Related papers: Approaching a parameter-free metadynamics
We summarize the original formulation of the free energy principle, and highlight some technical issues. We discuss how these issues affect related results involving generalised coordinates and, where appropriate, mention consequences for…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
The basics of the premetric approach are discussed, including the essential details of the formalism and some of its beautiful consequences. We demonstrate how the classical electrodynamics can be developed without a metric in a quite…
This paper presents a coordinate free pre-metric formulation of charge free Maxwell-Minkowski electrodynamics, and of the developed by the authors non-linear Extended Electrodynamics. First we introduce some formal relations from…
Thermodynamics is traditionally concerned with systems comprised of a large number of particles. Here we present a framework for extending thermodynamics to individual quantum systems, including explicitly a thermal bath and work-storage…
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the…
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.…
Inspired by the recent development on calculating the free energy change via a relaxation process [Nat. Phys. 14, 842 (2018)], we investigate the role of heat released in an irreversible relaxation following a large perturbation. Utilizing…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
We analyze an autonomous micro-engine as a closed quantum mechanical system, including the work it performs and the fuel it consumes. Our model system shows by example that it is possible to transfer energy steadily and spontaneously…
A unified treatment for the existence of free energy in several random energy models is presented. If the sequence of distributions associated with the particle systems obeys a large deviation principle, then the free energy exists almost…
We develop a novel data-driven approach to the inverse problem of classical statistical mechanics: given experimental data on the collective motion of a classical many-body system, how does one characterise the free energy landscape of that…
We study the classical electrodynamics of extended bodies. Currently, there is no self-consistent dynamical theory of such bodies in the literature. Electromagnetic energy-momentum is not conserved in the presence of charge and some…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
In traditional thermodynamical and statistical-mechanical approaches one has (some) detailed knowledge of the principles governing the microdynamics of a system. However in many instances we may not have a Hamiltonian or good information…
A manifestly gauge-invariant hamiltonian formulation of classical electrodynamics has been shown to be relativistic invariant by the construction of the adequate generators of the Poincare Lie algebra [Physica, 76, No. 3, 421-444 (1974)].…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
Inspired by thermodynamic integration, we propose a method for the calculation of time-independent free energy profiles from history-dependent biased simulations via Mean Force Integration (MFI). MFI circumvents the need for computing the…
The metriplectic formalism is useful for describing complete dynamical systems which conserve energy and produce entropy. This creates challenges for model reduction, as the elimination of high-frequency information will generally not…
We describe in detail how to eliminate nonphysical degrees of freedom in the Lagrangian and Hamiltonian formulations of a constrained system. Two important and distinct steps in our method are the fixing of ambiguities in the dynamics and…