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Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose,…
In many biological systems, the movement of individual agents is commonly characterized as having multiple qualitatively distinct behaviors that arise from various biophysical states. This is true for vesicles in intracellular transport,…
Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption.…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
Stochastic systems often exhibit multiple viable metastable states that are long-lived. Over very long timescales, fluctuations may push the system to transition between them, drastically changing its macroscopic configuration. In realistic…
Stochastic resetting, a method for accelerating target search in random processes, often incurs temporal and energetic costs. For a diffusing particle, a lower bound exists for the energetic cost of reaching the target, which is attained at…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
The theory of slow manifolds is an important tool in the study of deterministic dynamical systems, giving a practical method by which to reduce the number of relevant degrees of freedom in a model, thereby often resulting in a considerable…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Efficient energy transduction is one driver of evolution; and thus understanding biomolecular energy transduction is crucial to understanding living organisms. As an energy-orientated modelling methodology, bond graphs provide a useful…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…