Related papers: Modeling and Modifying Response of Biochemical Pro…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Over the last decade we have witnessed an increasing use of data processing in embedded systems. Where in the past the data processing was limited (if present at all) to the handling of a small number of "on-off control signals", more…
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
The reversible reactions like A+B <-> C in the many-component diffusive system affect the diffusive properties of the constituents. The effective conjugation of irreversible processes of different dimensionality takes place due to the…
In this work, we consider the problem of estimating summary statistics to characterise biochemical reaction networks of interest. Such networks are often described using the framework of the Chemical Master Equation (CME). For…
Synthetic biology is an interdisciplinary field aiming to design biochemical systems with desired behaviors. To this end, molecular controllers have been developed which, when embedded into a pre-existing ambient biochemical network,…
In chemical processing and bioprocessing, conventional online sensors are limited to measure only basic process variables like pressure and temperature, pH, dissolved O and CO$_2$ and viable cell density (VCD). The concentration of other…
Variations of physical and chemical characteristics of biomass reduce equipment utilization and increase operational costs of biomass processing. Biomass processing facilities use sensors to monitor the changes in biomass characteristics.…
We present a multimodal search tool that facilitates retrieval of chemical reactions, molecular structures, and associated text from scientific literature. Queries may combine molecular diagrams, textual descriptions, and reaction data,…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
There is a growing trend in molecular and synthetic biology of using mechanistic (non machine learning) models to design biomolecular networks. Once designed, these networks need to be validated by experimental results to ensure the…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
In this paper, we investigate how stochastic reaction processes are affected by external perturbations. We describe an extension of the deterministic metabolic control analysis (MCA) to the stochastic regime. We introduce stochastic…
The explosive demand for artificial intelligence (AI) workloads has led to a significant increase in silicon area dedicated to lower-precision computations on recent high-performance computing hardware designs. However, mixed-precision…
Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to…
Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…
The precise control of complex reactions is critical for biological processes yet our inability to design for specific outcomes limits the development of synthetic analogues. Here, we leverage differentiable simulators to design nontrivial…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
Researchers in the biological sciences nowadays often encounter the curse of high-dimensionality, which many previously developed statistical models fail to overcome. To tackle this problem, sufficient dimension reduction aims to estimate…