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Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to…
The convergence of artificial intelligence (AI) and synthetic biology is rapidly accelerating the pace of biological discovery and engineering. AI techniques, such as large language models and biological design tools, are enabling the…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
This paper presents an automatic formal controller synthesis method for nonlinear sampled-data systems with safety and reachability specifications. Fundamentally, the presented method is not restricted to polynomial systems and controllers.…
This study introduces the concept of finite element network analysis (FENA) which is a physics-informed, machine-learning-based, computational framework for the simulation of complex physical systems. The framework leverages the extreme…
Many computer models such as cellular automata and artificial neural networks have been developed and successfully applied. However, in some cases, these models might be restrictive on the possible solutions or their solutions might be…
Most chemical processes, such as distillation, absorption, extraction, and catalytic reactions, are extremely complex processes that are affected by multiple factors. The relationships between their input variables and output variables are…
In this study, we explore how the combination of synthetic biology, neuroscience modeling, and neuromorphic electronic systems offers a new approach to creating an artificial system that mimics the natural sense of smell. We argue that a…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
Propelling microorganisms through fluids and moving fluids along cellular surfaces are essential biological functions accomplished by long, thin structures called motile cilia and flagella, whose regular, oscillatory beating breaks the…
One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
Cellular automata are discrete and computational models thatcan be shown as general models of complexity. They are used in varied applications to derive the generalized behavior of the presented model. In this paper we have took one such…
The design and implementation of a new framework for adaptive mesh refinement (AMR) calculations is described. It is intended primarily for applications in astrophysical fluid dynamics, but its flexible and modular design enables its use…
Automated synthesis of histology images has several potential applications in computational pathology. However, no existing method can generate realistic tissue images with a bespoke cellular layout or user-defined histology parameters. In…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…
Digital Embedded Devices of next-generation safety-critical industrial automation systems require high levels of survivability and resilience against the hardware and software failure. One of the concepts for achieving this requirement is…