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Infrequent Metadynamics is a popular method to obtain the rates of long timescale processes from accelerated simulations. The inference procedure is based on rescaling the first-passage times of Metadynamics trajectories using a…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
Non-adiabatic molecular dynamics (NAMD) has become an essential computational technique for studying the photophysical relaxation of molecular systems after light absorption. These phenomena require approximations that go beyond the…
We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to…
While surface-hopping has emerged as a powerful method to simulate non-adiabatic dynamics in large molecules, the ad hoc nature of the necessary velocity adjustments and decoherence corrections in the algorithm somewhat reduces its…
We propose score dynamics (SD), a general framework for learning accelerated evolution operators with large timesteps from molecular-dynamics simulations. SD is centered around scores, or derivatives of the transition log-probability with…
The computer-assisted modeling of re-entrant production lines, and, in particular, simulation scalability, is attracting a lot of attention due to the importance of such lines in semiconductor manufacturing. Re-entrant flows lead to…
The athermal quasistatic deformation method provides an elegant solution to overcome the limitation of short time spans in molecular simulations. It provides overdamped conditions, allowing for the extraction of purely structural responses…
Molecular dynamics simulations of frictional sliding in an Atomic Force Microscope (AFM) show a clear dependence of superlubricity between incommensurate surfaces on tip compliance and applied normal force. While the kinetic friction…
Rapid processes of heat transfer are not described by the standard heat conduction equation. To take into account a finite velocity of heat transfer, we use the hyperbolic model of heat conduction, which is connected with the relaxation of…
Identifying phase transitions is one of the key challenges in quantum many-body physics. Recently, machine learning methods have been shown to be an alternative way of localising phase boundaries also from noisy and imperfect data and…
In this paper, we introduce a new machine learning (ML) model for nonlinear regression called the Boosted Smooth Transition Regression Trees (BooST), which is a combination of boosting algorithms with smooth transition regression trees. The…
Inertial microfluidic devices (IMDs) offer low-cost, high-throughput alternative techniques for many traditional particle- (or cell-) manipulation tasks, but simulating them requires being able to predict particle migration, and thus…
State estimation is crucial for the performance and safety of numerous robotic applications. Among the suite of estimation techniques, particle filters have been identified as a powerful solution due to their non-parametric nature. Yet, in…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
Dissipative particle dynamics (DPD) is an effective mesoscopic particle model with a lower computational cost than molecular dynamics because of the soft potentials that it employs. However, the soft potential is not strong enough to…
Given two distinct subsets $A,B$ in the state space of some dynamical system, Transition Path Theory (TPT) was successfully used to describe the statistical behavior of transitions from $A$ to $B$ in the ergodic limit of the stationary…
We present a novel approach to kinetic theory modeling enabling the simulation of a generic, real gas presented by its corresponding equation of state. The model is based on mass, momentum and energy conservation, and unlike the lattice…
Computational multi-scale methods capitalize on a large time-scale separation to efficiently simulate slow dynamics over long time intervals. For stochastic systems, one often aims at resolving the statistics of the slowest dynamics. This…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…