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Search · four archives
14 papers · ranked by Valyu relevance
Surya Narayanan Hari, Jackson Nyman, Nicita Mehta, Haitham Elmarakeby + 7 more
Computer vision (CV) approaches applied to digital pathology have informed biological discovery and development of tools to help inform clinical decision-making. However, batch effects in the images have the potential to introduce spurious confounders and represent a major challenge to effective analysis and…
Armin M. Zand, Ankit Gupta, Mustafa Khammash
Precise intracellular regulation and robust perfect adaptation can be achieved using biomolecular integral controllers and it holds enormous potential for synthetic biology applications. In this letter, we consider the cascaded implementation of a class of such integrator motifs. Our cascaded integrators underpin…
Vittoria Martinelli, Davide Fiore, Davide Salzano, Mario di Bernardo
Ensuring a stable and robust phenotype expression is a key challenge for the correct operation of synthetically engineered cells, and feedback has been highlighted as a key mechanism to achieve this goal. Biomolecular PID controllers have been extensively leveraged at a single cell level to regulate gene expression.…
Vittoria Martinelli, Davide Fiore, Davide Salzano, Mario di Bernardo
This paper presents the first implementation of a Proportional-Integral-Derivative (PID) biomolecular controller within a consortium of different cell populations, aimed at robust regulation of biological processes. By leveraging the modularity and cooperative dynamics of multiple engineered cell populations, we…
Armin M. Zand, Ankit Gupta, Mustafa Khammash
Biomolecular integral feedback controllers offer precise regulation of molecular species copy numbers, making them valuable for synthetic biology applications. Antithetic integral feedback controllers, in particular, can be effective in low-copy-number regimes with stochastic dynamics. In this work, we introduce a…
Corentin Briat, Ankit Gupta, Mustafa Khammash
Homeostasis is a running theme in biology. Often achieved through feedback regulation strategies, homeostasis allows living cells to control their internal environment as a means for surviving changing and unfavourable environments. While many endogenous homeostatic motifs have been studied in living cells, some other…
Emmanouil Alexis, Clarence W. Rowley, José L. Avalos
Achieving complex multi-species control objectives is essential for engineering advanced autoregulated biomolecular devices. This paper addresses the problem of robust steady-state tracking for outputs defined as multiplicative combinations of biomolecular species concentrations. We first introduce a control…
Corentin Briat, Ankit Gupta, Mustafa Khammash
The antithetic integral feedback motif recently introduced in [6] is known to ensure robust perfect adaptation for the mean dynamics of a given molecular species involved in a complex stochastic biomolecular reaction network. However, it was observed that it also leads to a higher variance in the controlled network…
Fangzhou Xiao, John C. Doyle
For control in biomolecular systems, the most basic objective of maintaining a small error in a target variable, say the expression level of some protein, is often difficult due to the presence of both large uncertainty of every type and intrinsic limitations on the controller’s implementation. This paper explores the…
Alessandro Santuz, Leon Brüll, Antonis Ekizos, Arno Schroll + 4 more
Is the control of movement less stable when we walk or run in challenging settings? One might intuitively answer affirmatively, given that adding constraints to locomotion (e.g. rough terrain, age-related impairments, etc.) imply less stable movements. We investigated how young and old humans synergistically activate…
Maurice Filo, Mustafa Khammash
Proportional-Integral-Derivative (PID) feedback controllers have been the most widely used controllers in the industry for almost a century. This is mainly due to their simplicity and intuitive operation. Recently, motivated by their success in various engineering disciplines, PID controllers found their way into…
Steven A. Frank
As systems become more robust against perturbations, they can compensate for greater sloppiness in the performance of their components. That robust compensation reduces the force of natural selection on the system’s components, leading to component decay. The paradoxical coupling of robustness and decay predicts that…
Steven A. Frank
The evolutionary design of regulatory control balances various tradeoffs in performance. Fast reaction to environmental change tends to favor plastic responsiveness at the expense of greater sensitivity to perturbations that degrade homeostatic control. Greater homeostatic stability against unpredictable disturbances…
Corentin Briat, Mustafa Khammash
Controlling stochastic reactions networks is a challenging problem with important implications in various fields such as systems and synthetic biology. Various regulation motifs have been discovered or posited over the recent years, the most recent one being the so-called Antithetic Integral Control (AIC) motif [1].…