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Many systems occurring in real-world applications, such as controlling the motions of robots or modeling the spread of diseases, are switched impulsive systems. To ensure that the system state stays in a safe region (e.g., to avoid…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
We show that transport in the presence of entropic barriers exhibits peculiar characteristics which makes it distinctly different from that occurring through energy barriers. The constrained dynamics yields a scaling regime for the particle…
We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
Predictive maintenance is an effective tool for reducing maintenance costs. Its effectiveness relies heavily on the ability to predict the future state of health of the system, and for this survival models have shown to be very useful. Due…
Assessing the synthesizability of inorganic materials is a grand challenge for accelerating their discovery using computations. Synthesis of a material is a complex process that depends not only on its thermodynamic stability with respect…
Complex networks theory has commonly been used for modelling and understanding the interactions taking place between the elements composing complex systems. More recently, the use of generative models has gained momentum, as they allow…
Living systems are maintained out-of-equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
Energy system models based on linear programming have been growing in size with the increasing need to model renewables with high spatial and temporal detail. Larger models lead to high computational requirements. Furthermore, seemingly…
Network models are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of these systems are generally nonlinear, suggesting that…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
Development of robust dynamical systems and networks such as autonomous aircraft systems capable of accomplishing complex missions faces challenges due to the dynamically evolving uncertainties coming from model uncertainties, necessity to…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
Learning kinetic systems from data is one of the core challenges in many fields. Identifying stable models is essential for the generalization capabilities of data-driven inference. We introduce a computationally efficient framework, called…
Ammonia is a promising zero-carbon fuel for industrial and transport applications, but its combustion is hindered by flame instabilities, incomplete oxidation, and the formation of nitrogen oxides. Accurate and detailed kinetic models are…
We perform off-lattice, canonical ensemble molecular dynamics simulations of the self-assembly of long segmented copolymers consisting of alternating, tunably attractive and hydrophobic {\em binder} domains, connected by hydrophilic {\em…
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change…