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Performing cell-free expression (CFE) in tailored microfluidic environments is a powerful tool to investigate the organisation of biosystems from molecular to multicellular scales. While cell-free transcription-translation systems simplify…
Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…
In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such…
There is a high degree of compartmentalization in the living cell where various compartments sustain different chemical reactions and transport reactants among themselves. It is exactly such situation that is investigated. The main…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
Biological mixtures such as the cytosol may consist of thousands of distinct components. There is now a substantial body of evidence showing that, under physiological conditions, intracellular mixtures can phase separate into spatially…
Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
We study a stochastic two-species chemical reaction system with two mechanisms. One mechanism consists of chemical interactions which govern the overall drift of species amounts in the system; the other mechanism consists of resampling,…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive.…
Mixed-Criticality (MC) systems consolidate multiple functionalities with different criticalities onto a single hardware platform. Such systems improve the overall resource utilization while guaranteeing resources to critical tasks. In this…
System performance for networks composed of interconnected subsystems can be increased if the traditionally separated subsystems are jointly optimized. Recently, parallel and distributed optimization methods have emerged as a powerful tool…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Astrochemical simulations are a powerful tool for revealing chemical evolution in the interstellar medium. Astrochemical calculations require efficient processing of large matrices for the chemical networks. The large chemical reaction…
High-density microfluidics is becoming an important experimental platform for studying complex biological systems such as synthetic gene regulatory networks, molecular biocomputating of engineered cells, distributing rapid point-of-care…