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Let $P$ be a polygon with $r>0$ reflex vertices and possibly with holes and islands. A subsuming polygon of $P$ is a polygon $P'$ such that $P \subseteq P'$, each connected component $R$ of $P$ is a subset of a distinct connected component…
The reconfiguration problem for homomorphisms of digraphs to a reflexive digraph cycle, which amounts to deciding if a `reconfiguration graph' is connected, is known to by polynomially time solvable via a greedy algorithm based on certain…
We employ 3D Langevin Dynamics simulations to study the dynamics of polymer chains translocating through a nanopore in presence of asymmetric solvent conditions. Initially a large fraction ($>$ 50%) of the chain is placed at the…
Tightness is a generalisation of the notion of convexity: a space is tight if and only if it is "as convex as possible", given its topological constraints. For a simplicial complex, deciding tightness has a straightforward exponential time…
We consider the computation of the volume of the union of high-dimensional geometric objects. While showing that this problem is #P-hard already for very simple bodies (i.e., axis-parallel boxes), we give a fast FPRAS for all objects where…
We consider a class of pattern matching problems where a normalising transformation is applied at every alignment. Normalised pattern matching plays a key role in fields as diverse as image processing and musical information processing…
Lexicographically minimal string rotation is a fundamental problem in string processing that has recently garnered significant attention in quantum computing. Near-optimal quantum algorithms have been proposed for solving this problem,…
We propose the first algorithm for non-rigid 2D-to-3D shape matching, where the input is a 2D shape represented as a planar curve and a 3D shape represented as a surface; the output is a continuous curve on the surface. We cast the problem…
In this paper, we consider three hitting problems on a disk intersection graph: Triangle Hitting Set, Feedback Vertex Set, and Odd Cycle Transversal. Given a disk intersection graph $G$, our goal is to compute a set of vertices hitting all…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
We present an algorithm for the following problem. Given a triangulated 3-manifold M and a (possibly non-simple) closed curve on the boundary of M, decide whether this curve is contractible in M. Our algorithm runs in space polynomial in…
Let $\mathcal{A}$ be the subdivision of $\mathbb{R}^d$ induced by $m$ convex polyhedra having $n$ facets in total. We prove that $\mathcal{A}$ has combinatorial complexity $O(m^{\lceil d/2 \rceil} n^{\lfloor d/2 \rfloor})$ and that this…
The Largest Empty Circle problem seeks the largest circle centered within the convex hull of a set $P$ of $n$ points in $\mathbb{R}^2$ and devoid of points from $P$. In this paper, we introduce a query version of this well-studied problem.…
We study the problem of planning paths for $p$ distinguishable pebbles (robots) residing on the vertices of an $n$-vertex connected graph with $p \le n$. A pebble may move from a vertex to an adjacent one in a time step provided that it…
We study the problem of rotating a simple polygon to contain the maximum number of elements from a given point set in the plane. We consider variations of this problem where the rotation center is a given point or lies on a line segment, a…
One of basic difficulties of machine learning is handling unknown rotations of objects, for example in image recognition. A related problem is evaluation of similarity of shapes, for example of two chemical molecules, for which direct…
Given a boolean n by n matrix A we consider arithmetic circuits for computing the transformation x->Ax over different semirings. Namely, we study three circuit models: monotone OR-circuits, monotone SUM-circuits (addition of non-negative…
Given the n vertices of a convex polygon in cyclic order, can the triangle of maximum area inscribed in P be determined by an algorithm with O(n) time complexity? A purported linear-time algorithm by Dobkin and Snyder from 1979 has recently…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…