On the Complexity of an Unregulated Traffic Crossing

The steady development of motor vehicle technology will enable cars of the near future to assume an ever increasing role in the decision making and control of the vehicle itself. In the foreseeable future, cars will have the ability to communicate with one another in order to better coordinate their motion. This motivates a number of interesting algorithmic problems. One of the most challenging aspects of traffic coordination involves traffic intersections. In this paper we consider two formulations of a simple and fundamental geometric optimization problem involving coordinating the motion of vehicles through an intersection. We are given a set of $n$ vehicles in the plane, each modeled as a unit length line segment that moves monotonically, either horizontally or vertically, subject to a maximum speed limit. Each vehicle is described by a start and goal position and a start time and deadline. The question is whether, subject to the speed limit, there exists a collision-free motion plan so that each vehicle travels from its start position to its goal position prior to its deadline. We present three results. We begin by showing that this problem is NP-complete with a reduction from 3-SAT. Second, we consider a constrained version in which cars traveling horizontally can alter their speeds while cars traveling vertically cannot. We present a simple algorithm that solves this problem in $O(n \log n)$ time. Finally, we provide a solution to the discrete version of the problem and prove its asymptotic optimality in terms of the maximum delay of a vehicle

Shortest paths in nearly conservative digraphs

We introduce the following notion: a digraph D = (V, A) with arc weights c: A → R is called nearly conservative if every negative cycle consists of two arcs. Computing shortest paths in nearly conservative digraphs is NP-hard, and even deciding whether a digraph is nearly conservative is coNP-complete. We show that the “All Pairs Shortest Path” problem is fixed parameter tractable with various parameters for nearly conservative digraphs. The results also apply for the special case of conservative mixed graphs

Approximation Algorithms for Generalized MST and TSP in Grid Clusters

We consider a special case of the generalized minimum spanning tree problem (GMST) and the generalized travelling salesman problem (GTSP) where we are given a set of points inside the integer grid (in Euclidean plane) where each grid cell is $1 \times 1$. In the MST version of the problem, the goal is to find a minimum tree that contains exactly one point from each non-empty grid cell (cluster). Similarly, in the TSP version of the problem, the goal is to find a minimum weight cycle containing one point from each non-empty grid cell. We give a $(1+4\sqrt{2}+\epsilon)$ and $(1.5+8\sqrt{2}+\epsilon)$-approximation algorithm for these two problems in the described setting, respectively. Our motivation is based on the problem posed in [7] for a constant approximation algorithm. The authors designed a PTAS for the more special case of the GMST where non-empty cells are connected end dense enough. However, their algorithm heavily relies on this connectivity restriction and is unpractical. Our results develop the topic further

Algorithms for Stable Matching and Clustering in a Grid

We study a discrete version of a geometric stable marriage problem originally proposed in a continuous setting by Hoffman, Holroyd, and Peres, in which points in the plane are stably matched to cluster centers, as prioritized by their distances, so that each cluster center is apportioned a set of points of equal area. We show that, for a discretization of the problem to an $n\times n$ grid of pixels with $k$ centers, the problem can be solved in time $O(n^2 \log^5 n)$, and we experiment with two slower but more practical algorithms and a hybrid method that switches from one of these algorithms to the other to gain greater efficiency than either algorithm alone. We also show how to combine geometric stable matchings with a $k$-means clustering algorithm, so as to provide a geometric political-districting algorithm that views distance in economic terms, and we experiment with weighted versions of stable $k$-means in order to improve the connectivity of the resulting clusters.Comment: 23 pages, 12 figures. To appear (without the appendices) at the 18th International Workshop on Combinatorial Image Analysis, June 19-21, 2017, Plovdiv, Bulgari

A tight lower bound for steiner orientation

In the STEINER ORIENTATION problem, the input is a mixed graph G (it has both directed and undirected edges) and a set of k terminal pairs T. The question is whether we can orient the undirected edges in a way such that there is a directed s⇝t path for each terminal pair (s,t)∈T. Arkin and Hassin [DAM’02] showed that the STEINER ORIENTATION problem is NP-complete. They also gave a polynomial time algorithm for the special case when k=2 . From the viewpoint of exact algorithms, Cygan, Kortsarz and Nutov [ESA’12, SIDMA’13] designed an XP algorithm running in nO(k) time for all k≥1. Pilipczuk and Wahlström [SODA ’16] showed that the STEINER ORIENTATION problem is W[1]-hard parameterized by k. As a byproduct of their reduction, they were able to show that under the Exponential Time Hypothesis (ETH) of Impagliazzo, Paturi and Zane [JCSS’01] the STEINER ORIENTATION problem does not admit an f(k)⋅no(k/logk) algorithm for any computable function f. That is, the nO(k) algorithm of Cygan et al. is almost optimal. In this paper, we give a short and easy proof that the nO(k) algorithm of Cygan et al. is asymptotically optimal, even if the input graph has genus 1. Formally, we show that the STEINER ORIENTATION problem is W[1]-hard parameterized by the number k of terminal pairs, and, under ETH, cannot be solved in f(k)⋅no(k) time for any function f even if the underlying undirected graph has genus 1. We give a reduction from the GRID TILING problem which has turned out to be very useful in proving W[1]-hardness of several problems on planar graphs. As a result of our work, the main remaining open question is whether STEINER ORIENTATION admits the “square-root phenomenon” on planar graphs (graphs with genus 0): can one obtain an algorithm running in time f(k)⋅nO(k√) for PLANAR STEINER ORIENTATION, or does the lower bound of f(k)⋅no(k) also translate to planar graphs

Star Routing: Between Vehicle Routing and Vertex Cover

We consider an optimization problem posed by an actual newspaper company, which consists of computing a minimum length route for a delivery truck, such that the driver only stops at street crossings, each time delivering copies to all customers adjacent to the crossing. This can be modeled as an abstract problem that takes an unweighted simple graph $G = (V, E)$ and a subset of edges $X$ and asks for a shortest cycle, not necessarily simple, such that every edge of $X$ has an endpoint in the cycle. We show that the decision version of the problem is strongly NP-complete, even if $G$ is a grid graph. Regarding approximate solutions, we show that the general case of the problem is APX-hard, and thus no PTAS is possible unless P $=$ NP. Despite the hardness of approximation, we show that given any $\alpha$-approximation algorithm for metric TSP, we can build a $3\alpha$-approximation algorithm for our optimization problem, yielding a concrete $9/2$-approximation algorithm. The grid case is of particular importance, because it models a city map or some part of it. A usual scenario is having some neighborhood full of customers, which translates as an instance of the abstract problem where almost every edge of $G$ is in $X$. We model this property as $|E - X| = o(|E|)$, and for these instances we give a $(3/2 + \varepsilon)$-approximation algorithm, for any $\varepsilon > 0$, provided that the grid is sufficiently big.Comment: Accepted to the 12th Annual International Conference on Combinatorial Optimization and Applications (COCOA'18

The Complexity of Drawing a Graph in a Polygonal Region

We prove that the following problem is complete for the existential theory of the reals: Given a planar graph and a polygonal region, with some vertices of the graph assigned to points on the boundary of the region, place the remaining vertices to create a planar straight-line drawing of the graph inside the region. This strengthens an NP-hardness result by Patrignani on extending partial planar graph drawings. Our result is one of the first showing that a problem of drawing planar graphs with straight-line edges is hard for the existential theory of the reals. The complexity of the problem is open in the case of a simply connected region. We also show that, even for integer input coordinates, it is possible that drawing a graph in a polygonal region requires some vertices to be placed at irrational coordinates. By contrast, the coordinates are known to be bounded in the special case of a convex region, or for drawing a path in any polygonal region.Comment: Appears in the Proceedings of the 26th International Symposium on Graph Drawing and Network Visualization (GD 2018

A two-domain elevator mechanism for sodium/proton antiport

Sodium/proton (Na+/H+) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis1. In humans, their dysfunction has been linked to diseases, such as hypertension, heart failure and epilepsy, and they are well-established drug targets2. The best understood model system for Na+/H+ antiport is NhaA from Escherichia coli1, 3, for which both electron microscopy and crystal structures are available4, 5, 6. NhaA is made up of two distinct domains: a core domain and a dimerization domain. In the NhaA crystal structure a cavity is located between the two domains, providing access to the ion-binding site from the inward-facing surface of the protein1, 4. Like many Na+/H+ antiporters, the activity of NhaA is regulated by pH, only becoming active above pH 6.5, at which point a conformational change is thought to occur7. The only reported NhaA crystal structure so far is of the low pH inactivated form4. Here we describe the active-state structure of a Na+/H+ antiporter, NapA from Thermus thermophilus, at 3 Å resolution, solved from crystals grown at pH 7.8. In the NapA structure, the core and dimerization domains are in different positions to those seen in NhaA, and a negatively charged cavity has now opened to the outside. The extracellular cavity allows access to a strictly conserved aspartate residue thought to coordinate ion binding1, 8, 9 directly, a role supported here by molecular dynamics simulations. To alternate access to this ion-binding site, however, requires a surprisingly large rotation of the core domain, some 20° against the dimerization interface. We conclude that despite their fast transport rates of up to 1,500 ions per second3, Na+/H+ antiporters operate by a two-domain rocking bundle model, revealing themes relevant to secondary-active transporters in general

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon