Related papers: Athena: Modular CAM/CAD Software for Synthetic Bio…
The Science Products Module (SPM), a US contribution to the Athena Wide Field Imager, is a highly capable secondary CPU that performs special processing on the science data stream. The SPM will have access to both accepted X-ray events and…
Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological {\em networks} holds similar promise. Biological networks generally model interactions between biomolecules…
Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies,…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Associative learning is one of the key mechanisms displayed by living organisms in order to adapt to their changing environments. It was early recognized to be a general trait of complex multicellular organisms but also found in "simpler"…
Chemistry plays a key role in many aspects of astrophysical fluids. Atoms and molecules are agents for heating and cooling, determine the ionization fraction, serve as observational tracers, and build the molecular foundation of life. We…
We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy,…
Large scale simulations are a key pillar of modern research and require ever-increasing computational resources. Different novel manycore architectures have emerged in recent years on the way towards the exascale era. Performance…
Athena is the ATLAS off-line software framework, based upon the GAUDI architecture from LHCb. As part of ATLAS' continuing efforts to enhance and customise the architecture to meet our needs, we have developed a data object description tool…
Concurrent advances across fields such as organoid technology, Microelectrode Arrays (MEAs), neuromorphic computing, and machine learning have given rise to a groundbreaking research paradigm: Synthetic Biological Intelligence (SBI). SBI…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
The design of genetic networks with specific functions is one of the major goals of synthetic biology. However, constructing biological devices that work "as required" remains challenging, while the cost of uncovering flawed designs…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
ATHENA is an open source Python package for reduction in parameter space. It implements several advanced numerical analysis techniques such as Active Subspaces (AS), Kernel-based Active Subspaces (KAS), and Nonlinear Level-set Learning…
This paper introduces a new concept. We intend to give life to a software agent. A software agent is a computer program that acts on a user's behalf. We put a DNA inside the agent. DNA is a simple text, a whole roadmap of a network of…
Biology-derived algorithms are an important part of computational sciences, which are essential to many scientific disciplines and engineering applications. Many computational methods are derived from or based on the analogy to natural…
Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…
Cellular Agent-Based Models are commonly employed to describe a variety biological systems. Over the course of the past years, many modeling tools have emerged which solve particular research questions. In this short opinion piece, we argue…