Future systems and control research in synthetic biology

D Del Vecchio, Y Qian, RM Murray, ED Sontag - Annual Reviews in Control, 2018 - Elsevier
Synthetic biology is the application of engineering principles to the fundamental components
of biology, with the aim of creating systems with novel functionalities that can be used for …

Quasi-entropy closure: a fast and reliable approach to close the moment equations of the chemical master equation

V Wagner, B Castellaz, M Oesting, N Radde - Bioinformatics, 2022 - academic.oup.com
Abstract Motivation The Chemical Master Equation is a stochastic approach to describe the
evolution of a (bio) chemical reaction system. Its solution is a time-dependent probability …

A provably convergent control closure scheme for the Method of Moments of the Chemical Master Equation

V Wagner, R Strässer, F Allgöwer… - Journal of Chemical …, 2023 - ACS Publications
In this article, we introduce a novel moment closure scheme based on concepts from model
predictive control (MPC) to accurately describe the time evolution of the statistical moments …

Optimal network transmission to minimize state-estimation error

S Rezaee, C Nieto, A Singh - 2022 - osf.io
We consider the problem of transmitting the state value of a dynamical system through a
communication network. The dynamics of the error in state estimation is modeled using a …

Robust Model Invalidation for Chemical Reaction Networks Using Generalized Moments

TW Grunberg, D Del Vecchio - 2023 62nd IEEE Conference on …, 2023 - ieeexplore.ieee.org
Many biomolecular systems can be described by chemical reaction networks, however,
there may be several candidate networks based on the known biology for a particular …

Robust model invalidation for chemical reaction networks using generalized moments (extended version)

TW Grunberg, D Del Vecchio - 2023 - dspace.mit.edu
Many biomolecular systems can be described by chemical reaction networks. Determining
which chemical reaction network models are inconsistent with observed data can be done …

Approximation of the chemical master equation using conditional moment closure and time-scale separation

U Kwon, M Naghnaeian… - 2019 American Control …, 2019 - ieeexplore.ieee.org
To describe the stochastic behavior of biomolecular systems, the Chemical Master Equation
(CME) is widely used. The CME gives a complete description of the evolution of a system's …

Using semidefinite programming to bound distributions in chemical engineering systems

GR Dowdy - 2019 - dspace.mit.edu
Distributions appear in many forms in models of chemical engineering systems. Such
distributions account for microscopic variability in the system while simultaneously …

Solutions to the Minimum Variance Problem Using Delaunay Triangulation

A Strang - SIAM Journal on Discrete Mathematics, 2020 - SIAM
We consider the problem of minimizing the variance of a distribution supported on a finite set
of points Ω in R^n given the expected value of the distribution. This produces the distribution …

The Enhanced Finite State Projection algorithm, using conditional moment closure and time-scale separation

U Kwon, M Naghnaeian… - 2020 59th IEEE …, 2020 - ieeexplore.ieee.org
The Chemical Master Equation (CME) is commonly used to describe the stochastic behavior
of biomolecular systems. However, in general, the CME's dimension is very large or infinite …