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CA has grown as potential classifier for addressing major problems in bioinformatics. Lot of bioinformatics problems like predicting the protein coding region, finding the promoter region, predicting the structure of protein and many other…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
In biological data, it is often the case that observed data are available only for a subset of samples. When a kernel matrix is derived from such data, we have to leave the entries for unavailable samples as missing. In this paper, we make…
The microstructure of materials evolves through chemical reactions and mechanical stress, often strongly coupled in phenomena such as pressure solution or crystallization pressure. This article presents MASKE: a simulator to address the…
We ask the question of how small a self-assembling set of tiles can be yet have interesting computational behaviour. We study this question in a model where supporting walls are provided as an input structure for tiles to grow along: we…
This research is aimed to propose an artificial intelligence algorithm comprising an ontology-based design, text mining, and natural language processing for automatically generating gap-fill multiple choice questions (MCQs). The simulation…
Membrane systems are a biologically-inspired computational model based on the structure of biological cells and the way chemicals interact and traverse their membranes. Although their dynamics are described by rules, encoding membrane…
Many forms of programmable matter have been proposed for various tasks. We use an abstract model of self-organizing particle systems for programmable matter which could be used for a variety of applications, including smart paint and…
A recursive method is given for finding generating functions which enumerate rooted hypermaps by number of vertices, edges and faces for any given number of darts. It makes use of matrix-integral expressions arising from the study of…
Stochastic models of gene expression are typically formulated using the chemical master equation, which can be solved exactly or approximately using a repertoire of analytical methods. Here, we provide a tutorial review of an alternative…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
The Turing machine, as it was presented by Turing himself, models the calculations done by a person. This means that we can compute whatever any Turing machine can compute, and therefore we are Turing complete. The question addressed here…
Mobile genetic elements like conjugative plasmids play a crucial role in shaping the genetic content and population dynamics of bacterial species. Bacterial populations often contain not one, but multiple co-circulating MGEs, which modify…
The past decade has seen rapid growth in the number of experimentally realized two-dimensional (2D) materials with diverse chemical and physical properties. However, information on their crystal structure, synthesis routes, and measured or…
Mesh generation remains a key technology in many areas where numerical simulations are required. As numerical algorithms become more efficient and computers become more powerful, the percentage of time devoted to mesh generation becomes…
To solve Math Word Problems, human students leverage diverse reasoning logic that reaches different possible equation solutions. However, the mainstream sequence-to-sequence approach of automatic solvers aims to decode a fixed solution…
Many scientific computing problems can be reduced to Matrix-Matrix Multiplications (MMM), making the General Matrix Multiply (GEMM) kernels in the Basic Linear Algebra Subroutine (BLAS) of interest to the high-performance computing…
We computationally resolve an open problem concerning the expressibility of $4 \times 4$ full-rank matrices as Hadamard products of two rank-2 matrices. Through exhaustive search over $\mathbb{F}_2$, we identify 5,304 counterexamples among…
The mechanism of bacterial cell size control has been a mystery for decades, which involves the well-coordinated growth and division in the cell cycle. The revolutionary modern techniques of microfluidics and the advanced live imaging…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…