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Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to…
The use of stochastic models, in effect piecewise deterministic Markov processes (PDMP), has become increasingly popular especially for the modeling of chemical reactions and cell biophysics. Yet, exact simulation methods, for the…
We present a highly efficient method to directly simulate the photodissociation followed by Coulomb explosion of methyl iodide. In order to achieve statistical reliability, more than 40,000 trajectories are calculated on accurate potential…
Understanding molecular state evolution is central to many disciplines, including molecular dynamics, precision measurement, and molecule-based quantum technology. Details of the evolution are obscured when observing a statistical ensemble…
Molecular dynamics is a versatile and powerful method to study diffusion in solid-state ionic conductors, requiring minimal prior knowledge of equilibrium or transition states of the system's free energy surface. However, the analysis of…
Biological macromolecules have complex and non-trivial energy landscapes, endowing them a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is…
Quantum-logic techniques used to manipulate quantum systems are now increasingly being applied to molecules. Previous experiments on single trapped diatomic species have enabled state detection with excellent fidelities and highly precise…
In this article we demonstrate a general protocol for constructing systematically experimental steady-state bifurcation diagrams for electrophysiologically active cells. We perform our experiments on entorhinal cortex neurons, both…
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…
Single-molecule tracking (SMT) methods are under considerable expansion in many fields of cell biology, as the dynamics of cellular components in biological mechanisms becomes increasingly relevant. Despite the development of SMT…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions. We start by introducing the formalism of the new…
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…
We first use the quantum method to replicate the well-known results of a single atom relaxing, whilst demonstrating the intuitive picture it provides for dissipative dynamics. By use of individual "quantum trajectories", the method allows…
Recent advances in non-equilibrium statistical mechanics and single molecule technologies make it possible to extract free energy differences from irreversible work measurements in pulling experiments. To date, free energy recovery has been…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
Scalable atom-based quantum platforms for simulation, computing, and metrology require fast high-fidelity, low-loss imaging of individual atoms. Standard fluorescence detection methods rely on continuous cooling, limiting the detection…
We consider the problem of detecting jumps in an otherwise smoothly evolving trend whilst the covariance and higher-order structures of the system can experience both smooth and abrupt changes over time. The number of jump points is allowed…
We present theoretical and experimental progress towards a new approach for the precision spectroscopy, coherent manipulation and state-to-state chemistry of single isolated molecular ions in the gas phase. Our method consists of a…
We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. We…