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Characterization of qubit couplings in many-body quantum systems is essential for benchmarking quantum computation and simulation. We propose a tomographic measurement scheme to determine all the coupling terms in a general many-body…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
Temperature estimation, known as thermometry, is a critical sensing task for physical systems operating in the quantum regime. Indeed, thermal fluctuations can significantly degrade quantum coherence. Therefore, accurately determining the…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
Quantum technology is approaching a level of maturity, recently demonstrated in space-borne experiments and in-field measurements, which would allow for adoption by non-specialist users. Parallel advancements made in microprocessor-based…
Temperature estimation plays a vital role across natural sciences. A standard approach is provided by probe thermometry, where a probe is brought into contact with the sample and examined after a certain amount of time has passed. In many…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Entanglement is the key feature of many-body quantum systems, and the development of new tools to probe it in the laboratory is an outstanding challenge. Measuring the entropy of different partitions of a quantum system provides a way to…
Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these…
Symmetries in a Hamiltonian play an important role in quantum physics because they correspond directly with conserved quantities of the related system. In this paper, we propose quantum algorithms capable of testing whether a Hamiltonian…
A roughly constant temperature over a wide range of densities is maintained in molecular clouds through radiative heating and cooling. An isothermal equation of state is therefore frequently employed in molecular cloud simulations. However,…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
Virtually all aspects of many-body atomic physics are challenging: experiments are technically demanding, datasets have become enormous, and the memory and CPU requirements for classical simulation of generic quantum systems often scale…
Preparing thermal equilibrium states is an essential task for finite-temperature quantum simulations. In statistical mechanics, microstates in thermal equilibrium can be obtained from statistical ensembles. To date, numerous ensembles have…
We propose an ensemble algorithm, which provides a new approach for evaluating and summing up a set of function samples. The proposed algorithm is not a quantum algorithm, insofar it does not involve quantum entanglement. The query…
Statistical analysis is used throughout biomedical research and elsewhere to assess strength of evidence. We have previously argued that typical outcome statistics (including p-values and maximum likelihood ratios) have poor…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
The thermal conductivity of nanometric objects or nanostructured materials can be determined using non equilibrium molecular dynamics (NEMD) simulations. The technique is simple in its principle, and resembles a numerical guarded hot plate…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…