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Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
We develop randomized quantum algorithms to simulate quantum collision models, also known as repeated interaction schemes, which provide a rich framework to model various open-system dynamics. The underlying technique involves composing…
The stochastic dynamics of biochemical networks are usually modelled with the chemical master equation (CME). The stationary distributions of CMEs are seldom solvable analytically, and numerical methods typically produce estimates with…
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…
Differential geometry offers a powerful framework for optimising and characterising finite-time thermodynamic processes, both classical and quantum. Here, we start by a pedagogical introduction to the notion of thermodynamic length. We…
Simulations of chemical dynamics are a powerful means for understanding chemistry. However, classical computers struggle to simulate many chemical processes, especially non-adiabatic ones, where the Born-Oppenheimer approximation breaks…
Applying the method of moments to the chemical master equation (CME) appearing in stochastic chemical kinetics often leads to the so-called closure problem. Recently, several authors showed that this problem can be partially overcome using…
We develop tools from computational algebraic geometry for the study of steady state features of autonomous polynomial dynamical systems via elimination of variables. In particular, we obtain nontrivial bounds for the steady state…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
Accurately quantifying the thermodynamic work costs of quantum operations is essential for the continued development and optimisation of emerging quantum technologies. This present a significant challenge in regimes of rapid control within…
The use of approximate solution techniques for the Chemical Master Equation is common practice for the analysis of stochastic chemical systems. Despite their widespread use, however, many such techniques rely on unverifiable assumptions and…
In this article, we present a novel approach to investigating entanglement in the context of quantum computing. Our methodology involves analyzing reduced density matrices at different stages of a quantum algorithm's execution and…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
Understanding and simulating how a quantum system interacts and exchanges information or energy with its surroundings is a ubiquitous problem, one which must be carefully addressed in order to establish a coherent framework to describe the…
A key objective in nuclear and high-energy physics is to describe nonequilibrium dynamics of matter, e.g., in the early universe and in particle colliders, starting from the Standard Model. Classical-computing methods, via the framework of…
We present an extensive introduction to quantum collision models (CMs), also known as repeated interactions schemes: a class of microscopic system-bath models for investigating open quantum systems dynamics whose use is currently spreading…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Markov jump processes are widely used to model natural and engineered processes. In the context of biological or chemical applications one typically refers to the chemical master equation (CME), which models the evolution of the probability…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication or locomotion. Given time series observations of intra-, inter- or multicellular processes,…