Finding a Hamiltonian Path in a Cube with Specified Turns is Hard

We prove the NP-completeness of finding a Hamiltonian path in an N × N × N cube graph with turns exactly at specified lengths along the path. This result establishes NP-completeness of Snake Cube puzzles: folding a chain of N3 unit cubes, joined at face centers (usually by a cord passing through all the cubes), into an N × N × N cube. Along the way, we prove a universality result that zig-zag chains (which must turn every unit) can fold into any polycube after 4 × 4 × 4 refinement, or into any Hamiltonian polycube after 2 × 2 × 2 refinement

Continuously Flattening Polyhedra Using Straight Skeletons

We prove that a surprisingly simple algorithm folds the surface of every convex polyhedron, in any dimension, into a flat folding by a continuous motion, while preserving intrinsic distances and avoiding crossings. The flattening respects the straight-skeleton gluing, meaning that points of the polyhedron touched by a common ball inside the polyhedron come into contact in the flat folding, which answers an open question in the book Geometric Folding Algorithms. The primary creases in our folding process can be found in quadratic time, though necessarily, creases must roll continuously, and we show that the full crease pattern can be exponential in size. We show that our method solves the fold-and-cut problem for convex polyhedra in any dimension. As an additional application, we show how a limiting form of our algorithm gives a general design technique for flat origami tessellations, for any spiderweb (planar graph with all-positive equilibrium stress)

Folding equilateral plane graphs

22nd International Symposium, ISAAC 2011, Yokohama, Japan, December 5-8, 2011. ProceedingsWe consider two types of folding applied to equilateral plane graph linkages. First, under continuous folding motions, we show how to reconfigure any linear equilateral tree (lying on a line) into a canonical configuration. By contrast, such reconfiguration is known to be impossible for linear (nonequilateral) trees and for (nonlinear) equilateral trees. Second, under instantaneous folding motions, we show that an equilateral plane graph has a noncrossing linear folded state if and only if it is bipartite. Not only is the equilateral constraint necessary for this result, but we show that it is strongly NP-complete to decide whether a (nonequilateral) plane graph has a linear folded state. Equivalently, we show strong NP-completeness of deciding whether an abstract metric polyhedral complex with one central vertex has a noncrossing flat folded state with a specified “outside region”. By contrast, the analogous problem for a polyhedral manifold with one central vertex (single-vertex origami) is only weakly NP-complete

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

On folding and unfolding with linkages and origami

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mathematics, 2016.Cataloged from PDF version of thesis.Includes bibliographical references (pages 121-127).We revisit foundational questions in the kinetic theory of linkages and origami, investigating their folding/unfolding behaviors and the computational complexity thereof. In Chapter 2, we exactly settle the complexity of realizability, rigidity, and global rigidy for graphs and linkages in the plane, even when the graphs are (1) promised to avoid crossings in all configurations, or (2) equilateral and required to be drawn without crossings ("matchstick graphs"): these problems are complete for the class IR defined by the Existential Theory of the Reals, or its complement. To accomplish this, we prove a strong form of Kempe's Universality Theorem for linkages that avoid crossings. Chapter 3 turns to "self-touching" linkage configurations, whose bars are allowed to rest against each other without passing through. We propose an elegant model for representing such configurations using infinitesimal perturbations, working over a field R(e) that includes formal infinitesimals. Using this model and the powerful Tarski-Seidenberg "transfer" principle for real closed fields, we prove a self-touching version of the celebrated Expansive Carpenter's Rule Theorem. We switch to folding polyhedra in Chapter 4: we show a simple technique to continuously flatten the surface of any convex polyhedron without distorting intrinsic surface distances or letting the surface pierce itself. This origami motion is quite general, and applies to convex polytopes of any dimension. To prove that no piercing occurs, we apply the same infinitesimal techniques from Chapter 3 to formulate a new formal model of self-touching origami that is simpler to work with than existing models. Finally, Chapter 5 proves polyhedra are hard to edge unfold: it is NP-hard to decide whether a polyhedron may be cut along edges and unfolded into a non-overlapping net. This edge unfolding problem is not known to be solvable in NP due to precision issues, but we show this is not the only obstacle: it is NP complete for orthogonal polyhedra with integer coordinates (all of whose unfolding also have integer coordinates)by Zachary Abel.Ph. D

Shape replication through self-assembly and RNase enzymes

We introduce the problem of shape replication in the Wang tile self-assembly model. Given an input shape, we consider the problem of designing a self-assembly system which will replicate that shape into either a specific number of copies, or an unbounded number of copies. Motivated by practical DNA implementations of Wang tiles, we consider a model in which tiles consisting of DNA or RNA can be dynamically added in a sequence of stages. We further permit the addition of RNase enzymes capable of disintegrating RNA tiles. Under this model, we show that arbitrary genus-0 shapes can be replicated infinitely many times using only O(1) distinct tile types and O(1) stages. Further, we show how to replicate precisely n copies of a shape using O(log n) stages and O(1) tile types.National Science Foundation (U.S.) (NSF CAREER award CCF-0347776)United States. Dept. of Energy (DOE grant DE-FG02-04ER25647