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The process of dynamic state estimation (filtering) based on point process observations is in general intractable. Numerical sampling techniques are often practically useful, but lead to limited conceptual insight about optimal…
Progress in experimental techniques at nanoscale made measurements of noise in molecular junctions possible. These data are important source of information not accessible through average flux measurements. Emergence of optoelectronics,…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Energy consumption in residential and commercial buildings has increased dramatically worldwide in the last decade, due to the constant population and economic growth, the proliferation of electronic and consumer appliances. This has…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Sensor-based human activity recognition is a key technology for many human-centered intelligent applications. However, this research is still in its infancy and faces many unresolved challenges. To address these, we propose a comprehensive…
Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…
Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…
Traditional microbial detection methods often rely on the overall property of microbial cultures and cannot resolve individual growth event at high spatiotemporal resolution. As a result, they require bacteria to grow to confluence and then…
Building performance has been shown to degrade significantly after commissioning, resulting in increased energy consumption and associated greenhouse gas emissions. Continuous Commissioning using existing sensor networks and IoT devices has…
Centrifugation is a widespread laboratory technique used to separate mixtures into fractions characterized by a specific size, weight or density. We demonstrate that centrifugation can be also used to separate swimming cells having…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Numerous biological functions-such as enzymatic catalysis, the immune response system, and the DNA-protein regulatory network-rely on the ability of molecules to specifically recognize target molecules within a large pool of similar…
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…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
The prediction of battery rate performance traditionally relies on computation-intensive numerical simulations. While simplified analytical models have been developed to accelerate the calculation, they usually assume battery performance to…
In cell culture bioprocessing, real-time batch process monitoring (BPM) refers to the continuous tracking and analysis of key process variables such as viable cell density, nutrient levels, metabolite concentrations, and product titer…