Related papers: Non-Parametric Analysis of Non-Equilibrium Simulat…
Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…
We present a model independent, operator algebraic approach to non-equilibrium quantum thermodynamics within the framework of two-dimensional Conformal Field Theory. Two infinite reservoirs in equilibrium at their own temperatures and…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…
We propose a method to study dynamical response of a quantum system by evolving it with an imaginary-time dependent Hamiltonian. The leading non-adiabatic response of the system driven to a quantum-critical point is universal and…
Many state of the art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are…
With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into some metastable conformational regions by high free energy…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
Existing optimal estimators of nonequilibrium path-ensemble averages are shown to fall within the framework of extended bridge sampling. Using this framework, we derive a general minimal-variance estimator that can combine nonequilibrium…
Non-equilibrium transport properties of quantum systems have recently become experimentally accessible in a number of platforms in so-called full-counting experiments that measure transient and steady state non-equilibrium transport…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with…
Model-based reinforcement learning is a powerful tool, but collecting data to fit an accurate model of the system can be costly. Exploring an unknown environment in a sample-efficient manner is hence of great importance. However, the…
We propose a setup of an open quantum system in which the environment can be tuned such that either Markovian or non-Markovian system dynamics can be achieved. The implementation uses ultracold Rydberg atoms, relying on their strong…
In this paper we propose a new state observer design technique for nonlinear systems. It consists of an extension of the recently introduced parameter estimation-based observer, which is applicable for systems verifying a particular…
The formalism of linear response theory can be extended to encompass physical situations where an open quantum system evolves towards a non-equilibrium steady-state. Here, we use the framework put forward by Konopik and Lutz [Phys. Rev.…
Different dynamical states ranging from coherent, incoherent to chimera, multichimera, and related transitions are addressed in a globally coupled nonlinear continuum chemical oscillator system by implementing a modified complex…
The computation of free energy differences through an exponential weighting of out of equilibrium paths (known as the Jarzynski equality) is often used for transitions between states described by an external parameter $\lambda$ in the…
A nonequilibrium statistical operator method is developed for ensembles of particles obeying non-Hamiltonian equations of motion in classical phase space. The main consequences of non-zero compressibility of phase space are examined in…
We propose and analyze a sample-efficient protocol to estimate the fidelity between an experimentally prepared state and an ideal target state, applicable to a wide class of analog quantum simulators without advanced sophisticated…