20 papers · ranked by Valyu relevance
Léa C. Girard, Walter G. Joyce
Softshell turtles (Pan-Trionychidae) are an early branching clade of hidden-necked turtles (Cryptodira) with a rich fossil record extending back to the Early Cretaceous. The evolutionary history of softshell turtles is still unresolved because of their conservative morphology combined with high levels of polymorphism…
Hugo Daniel Macedo, José N. Oliveira
Interested in formalizing the generation of fast running code for linear algebra applications, the authors show how an index-free, calculational approach to matrix algebra can be developed by regarding matrices as morphisms of a category with biproducts. This shifts the traditional view of matrices as indexed…
Christian Pech, Maja Pech
A relational structure is homomorphism-homogeneous if every homomorphism between finite substructures extends to an endomorphism of the structure. This notion was introduced recently by Cameron and Neˇsetˇril. In this paper we consider a strengthening of homomorphism-homogeneity — we call a relational structure…
Tamás Varga, József Garay
One of the main result in the theory of classical evolutionary matrix games (13, 12) claims that monomorphic ESS condition implies the stability of the corresponding state of the polymorphic replicator dynamics (9, 20). The picture was then refined by 4 introducing the strong stability concept which says that if there…
Aaron T. L. Lun, Hervé Pagès, Mike L. Smith, Mihaela Pertea
Biological experiments involving genomics or other high-throughput assays typically yield a data matrix that can be explored and analyzed using the R programming language with packages from the Bioconductor project. Improvements in the throughput of these assays have resulted in an explosion of data even from routine…
Dey, Sourin, Miklaucic, Nicholas + 12 more
Polymorphism, the ability of a compound to crystallize in multiple distinct structures, which plays a vital role in determining the physical, chemical, and functional properties of materials. Accurate identification and prediction of polymorphic structures are critical for materials design, drug development, and device…
Authors not listed
Organic semiconductors (OSCs) can exhibit polymorphism, which may impact the physichochemical properties of the material, including the bandgap. With the advent of machine learning, graph neural networks have been used to predict the bandgap of OSCs. However, these frameworks struggle with differentiating between…
Jeremy G Sumner, Peter D Jarvis, Barbara R Holland
Background Hadamard conjugation is part of the standard mathematical armoury in the analysis of molecular phylogenetic methods. For group-based models, the approach provides a one-to-one correspondence between the so-called “edge length” and “sequence” spectrum on a phylogenetic tree. The Hadamard conjugation has been…
Johannes J. Cartus, Andreas Jeindl, Anna Werkovits, Lukas Hörmann + 1 more
Organic/inorganic interfaces are known to exhibit rich polymorphism, where different polymorphs often possess significantly different properties. Which polymorph forms during an experiment depends strongly on environmental parameters such as deposition temperature and partial pressure of the molecule to be adsorbed. To…
Melvyn B. Nathanson
The process of alternately row scaling and column scaling a positive n × n matrix A converges to a doubly stochastic positive n × n matrix S(A), called the Sinkhorn limit of A. Exact formulae for the Sinkhorn limits of certain symmetric positive 3 × 3 matrices are computed, and related problems in diophantine…
Yamato Arai, Yuma Ichikawa, Koji Hukushima
This study proposes the "adaptive flip graph algorithm", which combines adaptive searches with the flip graph algorithm for finding fast and efficient methods for matrix multiplication. The adaptive flip graph algorithm addresses the inherent limitations of exploration and inefficient search encountered in the original…
Shu-Xin Miao, Dan Zhang
Recently, based on the Hadjidimos preconditioner, a preconditioned GAOR method was proposed for solving the linear complementarity problem (Liu and Li in East Asian J. Appl. Math. 2:94-107, [13]). In this paper, we propose a new preconditioned GAOR method for solving the linear complementarity problem with an M-matrix.…
Łukasz Matysiak, Weronika Przewozniak, Natalia Rulinska
Matrices are very popular and widely used in mathematics and other fields of science. Every mathematician has known the properties of finite-sized matrices since the time of study. In this paper, we consider the basic theory of infinite matrices. So far, there have been references and few results in certain scientific…
Alena Khmelinskaia, Neville P. Bethel, Farzad Fatehi, Aleksandar Antanasijevic + 15 more
Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. For example, clathrin coats adopt a wide variety of architectures to adapt to vesicular cargos of various sizes. Although computational methods for designing novel self-assembling proteins have advanced…
Yves Fomatati
Let K be a field. Let f ∈ K[[x1, ..., xr]] and g ∈ K[[y1, ..., ys]] be nonzero elements. If X (resp. Y) is a matrix factorization of f (resp. g), Yoshino had constructed a tensor product (of matrix factorizations) b⊗ such that Xb⊗Y is a matrix factorization of f + g ∈ K[[x1, ..., xr , y1, ..., ys]]. In this paper, we…
Imran S. Haque, Kyle A. Beauchamp, Vijay S. Pande
The bottleneck for the rapid calculation of the root-mean-square deviation in atomic coordinates (RMSD) between pairs of protein structures for large numbers of conformations is the evaluation of a 3 × N × N × 3 matrix product over conformation pairs. Here we describe two matrix multiply routines specialized for the 3…
Lukas Frey, Dhiman Ghosh, Bilal M. Qureshi, David Rhyner + 7 more
The aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly…
Yves Fomatati
Let R = K[x1, x2, · · · , xm] where K is a field. In this paper, we give some properties of nmatrix factorizations of polynomials in R. We also derive some results giving some lower bounds on the number of n-matrix factors of polynomials. In particular, we give a lower bound on the number of matrix factors of minimal…
Gökhan Tuncay, Fatma Büyüksaraçoğlu Sakallı, Meltem Kurt Pehlivanoğlu, Gülsüm Gözde Yılmazgüç + 3 more
'Gülsüm Gözde Yılmazgüç' 'Sedat Akleylek' 'Muharrem Tolga Sakallı' 'Vimal Shanmuganathan'] This article presents a new hybrid method (combining search based methods and direct construction methods) to generate all \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts}…
Benjamin Lieser, Georgy Belousov, Johannes Söding
Background Most popular tools for reconstructing phylogenetic trees from multiple sequence alignments use a model of molecular evolution in which a single substitution matrix or a small set of fixed matrices are shared between all columns. Models with column-specific rate matrices can in principle be fit by automatic…