相关论文: Biochemical Filter with Sigmoidal Response: Increa…
A dynamical system obtains a wide variety of kinetic realizations, which is advantageous for the analysis of biochemical systems. A reaction network, derived from a dynamical system, may or may not possess some properties needed for a…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
Background: Stochastic biochemical reaction networks are commonly modelled by the chemical master equation, and can be simulated as first order linear differential equations through a finite state projection. Due to the very high state…
Capturing the microscopic interactions that determine molecular reactivity poses a challenge across the physical sciences. Even a basic understanding of the underlying reaction mechanisms can substantially accelerate materials and compound…
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…
Cooperative collective dynamics is a principal determinant of the ability of synthetic micromotors to perform specific functions. However, realizing controllable and predictable collective behavior in complex physiological environments…
We consider the problem of estimating the dynamic latent states of an intracellular multiscale stochastic reaction network from time-course measurements of fluorescent reporters. We first prove that accurate solutions to the filtering…
Technical challenges in molecule sensing and chemical detection have created an increasing demand for transformative materials with high sensitivity and specificity. Biohybrid nanopores have attracted growing interest as they can ideally…
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,…
Biomolecular condensates organize biochemical processes by spatially concentrating molecules while allowing for dynamic exchange with their surroundings. However, transport across their interface can be strongly attenuated, leading to…
The chemotactic network of Escherichia coli has been studied extensively both biophysically and information-theoretically. Nevertheless, the connection between these two aspects is still elusive. In this work, we report such a connection by…
The design and synthesis of complex and large mimicked biochemical networks de novo is an unsolved problem in synthetic biology. To address this limitation without resorting to ad hoc computations and experiments, a predictive mathematical…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
A new type of microfluidic system for biological cell manipulation, a CMOS/microfluidic hybrid, is demonstrated. The hybrid system starts with a custom-designed CMOS (complementary metal-oxide semiconductor) chip fabricated in a…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Can we objectively distinguish chemical systems that are able to process meaningful information from those that are not suitable for information processing? Here, we present a formal method to assess the semantic capacity of a chemical…
The control of Biomedical Systems in Physical Human-Robot Interaction (pHRI) plays a pivotal role in achieving the desired behavior by ensuring the intended transfer function and stability of subsystems within the overall system.…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…