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Thermo-osmotic slip -- the flow induced by a thermal gradient along a surface -- is a well-known phenomenon, but curiously there is a lack of robust molecular-simulation techniques to predict its magnitude. Here, we compare three different…
A thermodynamic formulation of jammed matter is reviewed. Experiments and simulations of compressed emulsions and granular materials are then used to provide a foundation for the thermodynamics.
We initiate the systematic study of experimental quantum physics from the perspective of computational complexity. To this end, we define the framework of quantum algorithmic measurements (QUALMs), a hybrid of black box quantum algorithms…
We demonstrate that is it possible to simulate a system in thermal equilibrium even when the energy cannot be evaluated exactly, provided the error distribution is known. This leads to an effective optimisation strategy for problems where…
Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to…
Experimental comparisons of performance represent an important aspect of research on optimization algorithms. In this work we present a methodology for defining the required sample sizes for designing experiments with desired statistical…
Modern neural networks do not always produce well-calibrated predictions, even when trained with a proper scoring function such as cross-entropy. In classification settings, simple methods such as isotonic regression or temperature scaling…
Quantum annealers are emerging as programmable, dynamical experimental platforms for probing strongly correlated spin systems. Yet key thermal assumptions, chiefly a Gibbs-distributed output ensemble, remain unverified in the large-scale…
Molecular dynamics simulations of a quasi-harmonic solid are conducted to elucidate the meaning of temperature fluctuations in canonical systems and validate a well-known but frequently contested equation predicting the mean square of such…
We present a new method of conducting molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way,…
A model for comminution processes in ball mills is presented. The model provides an empirical approach using the physically realistic modelization of the ball mill system, but also deployes the statistical method to extract relevant…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
The claim that there is an inconsistency of quantum-classical dynamics [1] is investigated. We point out that a consistent formulation of quantum and classical dynamics which can be used to describe quantum measurement processes is already…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
This work explores the trade-off between the number of samples required to accurately build models of dynamical systems and the degradation of performance in various control objectives due to a coarse approximation. In particular, we show…
Concolic testing is a popular dynamic validation technique that can be used for both model checking and automatic test case generation. We have recently introduced concolic testing in the context of logic programming. In contrast to…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
As genomic scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process are essential for the testing and evaluation of new inference methods. However, the simulators themselves must be…
Algorithms for simulating complex physical systems or solving difficult optimization problems often resort to an annealing process. Rather than simulating the system at the temperature of interest, an annealing algorithm starts at a…