Related papers: Simple quantitative tests to validate sampling fro…

To quantify the progress in development of algorithms and forcefields used in molecular simulations, a method for the assessment of the sampling quality is needed. We propose a general method to assess the sampling quality through the…

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…

Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…

All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…

Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…

Machine learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale and complexity. Given the interpolative nature of…

Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…

Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…

Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…

Compressed sensing is a method that allows a significant reduction in the number of samples required for accurate measurements in many applications in experimental sciences and engineering. In this work, we show that compressed sensing can…

Irreversible thermodynamics of simple fluids have been connected recently to the theory of dynamical systems and some interesting assumptions have been made about the nature of the associated invariant measures. We show that the tests of…

Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…

Modern thermodynamic theories can be used to study highly complex quantum dynamics. Here, we experimentally demonstrate that the violation of thermodynamic constraints allows to detect the coupling of a quantum system to a hidden…

In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…

Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…

Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…

The resources required to characterise the dynamics of engineered quantum systems-such as quantum computers and quantum sensors-grow exponentially with system size. Here we adapt techniques from compressive sensing to exponentially reduce…

In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…

Many applications of computational fluid dynamics require multiple simulations of a flow under different input conditions. In this paper, a numerical algorithm is developed to efficiently determine a set of such simulations in which the…

In the light of the progress in quantum technologies, the task of verifying the correct functioning of processes and obtaining accurate tomographic information about quantum states becomes increasingly important. Compressed sensing, a…