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Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
Low-dimensional representations of underdamped systems often provide insightful grasps and analytical tractability. Here, we build such representations via information projections, obtaining an optimal model that captures the most…
Visual observations of dynamic phenomena, such as human actions, are often represented as sequences of smoothly-varying features . In cases where the feature spaces can be structured as Riemannian manifolds, the corresponding…
Physical systems evolve from one state to another along paths of least energy barrier. Without a priori knowledge of the energy landscape, multidimensional search methods aim to find such minimum energy pathways between the initial and…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts make sense of the complex outputs of folding pathway…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
Robotic systems are transforming image-guided interventions by enhancing accuracy and minimizing radiation exposure. A significant challenge in robotic assistance lies in surgical path planning, which often relies on the registration of…
A model Hamiltonian for the reaction CH$_4^+ \rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose…
The discovery of transition pathways to unravel distinct reaction mechanisms and, in general, rare events that occur in molecular systems is still a challenge. Recent advances have focused on analyzing the transition path ensemble using the…
Machine-learning generative methods for material design are constructed by representing a given chemical structure, either a solid or a molecule, over appropriate atomic features, generally called structural descriptors. These must be fully…
Due to the vastly different energy consumption between up-slope and down-slope, a path with the shortest length on a complex off-road terrain environment (2.5D map) is not always the path with the least energy consumption. For any…
Shortest-path roadmaps, also known as reduced visibility graphs, provides a highly efficient multi-query method for computing optimal paths in two-dimensional environments. Combined with Minkowski sum computations, shortest-path roadmaps…
The explicit evaluation of linear response coefficients for interacting many-particle systems still poses a considerable challenge to theoreticians. In this work we use a novel many-particle renormalization technique, the so-called…
The use of machine learning algorithms to predict behaviors of complex systems is booming. However, the key to an effective use of machine learning tools in multi-physics problems, including combustion, is to couple them to physical and…
Global dynamics in nonlinear stochastic systems is often difficult to analyze rigorously. Yet, many excellent numerical methods exist to approximate these systems. In this work, we propose a method to bridge the gap between computation and…
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of…
Pathways-reduced analysis is one of the techniques used by the Fispact-II nuclear activation and transmutation software to study the sensitivity of the computed inventories to uncertainties in reaction cross-sections. Although deciding…
The rate-distortion (RD) theory is one of the key concepts in information theory, providing theoretical limits for compression performance and guiding the source coding design, with both theoretical and practical significance. The…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…