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We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
In this paper, we present a generalized version of the matrix chain algorithm to generate efficient code for linear algebra problems, a task for which human experts often invest days or even weeks of works. The standard matrix chain problem…
Computer experiments can emulate the physical systems, help computational investigations, and yield analytic solutions. They have been widely employed with many engineering applications (e.g., aerospace, automotive, energy systems.…
We investigate algorithmic control of a large swarm of mobile particles (such as robots, sensors, or building material) that move in a 2D workspace using a global input signal (such as gravity or a magnetic field). We show that a maze of…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions…
This work aims to study and explore the use of Gene Expression Programming (GEP) in solving the on-line Bin-Packing problem. The main idea is to show how GEP can automatically find acceptable heuristic rules to solve the problem efficiently…
This work presents twelve fine-tuned deep learning architectures to solve the bacterial classification problem over the Digital Image of Bacterial Species Dataset. The base architectures were mainly published as mobile or efficient…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
Nonlinear constrained optimization problems are encountered in many scientific fields. To utilize the huge calculation power of current computers, many mathematic models are also rebuilt as optimization problems. Most of them have…
There is a growing interest towards implementation of maze solving in spatially-extended physical, chemical and living systems. Several reports of prototypes attracted great publicity, e.g. maze solving with slime mould and epithelial…
In \cite{entombed}, John Aycock and Tara Copplestone pose an open question, namely the explanation of the mysterious lookup table used in the Entombed Game's Algorithm for two dimensional maze generation. The question attracted media…
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the…
Biocomputing systems based on engineered bacteria can lead to novel tools for environmental monitoring and detection of metabolic diseases. In this paper, we propose a Bacterial Molecular Computing on a Chip (BMCoC) using microfluidic and…
The Cell Formation Problem has been studied as an optimization problem in manufacturing for more than 90 years. It consists of grouping machines and parts into manufacturing cells in order to maximize loading of cells and minimize movement…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for…
The diffusion-driven Turing instability is a potential mechanism for spatial pattern formation in numerous biological and chemical systems. However, engineering these patterns and demonstrating that they are produced by this mechanism is…
Rearrangements of bacterial chromosomes can be studied mathematically at several levels, most prominently at a local, or sequence level, as well as at a topological level. The biological changes involved locally are inversions, deletions,…