Science and
2
Department of Chemistry and Chemical Biology, Rutgers University,
Piscataway, NJ 08854, USA (bcoleman@jove.rutgers.edu; swigon@jove.rutgers.edu)
Published online 14 May 2004
There are circumstances under which it is useful to model a molecule of duplex DNA
as a homogeneous, inextensible, intrinsically straight, impenetrable elastic rod of cir-
cular cross-section obeying the theory of Kirchho. For such rods recent research has
yielded exact analytical solutions of Kirchhos equations of mechanical equilibrium
with the eects of impenetrability taken into account, and criteria have been derived
for determining whether an equilibrium conguration is stable in the sense that it
gives a strict local minimum to the elastic energy. This paper contains a summary
of published results on equilibrium congurations for the case in which a rod has
been pre-twisted and closed to form a knot-free ring. Emphasis is placed on the way
the writhe Wr of the ring, the number of its discrete points of self-contact, and the
presence or absence of lines of contact, depend on the excess link, Lk, which is a
measure of the amount the rod was twisted before its ends were joined. Bifurcation
diagrams are presented and a summary is given of the properties of the primary,
secondary and tertiary branches that arise by successive bifurcations from the triv-
ial branch comprised of congurations for which the axial curve is a circle. New
results are presented in the theory of equilibrium congurations of closed rods with
the topology of torus knots. It is remarked that examples of equilibrium congura-
tions of closed rods of one knot type can be obtained from examples of other knot
types using methods previously employed to calculate isolas of equilibrium congu-
rations of knot-free rings. Bifurcation diagrams are shown for supercoiled (2, 3) torus
knots (trefoil knots). It is observed that for suciently large and suciently small
Lk the minimum elastic energy conguration of a trefoil knot contains plectonemic
loops with straight contact lines, although the conguration that minimizes the elas-
tic energy of a general (2, q) torus knot over the entire range of Lk has self-contact
along a closed curve. As the ratio of the diameter of the rod to its length approaches
zero, that contact curve becomes a circle, and there is an open interval of values of
Lk for which stable equilibrium congurations with such circular contact curves
exist. Examples of minimum energy congurations are presented for both torus knots
and catenates formed by linking two unknots.
Keywords: DNA topology; elastic rods; contact problems
One contribution of 16 to a Theme The mechanics of DNA.
Phil. Trans. R. Soc. Lond. A (2004) 362, 12811299
1281
c 2004 The Royal Society
1282 B. D. Coleman and D. Swigon
1. Introduction
A duplex DNA molecule contains two complementary polynucleotide strands joined
together in a WatsonCrick double-helical structure. Each of the strands has a sugar
phosphate chain to which there are attached nucleotide bases of four types: A, T, C,
G, with A complementary to T, and C complementary to G. The duplex structure
forms when the bases on one strand bind to their complements on the other. The
resulting base pairs are, in an approximate sense, at, rigid, rectangular objects,
which are stacked with their mid-planes separated by 3.4

A and their centres on
a curve called the duplex axis. In the form DNA assumes under conditions that
mimic those in living cells, each base pair is rotated relative to its predecessor by
ca. 34
. In a rough sketch, the DNA duplex structure appears as a tube with an

approximate diameter of 20

A and with two parallel helical indentations, called the
major and minor grooves. The base pairs are in the interior of the tube, while the
sugarphosphate chains lie on its surface and constitute the material between the two
grooves. The base pairs, or, equivalently, the bases on one of the two complementary
strands, are the units of the genome.
A DNA molecule that is closed, in the sense that each strand forms a closed curve,
is called a plasmid or DNA ring, and is said to be circularized. A bacterium has no
nucleus and its entire genome is in a single plasmid. In a cell with a nucleus, the
DNA is compacted into chromosomes in which it is anchored at several sites in such
a way that the segments between the sites are topologically equivalent to plasmids.
The attainment of an understanding of the way in which highly compacted DNA in
bacteria or cell nuclei is made available for the processes of transcription, replication
and recombination is, in part, a problem in theoretical mechanics. This becomes
clear once one notes that the conguration, and hence the compaction, of a plasmid
depends on a topological parameter, Lk, dened as the Gauss linking number of two
closed curves: the duplex axis and (an arbitrarily chosen) one of the two strands that
form the DNA double helix. Plasmids that have the same size and base-pair sequence
but dier in such topological properties as the knot type of the duplex axis and the
linking number Lk are called topoisomers. The enzymes that convert one topoisomer
into another are called topoisomerases.
The various types of topoisomerases dier in their function (see, for example,
Wang 2002). Topoisomerases of type I cut and ligate a single strand. Whereas topoi-
somerases of type IA can increase Lk by 1, those of type IB can raise and lower Lk
and bring a mixture of topoisomers into an equilibrium state in which the ratio of
the concentrations of two topoisomers with dierent Lk and the same knot type is
given, in accord with the laws of chemical equilibrium, by an exponential function
of their free energy dierence. Topoisomerases of type II cut and ligate both strands
and change Lk by 2. The enzyme called DNA topoisomerase IV is of type II and can
change both linking number and knot type.
We here discuss an elastic rod model for DNA which is based on the assump-
tion that the rod under consideration obeys Kirchhos theory and is homogeneous,
inextensible, straight when stress free, and transversely isotropic. In such a model,
the rod axis ( is identied with the duplex axis; the vectors d that are embedded
in the rods cross-sections and are employed to dene twist density are identied
In crystals this rotation angle is closer to 36
.
Phil. Trans. R. Soc. Lond. A (2004)
Supercoiling of knotted and unknotted DNA plasmids 1283
with vectors that are normal to the duplex axis and point from that axis to the
sugarphosphate chain of one of the two DNA strands.
In early attempts to employ elastic rod models to calculate the dependence of DNA
congurations on Lk a diculty was encountered. The congurations of principal
interest are supercoiled congurations in which the DNA makes contact with itself,
and, for even the simplest case of Kirchhos theory of elastic rods, the problem of
nding with precision and analysing the stability of equilibrium congurations in
which self-contact occurs was open.
After investigations by Le Bret (1984) and J ulicher (1994) of congurations with
self-contact in the theory of closed rods with zero cross-sectional diameter, Stump
et al . (1998) used an approximate method to calculate, for rods of non-zero diam-
eter, congurations in which lines of contact are present. In our research on these
problems, which has had as its goal the attainment of explicit and exact expressions
for supercoiled congurations of rods of nite diameter, we have made use of known
analytical expressions for the congurations of contact-free rod segments (see, for
example, Ilyukhin 1969; Landau & Lifshitz 1970) and a newly derived exact expres-
sion for the conguration of a segment that is in contact with another along a straight
line (Coleman & Swigon 2000). Also preliminary to our study of contact problems
was the development of a theory of the inuence of end conditions on self-contact in
DNA loops (Tobias et al . 1994; Coleman et al . 1995). That theory, as it permits one
to relate both the shape and elastic energy of a DNA loop to geometric boundary
conditions imposed on it by, say, a DNA-binding protein, has been applied to the
problem of calculating the conguration of small rings of DNA in mononucleosomes
and has suggested a method of calculating DNA-histone binding energies from mea-
sured equilibrium distributions of linking number (Swigon et al . 1998; Tobias et al .
2000).
2. Variational inequalities for equilibrium
congurations of impenetrable rods
As is the case for Signorinis problem in the linear theory of three-dimensional elastic
bodies, the self-contact problem in nonlinear rod theory leads to a consideration of
variational inequalities.
Here, as in recent studies (Tobias et al . 2000; Coleman et al . 2000; Coleman &
Swigon 2000), we treat the self-contact problem for the case of a closed impenetra-
ble rod of circular cross-section that obeys Kirchhos theory and is homogeneous,
inextensible, intrinsically straight and transversely isotropic in such a way that it has
just two independent elastic constants: a bending modulus A and a twisting modulus
C. The conguration of a rod ! of that type is characterized by giving: (i) the axial
curve (, which is described by a smooth function x() with x(s) the spatial location
of the material point on ( with arc-length parameter s, and (ii) the twist density ,
which is, by denition,
= (s) = d(s) d
(s) t(s), 0 s 1. (2.1)

Here l is the length of (, t(s) = x
(s) is the unit tangent vector for ( at s, and d(s) is

a unit vector imbedded in the cross-section of ! at s. As ! is assumed to be closed,
i.e. is a ring (which need not be knot-free), in each conguration
x(l) = x(0), t(l) = t(0), d(l) = d(0). (2.2)
We write
u
for the twist density in a stress-free reference conguration. For an
arbitrary conguration, the total twist Tw and the excess twist Tw (in turns) are
Tw = Tw(()) =
1
2
l
0
(s) ds, Tw =
1
2
l
0
(s) ds, (2.3)
where =
u
is the density of excess twist. The total elastic energy of ! is
the sum of a bending energy
B
that depends on the curvature of ( and a twisting
energy
T
that depends on :
=
B
+
T
,
B
=
1
2
A
l
0
(s)
2
ds,
T
=
1
2
C
l
0
(s)
2
ds. (2.4)
We assume that ! is impenetrable, that cross-sections of ! are circular and of uni-
form diameter D, and that when self-contact occurs the contact forces are frictionless
reactive forces normal to the surface of !.
A closed rod is subject to the topological constraint that all of its congurations
give the same value to Lk, the Gauss linking number for two closed curves: ( and the
curve (
obtained by displacing each point x(s) of ( along d(s) by a xed distance

less than
1
2
D. There are several equivalent ways to dene Lk; one way is to set
Lk equal to one-half of the total number of signed crossings of ( and (
seen in a
projection of the two curves on an (arbitrary) plane. It follows from a result of White
(1969) and Calugareanu (1961) that the topological constant Lk obeys the relation
Lk = Wr +Tw, (2.5)
in which Wr is the writhe of the (closed) curve ( and equals the average, over all
orientations of a plane, of the sum of the signed self-crossings of the projection of (
on the plane (Fuller 1971). Of course, although Lk is an integer, Wr and Tw need
not be.
Equivalent to equation (2.5) is the relation
Lk = Wr + Tw, (2.6)
in which Lk, called the excess link, is, by denition, Lk Tw(
u
()) and is a
topological constant that need not be an integer.
A pair ((, ) is called a conguration only if it obeys the constraints imposed on
the rod; these include the end conditions (2.2), the assumption of impenetrability,
and the assumed knot type and value of Lk. A homotopy 1 : ((
) of
congurations is said to be admissible if it is compatible with the constraints. The
familiar denition of an equilibrium conguration, in which a conguration ((, )
is said to be in equilibrium if, for each smooth admissible homotopy 1 with a domain
containing the point = 0 in its interior and with
((
)[
=0
= ((, ), (2.7)
there holds
d
d
((
=0
= 0, (2.8)
is not appropriate when ((, ) is a conguration in which the rod makes contact
with itself. Such a conguration is in equilibrium if, for each admissible homotopy
1 obeying (2.7) with a domain of the form 0 , there holds the variational
inequality
d
d
((
=0
0. (2.9)
When ((, ) is in equilibrium according to this criterion, the equation (2.8) holds
for those homotopies that, for small > 0, can be smoothly extended from 0 <
to < < .
We are considering a rod ! of length l that was closed to form a ring. If the ring
is knot-free, the excess link Lk in equation (2.6) will be a natural measure of the
amount that the rod was pre-twisted before it was closed to form a ring, and for each
value of Lk there will be an equilibrium conguration in which ( is a circle and
hence Wr = 0. For Lk suciently large, there will be equilibrium congurations
with Wr ,= 0 in which the ring makes contact with itself. Whether or not the ring is
knotted, at a point of self-contact, say, that at which the cross-section with s = s
touches the cross-section with s = s
,= s
, there holds
[x(s
) x(s
)[ = D, t(s
) (x(s
) x(s
)) = 0. (2.10)
We shall here conne attention to cases in which a given cross-section is in contact
with at most one other. As we assume that the contact force, f
(i.e. the force

exerted on the cross-section at s
by the cross-section at s
) is a reactive force that

is frictionless (and hence normal to the surface of the rod at s = s
), we have
f
= f
x(s
) x(s
)
D
. (2.11)
It can be shown that our present denition of equilibrium with as in (2.4) implies
that throughout open intervals of values of s corresponding to contact-free sub-
segments, there hold the equations
F
= 0, M
= F t, (2.12)
in which M(s), the resultant of moments of the internal forces acting on a cross-
section, is given by
M = At t
+Ct, (2.13)
and F(s), the resultant of the internal forces, is a reactive force not given by a
constitutive relation. In an early work on the subject, Kirchho (1876) observed
that equations (2.12) and (2.13) are mathematically equivalent to Eulers equations
for the motion of a symmetric top, a fact which has been employed in research on
DNA congurations (e.g. Benham 1977; Le Bret 1984). It is known that use of a
particular cylindrical coordinate system greatly simplies the problem of obtaining
an exact and explicit expression for a contact-free conguration of a rod segment
obeying (2.4) (e.g. Landau & Lifshitz 1970; Tobias et al . 1994).
Contact can occur at isolated points or along contact curves. If s
is an isolated
value or an endpoint of an interval of values of s characterizing contact points, f
,
the contact force at s
, is a concentrated force, and balance of forces and moments

yields
F(s
+ 0) F(s
0) +f
= 0, M(s
+ 0) M(s
0) = 0. (2.14)
In the interior of the contact force has a continuous density f, equation (2.13)
holds, and in place of the equations (2.12) one has
F
(s
) +f(s
) = 0, M
(s
) = F(s
) t(s
), (2.15)
with M and F again smooth functions of s.
In a contact-free subsegment of ! the equations (2.12) with M as in (2.13) are a
system of dierential equations for ( and with solutions that can be expressed
in terms of elliptic functions (and integrals) and six parameters.
In cases in which ! contains a pair of subsegments !
, !
that meet at a con-

tact curve (
c
, the relations (2.14) hold in the interior of the interval of values of s
corresponding to the axial curve (
of !
. If for one of these values of s we write

v for the unit vector [x(s
) x(s
)]/D along the line connecting the centroids of

two cross-sections in contact, write u for the unit tangent vector for (
c
, and put
w = u v, then in the equation
t(s
) = u(s
) cos (s
) w(s
) sin (s
) (2.16)
is the angle of winding of (
about (
c
. There are cases in which one can combine this
last equation with equations (2.10), (2.11), (2.13) and (2.15) to obtain a tractable
dierential equation for . When (
c
is a straight line (i.e. a contact line), as is the
case for contact curves in knot-free rods, the vector u is independent of s, and the
dierential equation for , which then takes the form
=
8
D
2
sin
3
cos +
2C
AD
cos 2, (2.17)
has a solution,
(s
) = arccot
q cot
0
p tan
2
(
1
2
sn(s
s
0
)
pq) cot
1
q p tan
2
(
1
2
sn((s
s
0
)
pq))
(2.18)
in which p, q,
1
and the modulus of the elliptic function sn are functions of the
material parameters D, C/A and the numbers
0
, , where
0
is the value of at
a point s
0
where
= 0. Thus, the congurations of the subsegments !
and !
can be expressed in terms of elliptic functions and four solution parameters, which
are
0
, and the arc-length coordinates of the endpoints of (
.
As ! is a ring, if ! has n isolated points of self-contact and m contact lines, it
has 2(n + m) contact-free subsegments. Because there are six solution parameters
per contact-free subsegment and four per contact line, the conguration of ! is
determined when 12n+16m solution parameters are specied. The requirement that
Lk have its preassigned value and the equations (2.2), (2.10), (2.11) and (2.14)
yield 12n+16m algebraic equations that can be solved for those solution parameters
(Coleman et al . 2000). Thus one can obtain, for equilibrium congurations in which
self-contact occurs at isolated points and straight lines, (i) a value of (which the
governing equations require to be constant throughout !), (ii) a precise analytical
representation for (, and (iii) the value of f
at each contact point.

See Coleman & Swigon (2000, pp. 188190) for a detailed derivation of (2.18), and Thompson et
al . (2002) for a generalization of (2.17) to cases in which loads are imposed at the ends of the region of
continuous contact.
In order for a solution of equations (2.10)(2.15), obtained as just described, to
correspond to an equilibrium conguration it must be such that when the cross-
sections at s
and s
are in contact, f
in (2.11) is not negative; i.e. f
, if not zero,
tends to push apart cross-sections that contact each other. In addition, such a solution
must obey the condition of impenetrability, i.e. must be such that if two distinct cross-
sections of the rod have a point in common, that point is on the boundaries of the
two cross-sections. (Coleman & Swigon (2000, pp. 179, 180) give a mathematically
equivalent formulation of this condition.)
Two congurations ((
) and ((, ) are called equivalent if they have con-

gruent axial curves and equal distributions of twist. Here, a conguration of a rod
subject to appropriate end conditions is said to be stable if it gives a strict local min-
imum to in the class of congurations compatible with the imposed constraints.
In other words, ((, ) is stable when, for an appropriate topology, it has a neigh-
bourhood A such that ((
) > ((, ) for each conguration ((
) in
A that is not equivalent to ((, ) and, in addition, is accessible from ((, ) by
an admissible homotopy 1.
A conguration ((, ) is dierentially stable, if, for each admissible homotopy
1 with domain 0 < and obeying (2.7), either
d
d
((
=0
+
> 0 (2.19 a)
or
d
d
((
=0
+
= 0 and
d
2
d
2
((
=0
+
0. (2.19 b)
(A dierentially stable conguration obeys (2.9) and hence is in equilibrium.)
Tobias et al . (2000) showed that (whether or not self-contact is present), when
((, ) is a member of a family E of equilibrium congurations parametrized with
Lk, the following condition holds.
Condition (E). If ((, ) is stable, then, dLk/dWr, the slope at ((, ) of
the graph of Lk versus Wr for the family E, is not negative.
This condition, although necessary, is not sucient for even dierential stability.
However, in the same paper the following condition, condition (S), was shown to be
sucient for stability as dened here.
Condition (S). A conguration ((, ) that is a member of a family E of equi-
librium congurations is stable if
(1) on the graph of Lk versus Wr for the family E, dLk/dWr > 0 at ((, )
and, in addition,
(2) ((, ) strictly minimizes bending energy in a locally uniform way, i.e. in the
sense that ((, ) has a neighbourhood A such that, for each conguration
((
E
,
E
) in A and E, there holds
B
((
) >
B
((
E
) for every accessible
conguration ((
) in A for which (
has the same writhe as, but is not

congruent to, (
E
.
A necessary condition for stability equivalent to condition (E) was formulated by Le Bret (1984).
Verication of item 2 is a dicult matter. The following proposition (Tobias et al .
2000) gives a necessary condition for stability, called condition (), that is stronger
than condition (E) and is sucient for stability in several important cases.
Condition (). For each with 0 < l, let () be the minimum value of
dLk/dWr at ((, ) over the families of equilibrium congurations of ! that
obey the added imposed constraint that the subsegment of ! with s < l be held
rigid. In order that an equilibrium conguration ((, ) be stable, it is necessary
that () 0 for each , 0 < l.
Once one has in hand an explicit analytical representation for an equilibrium con-
guration, one can calculate () for 0 < l and determine whether condition ()
holds for that conguration. We have employed the theory of conjugate point criteria
for the stability of solutions of ordinary dierential equations (e.g. Manning et al .
1998) to prove that fullment of condition () is sucient for the dierential sta-
bility of a contact-free conguration, and we are working on an extension of results
of that type to congurations with self-contact. At the end of 3, in a discussion of
transitions between stable congurations, we shall assume that the fullment of the
slightly strengthened form of condition (), in which for each the relation () 0
is replaced by the strict inequality () > 0, is sucient not just for dierential
stability, but also stability as dened here.
3. Congurations and bifurcation diagrams for knot-free rings
The results summarized above tell us that in the present theory it is useful to draw
bifurcation diagrams as plots of Lk versus Wr. Some plots of this type, obtained
by the computational method discussed above and described in detail by Coleman &
Swigon (2000), are shown in gures 1 and 2 for a knot-free ring with C/A = 7/5 and
= 122, where = l/D. The chosen value of corresponds to a DNA molecule with
D = 20

A that has 718 nucleotides in each of its two strands. The employed value
of C/A is compatible with measurements of the width of experimentally determined
equilibrium distributions of topoisomers of DNA plasmids (see Horowitz & Wang
(1984) and the calculations of Frank-Kamenetskii et al . (1985)).
The reader may wish to compare the congurations and bifurcation diagrams
shown here for a knot-free ring with those we presented in an earlier paper (Coleman
& Swigon 2000) for such a ring with the same value of but with C/A = 2/3. On
p. 217 of that paper we derive implications of a rule (Tobias et al . 2000) relating the
congurations and the bifurcation diagrams of rings with the same but distinct
C/A. That rule, which is valid regardless of knot type or the presence or absence of
self-contact, states that there is a universal one-to-one correspondence between the
equilibrium congurations of two rings with distinct values C/A that preserves the
axial curve ( (and hence the writhe Wr) and the value of (C/A)Tw.
Although calculation of Wr by numerical evaluation of its representation as a double integral over
C is notoriously dicult, for the cases considered here one can obtain an analytical representation for
the integral along C of the geometric torsion and make use of the fact that Wr plus the torsion integral
is an integer, called the self-link of C (Pohl 1968; see also Calugareanu 1961), which is not dicult to
evaluate. For details see Swigon et al . (1998).

A
0

Wr
0
0
1
2
3
4
5
B
0
C
0
D
0
E
0
F
0
A
2
A
1
A
3
A
4
1 2 3 4 5
Lk
Figure 1. Graph of excess link, Lk, versus writhe, Wr, for the primary branch . Here and in
gure 2, = 122. For n = 0, 1, 2, 3, the congurations with n points of self-contact correspond to
points between A
n
and A
n+1
. At values of Lk greater than that at A
4
, the congurations have
an interval and two isolated points of self-contact (which are indiscernible at this scale of draw-
ing). Two examples are shown of congurations with Lk > Lk(A
4
), one with Lk = 3.55
and the other with Lk = 5.38. Families of stable congurations are shown as heavy curves.
Conguration A
1
has been called the gure-of-eight conguration; those with Wr > Wr(A
1
)
are said to be plectonemically supercoiled. The parameter Lk obeys equation (3.1) at cong-
urations A
0
, B
0
, . . . , of branch . Here and in gures 25 selected congurations are shown as
tubes of diameter 20

A. Here the line of view is at an angle of 45
to the axis of D
2
symmetry.
For knot-free rings of the type here under consideration, the bifurcation diagram
has a branch (called the trivial branch and labelled ) that is comprised of congu-
rations for which ( is a circle and hence Wr = 0. Each point of with
Lk =
A
C
m
2
1, m = 2, 3, . . . , (3.1)
is a bifurcation point at which a primary branch with Wr ,= 0 originates. The primary
branches with m = 2, 3, etc., are referred to as branch , branch , etc. For each
m 2 the symmetry group of the congurations in the primary branch with index m
is the dihedral group D
m
(which has order 2m). Hence, whether or not self-contact
S
R
Q
P
Wr
0
1
2
3
4
5
6
B
0
B
1
A
0
C
0
D
0
G
0
H
0
F
0
E
0

Lk
0 1 2 3 4 5 6
B
2
I
B
2
III
B
2
II
B
2
IV
B
2
I,II
B
3
I

II
II,I
III
IV
Figure 2. Graphs of Lk versus Wr for the primary branch (solid curve), the secondary
branches
I
,
II
,
III
,
IV
(long dashes) originating at , and the tertiary branch
II,I
(dots)
originating at
II
. The points B
0
, B
1
, P, Q, R are bifurcation points for branch , S is a
bifurcation point for branch
II
. For n = 0, 1, 2, 3, the congurations on branch with 3n points
of self-contact (i.e. with one such point in each lobe) correspond to points between B
n
and B
n+1
.
Not visible at this scale is a closed secondary branch
V
that meets at the bifurcation points
Q and R. A detailed graph of such a closed branch and views of congurations on it are given
by Coleman & Swigon (2002). Here, the line of view for B
n
(n = 1, 2, 3) is parallel to the axis
of highest symmetry; for all other congurations it is perpendicular to that axis.
is present, the curve ( for a conguration on the primary branch of index m has
a single m-fold symmetry axis that is perpendicular to a plane containing the 2m
points at which the curvature of ( has a local extremum. Each of the m lines that
intersect the m-fold symmetry axis and pass through two extrema of is a twofold
symmetry axis. Each primary branch, with the exception of branch of gure 1,
contains points of secondary bifurcation. Congurations on the secondary branches
originating at points on branch of gure 2, have C
2
symmetry. Congurations
on the tertiary branch
II,I
, previously called
II
(Coleman et al . 2000; Coleman &
Swigon 2000, 2002), that originates at the point S of secondary branch
II
have no
discernible symmetry.
Elsewhere (Coleman & Swigon 2000), we have described congurations on branch
(for which m = 4) and some secondary branches that originate on that primary
branch.
The congurations in the interior of regions of branches that are drawn as heavy
curves in gure 1 are stable. As condition (E) does not hold on the intervals of branch
that are there drawn as light curves, the congurations in those intervals are not
stable.
In gure 2 one sees the primary branch , the secondary branches that originate
at points on , and the tertiary branch
II,I
. On those branches, condition () holds
only for the congurations in the heavily drawn interval of branch that runs from
the bifurcation point B
1
to the bifurcation point P. No other congurations in those
branches can be stable.
The bifurcation diagrams presented by Swigon (1999), Coleman et al . (2000) and
Coleman & Swigon (2000, 2002) have sucient precision to reveal such features of
self-contact as the following: when changes in Lk result in rst one and then two
isolated points of self-contact in a lobe, further change results in three isolated points
and then a mixture of intervals and isolated points of self-contact.
A knot-free ring can have families of equilibrium congurations that are not on
primary, secondary or higher-order branches, i.e. that are isolas in the sense that they
are not connected to the trivial branch by a continuous path of equilibrium congu-
rations that obey the constraint arising from impenetrability. The isolas studied by
Coleman & Swigon (2000) are connected to one of the secondary branches originating
on branch , or to the tertiary branch
II,I
, by one-parameter families of solutions
of equations (2.10)(2.15) that contain subfamilies that do not obey the requirement
that, if distinct cross-sections have a point in common, that point must lie on the
surface of !. Such families occasionally contain subfamilies of congurations that
obey the constraint of impenetrability, but are knotted, and hence are not congura-
tions of the original knot-free ring. (The heavy solid curve seen in g. 24 of Coleman
& Swigon (2000) corresponds to a one-parameter family of trefoil knots obtained in
this way from the branch
I
of a knot-free ring.)
4. Congurations and bifurcation diagrams for torus knots
We now turn to the theory of equilibrium congurations of closed rods that have axial
curves with the topology of (p, q) torus knots, i.e. knots that can be drawn on the
surface of a torus as not self-intersecting curves that pass q times through the hole
in the torus and go p times around that hole, where p and q do not have a common
divisor and obey the relations q > p 2. The bifurcation diagrams we present in
For closed rods obeying the present assumptions, Domokos (1995) proved that each contact-free
equilibrium conguration has D
m
symmetry, which is what we found. In the same paper he conjectured
that the symmetry group of an equilibrium conguration with self-contact contains C
2
as a subgroup,
which is not the case for congurations on the tertiary branch
II,I
originating at the point S.
Because of their importance in molecular biology, we should mention here that there are classes
of catenated rings that can be treated as generalized torus knots for which p and q do have a common
divisor. When q is an even number, the generalized (2, q) torus knot is a link of two unknots, which we
may call the (2, q) torus link.
this section are for closed rods with C/A = 7/5 and = 170 (which corresponds to
a DNA molecule with D = 20

A and 1000 nucleotides in each strand).
Langer & Singer (1984) gave convincing arguments to the eect that a closed
rod can have a contact-free equilibrium conguration only if it is knot-free or has
the topology of a torus knot. Although they present their arguments assuming that
the elastic energy is the integral of
2
(they call rods with that property elastic
curves), their proof rests on the validity of a second-order dierential equation for
(s) which has been shown (Coleman et al . 1993) to hold for contact-free equilibrium
congurations (and also travelling waves) of rods of the type that we consider here
(i.e. rods for which the twisting modulus C in equation (2.4) need not be zero). In
other words, the propositions of Langer & Singer about the stability of contact-free
congurations have a broader range of validity than originally claimed. Contact-free
congurations of torus knots were calculated by Le Bret (1984) and Starostin (1996).
The relation between the families of contact-free equilibrium congurations of torus
knots and contact-free regions of primary branches of the bifurcation diagram for a
knot-free ring is shown in gure 3, in which one sees the trivial branch , segments
of the branches , , , , (for which m in equation (3.1) is, respectively, 2, 3,
4, 5, 6), and families of contact-free equilibrium congurations of (m 1, m) torus
knots with m = 3, 4, 5 that are labelled

, ,

. Each family of (m 1, m) torus
knots is connected to the primary branch for a knot-free ring with the same m by
a one-parameter family of solutions of the equations (2.10)(2.15) do not obey the
impenetrability constraint. Each such family contains a point (labelled / in gure 3)
at which the (axial) curve obtained by solving (2.10)(2.15) passes through itself and
hence Lk and Wr undergo a jump equal to the integer m
2
m.
A contact-free equilibrium conguration of a rod with the topology of a (p, q) torus
knot has D
q
symmetry. The rod can attain a contact-free conguration if and only
if the value of is larger than a critical value
that depends on p and q. We nd

that
(2, 3) = 26.47,
(3, 4) = 63.33,
(4, 5) = 120.19,
(5, 6) = 198.60. As the

value of employed for the calculations shown in gure 3 is 170, there a (5, 6) torus
knot can have no contact-free congurations.
Langer & Singer (1984) and Le Bret (1984) conjectured that contact-free congu-
rations of torus knots are unstable. As evidence tending to support this conjecture,
we observe that the families of contact-free equilibrium congurations of (m1, m)
torus knots shown in gure 3 do not obey condition (E) and hence contain only
unstable congurations.
We now focus on equilibrium congurations of trefoil (i.e. (2, 3) torus) knots which
occur in signicant concentration in DNA cyclization experiments under a broad
range of conditions. As the full bifurcation diagram for trefoil knots has a complex
topology with multiple bifurcation branches forming closed loops, a complete descrip-
tion of it is not presently available. Following the dissertation of Swigon (1999), we
here conne attention to the set / of equilibrium congurations dened as follows.
A tilde, as in

B
1
and

, generally indicates that the conguration (or family of congurations)
under consideration is knotted (or is comprised of knotted congurations). An exceptional case is that
of the family , which is topologically equivalent to the branch of a knot-free ring.
Of course,
>
, where
is the smallest value of for which a conguration without penetration

exists in a class of closed rods of prescribed knot type. Congurations with =
are called ideal knots

by Katritch et al . (1996) and maximally tightened knots by Grosberg et al . (1996).

A
0
C
0
D
0
E
0
B
0

0
1
2
3
4
5
Wr + J
L
k

+

J
0 1 2 3 4 5 6
E
1
D
1
D
0
D
1
~
C
0
~
C
1
~
B
1
~
B
0
~
A
0
~
A
1
~
C
1
B
1
~
A
1
/
/
/
/
/
Figure 3. Graphs of Lk+J versus Wr+J for one-parameter families of contact-free equilibrium
congurations of a closed rod. When the rod is knot-free, J = 0; when it has the topology of a
(m 1, m) torus knot, J = m
2
m. Here and in gure 4, = 170. The families of knot-free
congurations, , , , (solid curves) are connected to the families of torus knots:

, ,

(solid
curves) by families of congurations that fail the condition of impenetrability (dotted curves).
Congurations in the family

have the topology of (2, 3) torus knots (i.e. of trefoil knots), in
of (3, 4) torus knots, and in

of (4, 5) torus knots. Although the congurations in are mirror
images of congurations in and hence are not knotted, J = 2 for . With the exception of ,
all the families shown contain only unstable congurations. As the passage of the axial curve
through itself (at the point marked with /) results in a jump in Lk and Wr by the amount
mm
2
, each graph of Lk+J versus Wr +J is smooth. Points corresponding to congurations
in which contact occurs without penetration are shown as hollow circles. Solid circles give the
location of the depicted axial curves, and the line of view of is parallel to the axis of highest
symmetry. The axial curves for the torus knots are not all drawn on the same scale.
For each Wr an equilibrium conguration ((
) is in / if and only if (
mini-
mizes
B
(() over the set of axial curves ( with the same writhe (and of course the
same length and topology) as (
. The importance of / stems from the fact that it

contains every conguration that (globally) minimizes the total elastic energy for
preassigned Lk. However, /is strictly larger than the set of such global minimizers
of .
One-parameter families of congurations in /are shown in gure 4. The families
containing congurations with only isolated points of self-contact form two discon-
a
c b
a
a
a
a
b
c
a
a
b
c
a
Wr
5 4 3 2 1
7
6
5
4
3
2
1
L

B
0

O

M
1
N
1

K

C

Lk
~
N
2
~
N
3
~
N
4
~
~
II
III
~
~
~
~
~
M
2
~
M
3
~
M
4
~
~
~
B
1
Figure 4. Graphs of Lk versus Wr for congurations in the set M of congurations of the
trefoil knot. (M is dened in the text.) One-parameter families of stable congurations are
shown as heavy curves. The point

B
0
of the family

(which is also shown in gure 3) is the
bifurcation point at which the families

I
and

II
originate. The family

III
is not connected
to

by a continuous family of equilibrium congurations of the trefoil knot. The point

B
1
lies
on

but not

I
. The congurations corresponding to points in the family

C
(heavy dashed
vertical line) are stable; each has a contact curve that is close to a circle. Here, the line of view
for

B
0
,

B
1
,

K,

C is parallel to the axis of highest symmetry; for all other congurations it is
perpendicular to that axis.
nected sets: a set /
1
containing congurations with Wr < 3, and a set /
2
containing those with Wr > 3. The families in the set /
1
, labelled

I
and

II
, are
connected to the family

of contact-free congurations (shown in gure 4 as a light
dotted curve and as a solid curve in gure 3) at the bifurcation points

B
1
and

B
0
,
respectively; both of those points correspond to congurations with three points of
self-contact. (A more complete bifurcation diagram makes clear the fact that both
B
1
and

B
0
are termination points for families of congurations with 1, 2, or 3 points
of self-contact, but only

I
and

II
belong to /
1
and are shown in gure 4.) The
congurations in the family

I
have two points of self-contact and C
2
symmetry,
while those in the family

II
have three points of self-contact and D
3
symmetry.
Let us follow the family

I
in the direction of decreasing Wr. The D
3
symmetry of
the conguration at

B
0
is broken once one moves away from

B
0
and the congurations
in

I
between

B
0
and

K have two points of self-contact and C
2
symmetry. The
symmetry is broken again at the point

K, with the congurations between

K and
L showing two contact points but no discernible symmetry, and regained at the
point

L, with the congurations between

L and

M
1
showing three contact points
and C
2
symmetry. In gure 4 we have given the labels a, b and c to the three
points of maximum curvature (and to the loops containing those points) to help the
reader to visualize the transition

B
0

K

L. For the conguration at

K, the axis
of symmetry is perpendicular to the plane of the paper and passes through b, while
at

L that axis lies in the plane of the paper and passes through a. At

M
1
a new point
of self-contact appears in the loop labelled a, and the congurations between

M
1
and

M
4
follow the rule for the formation of points of self-contact in a plectonemic
loop: the one point of self-contact in loop a splits into two points at

M
2
, at

M
3
a third
contact point appears between the two, and for congurations with Wr < Wr(
M
4
)
the middle contact point spreads into a straight line of contact.
The situation is similar for the family

III
, the one family in the set /
2
. The
conguration

N
1
in

III
resembles the conguration

M
1
in

I
, except for a dierent
sign of crossing at the self-contact point in the loop labelled a. As one traverses
the family

III
in the direction of increasing Wr, one again nds that congurations
follow the rule for the formation of points of self-contact in a plectonemic loop, with
the congurations between

N
n
and

N
n+1
showing n self-contact points in the loop
a (i.e. n + 3 total points of self-contact). Computational complexities prohibited us
from obtaining congurations with 3 < Wr < Wr(
O).
The writhe of congurations in the family

B
II
originating at the point

B
0
increases
by a nearly undetectable amount as one traverses that family away from

B
0
in the
direction of increasing Lk. These congurations all have Wr < 3 and are in the
set /. Although the shape of the axial curve changes very little, new points of self-
contact do appear. The conguration

C, which contains 12 points of self-contact, is
at the limit of feasibility of our method of computing the integration constants in
our analytical solution of the equations (2.10)(2.15). We do not know how large
the value of Lk is at which the family

II
ceases to be a subset of /
1
, i.e. ceases
to be made up of congurations with only isolated points of self-contact, but we do
know that there is an interval of values of Lk (each greater than Lk(
C)) for which

the minimum energy conguration of a trefoil knot is one showing self-contact along
a closed curve. That one-parameter family

C
of congurations in / with closed
contact curves is shown in gure 4 as a heavy dashed line.
As exact analytical expressions for equilibrium congurations of rods with self-
contact along general curves are not available, we now derive approximate expressions
that are appropriate to rods with large , i.e. small d =
1
= D/l.
Let us consider a ply T formed by two rod segments !
, !
of equal lengths that

meet at a contact curve (
c
. When the two cross-sections at one end of T are glued to
the two cross-sections at the other end, (
c
becomes a closed curve, and the segments
!
, !
form either (i) one closed rod ! (with each end of !
glued to an end of
!
) or (ii) two closed rods !
, !
(with the ends of !
glued together, and the

ends of !
glued together). We here consider the cases in which (

c
is not knotted
and hence, in case (i), ! is either knot-free or a (2, q) torus knot, and, in case (ii),
!
and !
are knot-free and either unlinked or form a (2, q) torus link in which the
axial curves of !
and !
can be drawn as nonintersecting curves on the surface of

a torus with each passing once around the hole in the torus and q/2 times through
that hole.
The conguration of T is characterized by the contact curve (
c
(with arc-length
coordinate s
c
) and an angle = (s
c
) dened as follows. As in 2, we write v(s
c
) for
the unit vector along the line connecting the centroids of two cross-sections in contact
at s
c
, and u(s
c
) for the unit tangent vector for (
c
at s
c
, and we put w = uv. The
curvature
c
and torsion
c
of (
c
and the angle obey the relations
c
sin = w
u,
c
cos = u
v,
c
+
= v
w. (4.1)
It can be shown that when the diameter D of !
and !
is much smaller than their

length l, i.e. when d 1, the total elastic energy of T obeys the relation
= A
l
c
0
2
c
ds
c
+
4
2
C
l
c
( (Wr)
c
)
2
+O(d
2
), (4.2)
where l
c
and (Wr)
c
are, respectively, the length and the writhe of (
c
, and
=
1
2
(Lk q), (4.3)
with Lk the excess link of ! (and hence a topological constant independent of
the deformation of T). In (4.3) the minus (plus) sign is chosen for right-handed
(left-handed) (2, q) torus knots and links.
When we compare equation (4.2) with equation (2.4) and make use of the fact that
for a closed rod in equilibrium is a constant equal to = 2(Lk Wr)/l,
we conclude that (4.2) is identical to the equation for the total elastic energy of
a hypothetical knot-free closed rod with length l
c
, bending modulus 2A, twisting
modulus 2C and linking number that is in equilibrium with curvature
c
=
c
(s
c
),
writhe (Wr)
c
and (spatially uniform) twist density
c
= 2( (Wr)
c
)/l
c
. As it
is known that, for [[ < (A/C)
3, the minimum energy conguration of such a rod

is a circle, one may conclude the following.
Proposition 4.1. If the minimum energy conguration of a (2, q) torus knot or
link with (A/C)2
3 q < Lk < (A/C)2
3 q shows self-contact along a closed

curve (
c
, then, in the limit as d 0, (
c
is a circle.
When (
c
is a circle, the balance equations (2.15) yield, in the limit as d 0, a
fourth-order nonlinear dierential equation for (s
c
),
6(
)
2
3
c
C
A

+
1
2
2
c
(cos 23)
+
1
2
2
c
((
)
2
2
c
) sin 2 = 0, (4.4)
with the end-condition
(l
c
) (0) = q; (4.5)
here the plus sign is chosen for right-handed (2, q) torus knots and links. In order
for a solution of (4.4) and (4.5) to correspond to a stable equilibrium conguration
(2,3) (2,4)
(2,5) (2,6)
(2,7) (2,8)
Figure 5. Congurations of (2, q) torus knots and links
that minimize over the entire range of Lk.
of T, f
in (2.11) must not be negative. The balance equations (2.15) imply that, in
the limit as d 0,
f
=
AD
2
+

2
c
2
(sin 2)
)
4
+

2
c
2
(cos 2 + 3)(
)
2

4
c
2
(1 + cos 2)
C
c
D
2
[(
)
3
2
c
(1 + cos 2)]
. (4.6)
The equations (4.4) and (4.5) can be solved by expansion of the inverse function
s
c
= s
c
() as a sum of a term linear in and terms linear in sin 2n for n = 1, 2, . . . .
For the left-handed trefoil knot, which has q = 3, we nd that
s
c
=
2
3
c
( +B
1
sin 2 +B
2
sin 4 + ), (4.7)
Table 1. The coecients B
1
and B
2
in the solution (4.7) of
equation (4.4) obeyed by trefoil knots with d small
(Here q = 3, C/A = 7/5, 1/d = 170.)
Lk B
1
B
2
f
min
1.64 7.28 10
3
2.25 10
5
0
3.00 1.32 10
2
6.72 10
5
0.40AD/
c
3.97 3.03 10
2
3.26 10
4
0
with B
1
, B
2
, . . . constants that depend on Lk and C/A. Values of B
1
and B
2
for
selected values of Lk are given in table 1. By calculating f
min
, the minimum value of
f
in equation (4.6), we nd that for the trefoil with the present values of C/A and
the solution (4.7) describes a stable equilibrium conguration only if 3.97 < Lk <
1.64, i.e. only if the conguration is in the family

C
of gure 4. The conguration
that minimizes over the entire range of Lk, i.e. the conguration that minimizes
B
, has T = 0 and Lk 3.002. Elsewhere (Coleman & Swigon 2002, pp. 291
293) we discussed that conguration and gave examples of congurations of trefoil
knots with only isolated points of self-contact that minimize at specied values of
Lk outside of the range appropriate to the family

C
.
In gure 5 we show, for torus knots and links, the congurations that give a global
minimum to over the entire range of Lk. These congurations were obtained by
solving equations (4.4) and (4.5) for selected values of q. Whereas odd values of q
correspond to (2, q) torus knots (case (i)), even values of q correspond to (2, q) torus
links (case (ii)).
This research was supported by the National Science Foundation under Grant DMS-02-02668
and the US Public Health Service under research grant GM34809.
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Supercoiling of Knotted and Unknotted DNA Plasmids Contact in Kirchhoff Rods With Applications To Theory of Self

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Supercoiling of Knotted and Unknotted DNA Plasmids Contact in Kirchhoff Rods With Applications To Theory of Self

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doi: 10.1098/rsta.2004.

Bernard D. Coleman and David Swigon

supercoiling of knotted and unknotted DNA plasmids

. In a rough sketch, the DNA duplex structure appears as a tube with an

(s) t(s), 0 s 1. (2.1)

(s) is the unit tangent vector for ( at s, and d(s) is

obtained by displacing each point x(s) of ( along d(s) by a xed distance

touches the cross-section with s = s

(i.e. the force

) is a reactive force that

, is a concentrated force, and balance of forces and moments

that meet at a con-

. If for one of these values of s we write

)]/D along the line connecting the centroids of

= 0. Thus, the congurations of the subsegments !

at each contact point.

in (2.11) is not negative; i.e. f

) and ((, ) are called equivalent if they have con-

) > ((, ) for each conguration ((

has the same writhe as, but is not

that depends on p and q. We nd

(5, 6) = 198.60. As the

is the smallest value of for which a conguration without penetration

are called ideal knots

. The importance of / stems from the fact that it

C)) for which

of equal lengths that

form either (i) one closed rod ! (with each end of !

) or (ii) two closed rods !

(with the ends of !

glued together, and the

glued together). We here consider the cases in which (

can be drawn as nonintersecting curves on the surface of

is much smaller than their

3, the minimum energy conguration of such a rod

3 q < Lk < (A/C)2

3 q shows self-contact along a closed

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