Related papers: A Note on Spectral Map
Many biological processes occur on time scales longer than those accessible to molecular dynamics simulations. Identifying collective variables (CVs) and introducing an external potential to accelerate them is a popular approach to address…
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective…
Molecular dynamics (MD) simulations are increasingly being combined with machine learning (ML) to predict material properties. The molecular configurations obtained from MD are represented by multiple features, such as thermodynamic…
Global climate models (GCMs), typically run at ~100-km resolution, capture large-scale environmental conditions but cannot resolve convection and cloud processes at kilometer scales. Convection-permitting models offer higher-resolution…
Unraveling the connections between microscopic structure, emergent physical properties, and slow dynamics has long been a challenge when studying the glass transition. The absence of clear visible structural order in amorphous…
Machine learning methods provide a general framework for automatically finding and representing the essential characteristics of simulation data. This task is particularly crucial in enhanced sampling simulations. There we seek a few…
The prediction of product translational, vibrational, and rotational energy distributions for arbitrary initial conditions for reactive atom+diatom collisions is of considerable practical interest in atmospheric re-entry. Due to the large…
Collective variables (CVs) are low-dimensional projections of high-dimensional system states. They are used to gain insights into complex emergent dynamical behaviors of processes on networks. The relation between CVs and network measures…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Monte Carlo simulations are widely used to simulate complex molecular systems, but standard approaches suffer from metastability. Lately, the use of non-local proposal updates in a collective-variable (CV) space has been proposed in several…
The study of the rare transitions that take place between long lived metastable states is a major challenge in molecular dynamics simulations. Many of the methods suggested to address this problem rely on the identification of the slow…
Collective variables (CVs) play a crucial role in capturing rare events in high-dimensional systems, motivating the continual search for principled approaches to their design. In this work, we revisit the framework of quantitative coarse…
Enhanced sampling methods typically require predefined collective variables (CVs) that presuppose knowledge of reaction coordinates, restricting the discovery of unanticipated transition mechanisms or intermediates. Here, we show that a…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
A popular way to accelerate the sampling of rare events in molecular dynamics simulations is to introduce a potential that increases the fluctuations of selected collective variables. For this strategy to be successful, it is critical to…
Vibrational spectroscopy is a powerful technique to characterize the near-equilibrium dynamics of molecules in the gas- and the condensed-phase. This contribution summarizes efforts from computer-based methods to gain insight into the…