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Scanning transmission electron microscopy (STEM) provides high-resolution visualization of atomic structures as well as various functional imaging modes utilizing phase contrast. In this study we introduce a semicircular aperture in STEM bright field imaging, which gives a phase contrast transfer function that becomes complex and includes both lower and higher spatial frequency contrast transfer. This approach offers significant advantages over conventional phase plate methods, having no charge accumulation, degradation, or unwanted background noise, which are all problematic in the phase plate material. Also compared to the differential phase contrast or ptychography equipment, this semicircular aperture is far less costly. We apply this approach to visualization of polymer, biological and magnetic samples.

We give a complete classification of links up to clasp-pass moves, which coincides with Habiro's $C_3$-equivalence. We also classify links up to band-pass and band-# moves, which are versions of the usual pass- and #-move, respectively, where each pair of parallel strands belong to the same component. This recovers and generalizes widely a number of partial results in the study of these local moves. The proofs make use of clasper theory., Comment: 29 pages

We define numerical link-homotopy invariants of link maps of any number of components, which naturally generalize the Kirk invariant. The Kirk invariant is a link-homotopy invariant of 2-component link maps given by linking numbers of loops based at self-singularities of each component with the other spherical component; our invariants use instead ingredients from Milnor's higher order link invariants, and are extracted from the reduced fundamental groups of the exterior. We provide practical algorithms to compute these invariants from an appropriate cross-section, as well as families of examples that are therewith detected. The main proofs use the combinatorial theory of cut-diagrams previously developed by the authors., Comment: 24 pages

We develop a general diagrammatic theory of welded graphs, and provide an extension of Satoh's Tube map from welded graphs to ribbon surface-links. As a topological application, we obtain a complete link-homotopy classification of so-called \emph{knotted punctured spheres} in $4$--space, by means of the $4$--dimensional Milnor invariants introduced by the authors in \cite{cutAMY}. On the algebraic side, we show that the theory of welded graphs can be reinterpreted as a theory of Wirtinger group presentations, up to a natural set of transformations; these groups arise as the fundamental group of the exterior of the surface-link obtained from the given welded graph by the extended Tube map. Finally, we address the injectivity question for the Tube map, identifying a new family of local moves on welded links, called $\Upsilon$ moves, under which the (non extended) Tube map is invariant., Comment: 27 pages, many figures

We characterize, in an algebraic and in a diagrammatic way, Milnor string link invariants indexed by sequences where any index appears at most $k$ times, for any fixed $k\ge 1$. The algebraic characterization is given in terms of an Artin-like action on the so-called $k$-reduced free groups; the diagrammatic characterization uses the langage of welded knot theory. The link case is also addressed., Comment: 18 pages

We generalize Milnor link invariants to all types of surface-links in 4-space (possibly with boundary) and more generally to all codimension 2 embeddings. This is achieved by using the notion of cut-diagram, which is a higher dimensional generalization of Gauss diagrams, associated to codimension 2 embeddings in Euclidian spaces. We define a notion of group for cut-diagrams, which generalizes the fundamental group of the complement, and we extract Milnor-type invariants from the successive nilpotent quotients of this group. We show that the latter are invariant under an equivalence relation called cut-concordance, which encompasses the topological notion of concordance. We give several concrete applications of the resulting Milnor concordance invariants for surface-links, comparing their relative strength with previously known concordance invariants, and providing realization results. We also obtain several classification results up to link-homotopy, as well as a criterion for a surface-link to be ribbon. In connection with the k-slice conjecture proved by Igusa and Orr, we show that a classical link has vanishing Milnor invariants of length $\leq 2k$ if and only if it bounds disjoint surfaces in the 4-ball having vanishing Milnor invariants of length $\leq k$. Finally, the theory of cut-diagrams is further investigated, heading towards a combinatorial approach to the study of surfaces in 4-space., Comment: 49 pages

Dabkowski and Sahi defined an invariant of a link in the $3$-sphere, which is preserved under $4$-moves. This invariant is a quotient of the fundamental group of the complement of the link. It is generally difficult to distinguish the Dabkowski-Sahi invariants of given links. In this paper, we give a necessary condition for the existence of an isomorphism between the Dabkowski-Sahi invariant of a link and that of the corresponding trivial link. Using this condition, we provide a practical obstruction to a link to be trivial up to $4$-moves., Comment: 9 pages

For a classical link, Milnor defined a family of isotopy invariants, called Milnor $\overline{\mu}$-invariants. Recently, Chrisman extended Milnor $\overline{\mu}$-invariants to welded links by a topological approach. The aim of this paper is to show that Milnor $\overline{\mu}$-invariants can be extended to welded links by a combinatorial approach. The proof contains an alternative proof for the invariance of the original $\overline{\mu}$-invariants of classical links., Comment: 25 pages; v2: the title changed, Section 1 rewritten, remarks and references added; to appear in Michigan Mathematical Journal

Fixing two concordant links in $3$--space, we study the set of all embedded concordances between them, as knotted annuli in $4$--space. When regarded up to surface-concordance or link-homotopy, the set $\mathcal{C}(L)$ of concordances from a link $L$ to itself forms a group. In order to investigate these groups, we define Milnor-type invariants of $\mathcal{C}(L)$, which are integers defined modulo a certain indeterminacy given by Milnor invariants of $L$. We show in particular that, for a slice link $L$, these invariants classify $\mathcal{C}(L)$ up to link-homotopy., Comment: v4: final version. To appear in Indiana Univ. Math. J

In a previous paper, the authors proved that Milnor link-homotopy invariants modulo $n$ classify classical string links up to $2n$-move and link-homotopy. As analogues to the welded case, in terms of Milnor invariants, we give here two classifications of welded string links up to $2n$-move and self-crossing virtualization, and up to $V^{n}$-move and self-crossing virtualization, respectively., Comment: 16 pages, 18 figures. arXiv admin note: text overlap with arXiv:1902.06079

Two string links are equivalent up to $2n$-moves and link-homotopy if and only if their all Milnor link-homotopy invariants are congruent modulo $n$. Moreover, the set of the equivalence classes forms a finite group generated by elements of order $n$. The classification induces that if two string links are equivalent up to $2n$-moves for every $n>0$, then they are link-homotopic., Comment: 16 pages, 8 figures

Let $n$ be a positive integer. The aim of this paper is to study two local moves $V(n)$ and $V^{n}$ on welded links, which are generalizations of the crossing virtualization. We show that the $V(n)$-move is an unknotting operation on welded knots for any $n$, and give a classification of welded links up to $V(n)$-moves. On the other hand, we give a necessary condition for which two welded links are equivalent up to $V^{n}$-moves. This leads to show that the $V^{n}$-move is not an unknotting operation on welded knots except for $n=1$. We also discuss relations among $V^{n}$-moves, associated core groups and the multiplexing of crossings., Comment: 18 pages, many figures; entirely revised, Section 7 added

Let $n$ be a positive integer. M. K. Dabkowski and J. H. Przytycki introduced the $n$th Burnside group of links which is preserved by $n$-moves, and proved that for any odd prime $p$ there exist links which are not equivalent to trivial links up to $p$-moves by using their $p$th Burnside groups. This gives counterexamples for the Montesinos-Nakanishi $3$-move conjecture. In general, it is hard to distinguish $p$th Burnside groups of a given link and a trivial link. We give a necessary condition for which $p$th Burnside groups are isomorphic to those of trivial links. The necessary condition gives us an efficient way to distinguish $p$th Burnside groups of a given link and a trivial link. As an application, we show that there exist links, each of which is not equivalent to a trivial link up to $p$-moves for any odd prime $p$., Comment: 6 pages, 5 figures

We introduce the multiplexing of a crossing, replacing a classical crossing of a virtual link diagram with multiple crossings which is a mixture of classical and virtual. For integers $m_{i}$ $(i=1,\ldots,n)$ and an ordered $n$-component virtual link diagram $D$, a new virtual link diagram $D(m_{1},\ldots,m_{n})$ is obtained from $D$ by the multiplexing of all crossings. For welded isotopic virtual link diagrams $D$ and $D'$, $D(m_{1},\ldots,m_{n})$ and $D'(m_{1},\ldots,m_{n})$ are welded isotopic. From the point of view of classical link theory, it seems very interesting that $D(m_{1},\ldots,m_{n})$ could not be welded isotopic to a classical link diagram even if $D$ is a classical one, and new classical link invariants are expected from known welded link invariants via the multiplexing of crossings., Comment: 9 pages, 16 figures

We develop a calculus for diagrams of knotted objects. We define Arrow presentations, which encode the crossing informations of a diagram into arrows in a way somewhat similar to Gauss diagrams, and more generally w-tree presentations, which can be seen as `higher order Gauss diagrams'. This Arrow calculus is used to develop an analogue of Habiro's clasper theory for welded knotted objects, which contain classical link diagrams as a subset. This provides a 'realization' of Polyak's algebra of arrow diagrams at the welded level, and leads to a characterization of finite type invariants of welded knots and long knots. As a corollary, we recover several topological results due to K. Habiro and A. Shima and to T. Watanabe on knotted surfaces in 4-space. We also classify welded string links up to homotopy, thus recovering a result of the first author with B. Audoux, P. Bellingeri and E. Wagner., Comment: 40 pages, with many figures ; v.2: exposition revised, minor changes

We consider Milnor invariants for certain covering links as a generalization of covering linkage invariants formulated by R. Hartley and K. Murasugi. A set of Milnor invariants for covering links is a cobordism invariant of a link, and that this invariant can distinguish some links for which the ordinary Milnor invariants coincide. Moreover, for a Brunnian link $L$, the first non-vanishing Milnor invariants of $L$ is modulo-$2$ congruent to a sum of Milnor invariants of covering links. As a consequence, a sum of linking numbers of ' iterated' covering links gives the first non-vanishing Milnor invariant of $L$ modulo $2$., Comment: 11 pages, 10 figures

J.P. Levine introduced a clover link to investigate the indeterminacy of the Milnor invariants of a link. It is shown that for a clover link, the Milnor numbers of length at most $2k+1$ are well-defined if those of length at most $k$ vanish, and that the Milnor numbers of length at least $2k+2$ are not well-defined if those of length $k+1$ survive. For a clover link $c$ with the Milnor numbers of length at most $k$ vanishing, we show that the Milnor number $\mu_c(I)$ for a sequence $I$ is well-defined up to the greatest common devisor of $\mu_{c}(J)'s$, where $J$ is a subsequence of $I$ obtained by removing at least $k+1$ indices. Moreover, if $I$ is a non-repeated sequence with length $2k+2$, the possible range of $\mu_c(I)$ is given explicitly. As an application, we give an edge-homotopy classification of $4$-clover links., Comment: arXiv admin note: substantial text overlap with arXiv:1506.03922

Gordon and Litherland showed that all compact, unoriented, possibly non-orientable surfaces in $S^3$ bounded by a link are realted by attaching/deleting tubes and half twisted bands. In this note we give an elementary proof for this result., Comment: 4 pages, 7 figures

J.-B. Meilhan and the second author showed that any Milnor $\bar{\mu}$-invariant of length between 3 and $2k+1$ can be represented as a combination of HOMFLYPT polynomial of knots obtained by certain band sum of the link components, if all $\bar{\mu}$-invariants of length $\leq k$ vanish. They also showed that their formula does not hold for length $2k+2$. In this paper, we improve their formula to give the $\bar{\mu}$-invariants of length $2k+2$ by adding correction terms. The correction terms can be given by a combination of HOMFLYPT polynomial of knots determined by $\bar{\mu}$-invariants of length $k+1$. In particular, for any 4-component link the $\bar{\mu}$-invariants of length 4 are given by our formula, since all $\bar{\mu}$-invariants of length 1 vanish., Comment: 14 pages, 10 figures

The set SL(n) of n-string links has a monoid structure, given by the stacking product. When considered up to concordance, SL(n) becomes a group, which is known to be abelian only if n=1. In this paper, we consider two families of equivalence relations which endow SL(n) with a group structure, namely the C_k-equivalence introduced by Habiro in connection with finite type invariants theory, and the C_k-concordance, which is generated by C_k-equivalence and concordance. We investigate under which condition these groups are abelian, and give applications to finite type invariants., Comment: 20 pages

A C_k-move is a local move that involves (k+1) strands of a link. A C_k-move is called a C_k^d-move if these (k+1) strands belong to mutually distinct components of a link. Since a C_k^d-move preserves all k-component sublinks of a link, we consider the converse implication: are two links with common k-component sublinks related by a sequence of C_k^d-moves? We show that the answer is yes under certain assumptions, and provide explicit counter-examples for more general situations. In particular, we consider (n,k)-Brunnian links, i.e. n-component links whose k-component sublinks are all trivial. We show that such links can be deformed into a trivial link by C_k^d-moves, thus generalizing a result of Habiro and Miyazawa-Yasuhara, and deduce some results on finite type invariants of (n,k)-Brunnian links., Comment: 9 pages, 7 figures

We give formulas expressing Milnor invariants of an n-component link L in the 3-sphere in terms of the HOMFLYPT polynomial as follows. If the Milnor invariant \bar{\mu}_J(L) vanishes for any sequence J with length at most k, then any Milnor \bar{\mu}-invariant \bar{\mu}_I(L) with length between 3 and 2k+1 can be represented as a combination of HOMFLYPT polynomial of knots obtained from the link by certain band sum operations. In particular, the `first non vanishing' Milnor invariants can be always represented as such a linear combination., Comment: Entirely revised version (20 pages). The main result was generalized and extended to Milnor invariants of links, using new arguments. Several corollaries are given, in particular one containing the main result of the previous version. Example and References added

Link-homotopy and self Delta-equivalence are equivalence relations on links. It was shown by J. Milnor (resp. the last author) that Milnor invariants determine whether or not a link is link-homotopic (resp. self Delta-equivalent) to a trivial link. We study link-homotopy and self Delta-equivalence on a certain component of a link with fixing the rest components, in other words, homotopy and Delta-equivalence of knots in the complement of a certain link. We show that Milnor invariants determine whether a knot in the complement of a trivial link is null-homotopic, and give a sufficient condition for such a knot to be Delta-equivalent to the trivial knot. We also give a sufficient condition for knots in the complements of the trivial knot to be equivalent up to Delta-equivalence and concordance., Comment: 17 pages, 16 figures

In this paper, we give a complete set of finite type string link invariants of degree <5. In addition to Milnor invariants, these include several string link invariants constructed by evaluating knot invariants on certain closure of (cabled) string links. We show that finite type invariants classify string links up to C_k-moves for k<6, which proves, at low degree, a conjecture due to Goussarov and Habiro. We also give a similar characterization of finite type concordance invariants of degree <6.

A necessary and sufficient algebraic condition for a diffeomorphism over a surface embedded in the 3-sphere to be induced by a regular homotopic deformation is discussed, and a formula for the number of signed pass moves needed for this regular homotopy is given., Comment: 7 pages, 5 figures

We consider the operation of Whitehead double on a component of a link and study the behavior of Milnor invariants under this operation. We show that this operation turns a link whose Milnor invariants of length < k are all zero into a link with vanishing Milnor invariants of length < 2k, and we provide formulas for the first non-vanishing ones. As a consequence, we obtain statements relating the notions of link-homotopy and self Delta-equivalence via the Whitehead double operation. By using our result, we show that a Brunnian link L is link-homotopic to the unlink if and only if a link L with a single component Whitehed doubled is self Delta-equivalent to the unlink., Comment: 9 pages, 5 figures. Some minor modifications in this final version

For an $n$-component link $L$, the Milnor's isotopy invariant is defined for each multi-index $I=i_1i_2...i_m (i_j\in\n)$. Here $m$ is called the length. Let $r(I)$ denote the maximam number of times that any index appears. It is known that Milnor invariants with $r=1$ are link-homotopy invariant. N. Habegger and X. S. Lin showed that two string links are a link-homotopc if and only if their Milnor invariants with $r=1$ coincide. This gives us that a link in $S^3$ is link-homotopic to a trivial link if and only if the all Milnor invariants of the link with $r=1$ vanish. Although Milnor invariants with $r=2$ are not link-homotopy invariants, T. Fleming and the author showed that Milnor invariants with $r\leq 2$ are self $\Delta$-equivalence invariants. In this paper, we give a self $\Delta$-equivalence classification of the set of $n$-component links in $S^3$ whose Milnor invariants with length $\leq 2n-1$ and $r\leq 2$ vanish. As a corollary, we have that a link is self $\Delta$-equivalent to a trivial link if and only if the all Milnor invariants of the link with $r\leq 2$ vanish. This is a geometric characterization for links whose Milnor invariants with $\leq 2$ vanish. The chief ingredient in our proof is Habiro's clasper theory. We also give an alternate proof of a link-homotopy classification of string links by using clasper theory., Comment: 25 pages,18 figures, Changed the content (main result). Solved the conjecture given in previous version. Previous main result was a partial answer to the conjecture

A C_n-move is a local move on links defined by Habiro and Goussarov, which can be regarded as a `higher order crossing change'. We use Milnor invariants with repeating indices to provide several classification results for links up to C_n-moves, under certain restrictions. Namely, we give a classification up to C_4-moves of 2-component links, 3-component Brunnian links and n-component C_3-trivial links, and we classify n-component link-homotopically trivial Brunnian links up to C_{n+1}-moves., Comment: 16 pages

It has long been known that a Milnor invariant with no repeated index is an invariant of link homotopy. We show that Milnor's invariants with repeated indices are invariants not only of isotopy, but also of self C_k-moves. A self C_k-move is a natural generalization of link homotopy based on certain degree k clasper surgeries, which provides a filtration of link homotopy classes., Comment: 7 pages, 5 figures (low resolution)

K. Habiro gave a neccesary and sufficient condition for knots to have the same Vassiliev invariants in terms of $C_k$-move. In this paper we give another geometric condition in terms of Brunnian local move. The proof is simple and self-contained.

We give a classification of $n$-component links up to $C_n$-move. In order to prove this classification, we characterize Brunnian links, and have that a Brunnian link is ambient isotopic to a band sum of trivial link and Milnor's links.

Rotors were introduced in Graph Theory by W.Tutte. The concept was adapted to Knot Theory as a generalization of mutation by Anstee, Przytycki and Rolfsen in 1987. In this paper we show that Tristram-Levine signature is preserved by orientation-preserving rotations. Moreover, we show that any link invariant obtained from the characteristic polynomial of Goeritz matrix, including Murasugi signature, is not changed by rotations. In 2001, P. Traczyk showed that the Conway polynomials of any pair of orientation-preserving rotants coincide. But it was still an open problem if an orientation-reversing rotation preserves Conway polynomial. We show that there is a pair of orientation-reversing rotants with different Conway polynomials. This provides a negative solution to the problem., Comment: 23 pages, 22 figures

J.P. Levine showed that the Conway polynomial of a link is a product of two factors: one is the Conway polynomial of a knot which is obtained from the link by banding together the components; and the other is determined by the $\bar{\mu}$-invariants of a string link with the link as its closure. We give another description of the latter factor: the determinant of a matrix whose entries are linking pairings in the infinite cyclic covering space of the knot complement, which take values in the quotient field of ${\Bbb Z}[t,t^{-1}]$. In addition, we give a relation between the Taylor expansion of a linking pairing around $t=1$ and derivation on links which is invented by T.D. Cochran. In fact, the coefficients of the powers of $t-1$ will be the linking numbers of certain derived links in $S^3$. Therefore, the first non-vanishing coefficient of the Conway polynomial is determined by the linking numbers in $S^3$. This generalizes a result of J. Hoste., Comment: 9 pages, 2 figures

We study the linking numbers in a rational homology 3-sphere and in the infinite cyclic cover of the complement of a knot. They take values in $\Bbb Q$ and in ${Q}({\Bbb Z}[t,t^{-1}])$ respectively, where ${Q}({\Bbb Z}[t,t^{-1}])$ denotes the quotient field of ${\Bbb Z}[t,t^{-1}]$. It is known that the modulo-$\Bbb Z$ linking number in the rational homology 3-sphere is determined by the linking matrix of the framed link and that the modulo-${\Bbb Z}[t,t^{-1}]$ linking number in the infinite cyclic cover of the complement of a knot is determined by the Seifert matrix of the knot. We eliminate ` modulo $\Bbb Z$' and ` modulo ${\Bbb Z}[t,t^{-1}]$'. When the finite cyclic cover of the 3-sphere branched over a knot is a rational homology 3-sphere, the linking number of a pair in the preimage of a link in the 3-sphere is determined by the Goeritz/Seifert matrix of the knot., Comment: LaTeX, 24 pages, 6 figures

We give an algorithm for a surgery description of a $p$-fold cyclic branched cover of $B^3$ branched along a tangle. We generalize constructions of Montesinos and Akbulut-Kirby., Comment: LaTeX, 9 pages, 16 figures

We define $A_k$-moves for embeddings of a finite graph into the 3-sphere for each natural number $k$. Let $A_k$-equivalence denote an equivalence relation generated by $A_k$-moves and ambient isotopy. $A_k$-equivalence implies $A_{k-1}$-equivalence. Let ${\cal F}$ be an $A_{k-1}$-equivalence class of the embeddings of a finite graph into the 3-sphere. Let ${\cal G}$ be the quotient set of ${\cal F}$ under $A_k$-equivalence. We show that the set ${\cal G}$ forms an abelian group under a certain geometric operation. We define finite type invariants on ${\cal F}$ of order $(n;k)$. And we show that if any finite type invariant of order $(1;k)$ takes the same value on two elements of ${\cal F}$, then they are $A_k$-equivalent. $A_k$-move is a generalization of $C_k$-move defined by K. Habiro. Habiro showed that two oriented knots are the same up to $C_k$-move and ambient isotopy if and only if any Vassiliev invariant of order $\leq k-1$ takes the same value on them. The ` if' part does not hold for two-component links. Our result gives a sufficient condition for spatial graphs to be $C_k$-equivalent., Comment: LaTeX, 18 pages with figures, to appear in Pacific Journal of Mathematics

The $C_k$-equivalence is an equivalence relation generated by $C_k$-moves defined by Habiro. Habiro showed that the set of $C_k$-equivalence classes of the knots forms an abelian group under the connected sum and it can be classified by the additive Vassiliev invariant of order $\leq k-1$. We see that the set of $C_k$-equivalence classes of the spatial $\theta$-curves forms a group under the vertex connected sum and that if the group is abelian, then it can be classified by the additive Vassiliev invariant of order $\leq k-1$. However the group is not necessarily abelian. In fact, we show that it is nonabelian for $k\geq 12$. As an easy consequence, we have the set of $C_k$-equivalence classes of $m$-string links, which forms a group under the composition, is nonabelian for $k\geq 12$ and $m\geq 2$., Comment: LaTeX, 15 pages with 12 figures