Mario di Bernardo

Data-driven inference of digital twins for high-throughput phenotyping of motile and light-responsive microorganisms

The paper develops a platform to infer digital twins of light-responsive microorganisms using imaging data, enabling accurate simulation of their movement behaviors.

In silico analysis of metabolic burden effects on a multicellular integral controller

The paper models a multicellular antithetic integral controller to assess metabolic burden effects and compares it to a single-cell implementation using numerical analysis and simulations.

Root Contours Guided Design of a Multicellular PID Controller

The paper designs a multicellular PID controller using root contours for tuning control gains and validates it through in silico simulations.

Visual Influence Networks in Walking Crowds

The paper analyzes visual influence networks in human crowds, finding that leadership and influence are position-dependent within groups.

Multicellular Proportional-Integral-Derivative Control for Robust Regulation of Biological Processes

The paper develops a multicellular PID control strategy using engineered cell populations and validates its robustness through in silico experiments.

Ratiometric control of two microbial populations via a dual chamber bioreactor

This paper introduces a dual chamber bioreactor system to maintain stable coexistence of microbial populations with differing growth rates through feedback control.

In-vivo distributed multicellular control of gene expression in microbial consortia

This paper develops a distributed feedback control system in microbial consortia to precisely regulate gene expression across different cell populations.

Multicellular PD Control in Microbial Consortia

This paper designs a multicellular PD controller for gene expression regulation in microbial consortia using in silico experiments.

Controlling reversible cell differentiation for labor division in microbial consortia

The paper develops a control strategy to balance cell phenotypes in microbial consortia using reversible memory mechanisms and validates it through simulations.

Control-based continuation: a new approach to prototype synthetic gene networks

This paper introduces Control-Based Continuation (CBC) for analyzing synthetic gene networks, showing it can track bifurcation curves without relying on mathematical models and can identify bistability.

Embedded control of cell growth using tunable genetic systems

The paper develops a feedback control strategy using a tunable expression system and quorum sensing to regulate bacterial population density.

Multicellular PI control for gene regulation in microbial consortia

The paper designs multicellular PI controllers for gene regulation in microbial consortia using orthogonal quorum sensing and validates them through in silico experiments.

Feedback ratiometric control of two microbial populations in a single chemostat

The paper develops two feedback control strategies to regulate the ratio of two microbial populations in a chemostat through dilution rate control.

Cyber-yeast: Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control

This paper develops a cyber-genetic system to achieve long-term cell cycle synchronization in yeast using closed-loop feedback control.

Cheetah: a computational toolkit for cybergenetic control

Cheetah is a computational toolkit that integrates real-time microscopy analysis with cellular control algorithms, demonstrating improved segmentation accuracy over thresholding methods in bacterial and mammalian cells.

ChipSeg: an automatic tool to segment bacteria and mammalian cells cultured in microfluidic devices

ChipSeg segments bacterial and mammalian cells in microfluidic devices using thresholding, enabling fluorescence quantification and cell tracking in time-lapse experiments.

In vivo Feedback Control of an Antithetic Molecular-Titration Motif in Escherichia coli using Microfluidics

The paper demonstrates real-time feedback control of a molecular titration motif in E. coli using microfluidics and validates the approach with in silico simulations.

Multicellular feedback control of a genetic toggle-switch in microbial consortia

The paper designs a synthetic microbial consortium with three cell populations to control a bistable toggle-switch in target cells through orthogonal quorum sensing feedback.

Tunable genetic devices through simultaneous control of transcription and translation

This paper introduces genetic devices that can be dynamically tuned after construction to adjust their response functions and logic gate transitions.

Balancing cell populations endowed with a synthetic toggle switch via adaptive pulsatile feedback control

This paper proposes feedback control strategies to robustly balance synthetic toggle switch cell populations under stochastic and uncertain conditions using in-silico experiments and agent-based simulations.

Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells

The paper designs control strategies to synchronize yeast cell cycles using methionine levels, validated both in silico and experimentally.

Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation

This paper explores using control-based continuation to track dynamical features of biochemical systems, specifically bistable dynamics in gene regulation of pluripotency in embryonic stem cells.

Towards feedback control of the cell-cycle across a population of yeast cells

This paper develops and evaluates feedback control strategies to synchronize the cell cycle in yeast populations while minimizing volume growth.

A low cost, open source Turbidostat design for in-vivo control experiments in Synthetic Biology

The paper describes a low-cost, open-source turbidostat for in-vivo control experiments in synthetic biology and reports results from a 3-hour optical density control experiment.

Organisation of feed-forward loop motifs reveals architectural principles in natural and engineered networks

The paper analyzes how feed-forward loop motifs are organized in networks, revealing architectural principles and their functional implications in Escherichia coli metabolic networks.