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Locating transition states is crucial for investigating transition mechanisms in wide-ranging phenomena, from atomistic to macroscale systems. Existing methods, however, can struggle in problems with a large number of degrees of freedom,…
In body-centred-cubic (bcc) metals migrating 1/2<111> screw dislocations experience a periodic energy landscape with a triangular symmetry. Atomistic simulations, such as those performed using the nudged-elastic-band (NEB) method, generally…
The efficiency of minimum-energy configuration searching algorithms is closely linked to the energy landscape structure of complex systems. Here we characterize this structure by following the time evolution of two systems, vacancy…
Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where…
Numerical studies of ionic motion through solid electrolytes commonly involve static nudged-elastic band (NEB) methods or costly \emph{ab initio} molecular dynamics (AIMD). Building on a time-local model of current carrier-electrolyte…
Efficient algorithms for the calculation of minimum energy paths of magnetic transitions are implemented within the geodesic nudged elastic band (GNEB) approach. While an objective function is not available for GNEB and a traditional line…
The thermodynamic description of dislocation glide in crystals depends crucially on the shape of the Peierls barrier that the dislocation has to overcome when moving in the lattice. While the height of this barrier can be obtained…
Certain nematic liquid crystals, e.g., those formed by banana-shaped molecules, can exhibit a low-temperature twist-bend nematic (Ntb) phase. Upon addition of chiral dopants, a chiral version of the twist-bend phase (N*tb) can be observed…
Minimum energy path (MEP) search is a vital but often very time-consuming method to predict the transition states of versatile dynamic processes in chemistry, physics, and materials science. In this study, we reveal that the chemical bond…
In this work, we propose a multi-scale protocol for routine theoretical studies of chemical reaction mechanisms. The initial reaction paths of our investigated systems are sampled using the Nudged-Elastic Band (NEB) method driven by a cheap…
Nudging is a popular algorithmic strategy in numerical filtering to deal with the problem of inference in high-dimensional dynamical systems. We demonstrate in this paper that general nudging techniques can also tackle another crucial…
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states.…
Dielectric spectroscopy of a twist bend nematic phase of an achiral bent core liquid crystalline compound under DC bias is used to investigate its response to electric field. Two collective relaxation processes are revealed, these are…
In finite systems, such as nanoparticles and gas-phase molecules, calculations of minimum energy paths (MEPs) connecting initial and final states of transitions as well as searches for saddle points are complicated by the presence of…
The twist-bend nematic (Ntb) phase is a recent addition to the nematic (N) phases of liquid crystals (LCs). A net polar order in the Ntb phase under an external electric field was predicted in several recent theoretical studies but yet to…
Direct access to transition state energies at low computational cost unlocks the possibility of accelerating catalyst discovery. We show that the top performing graph neural network potential trained on the OC20 dataset, a related but…
We develop a novel peak detection algorithm for the analysis of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC$\times$GC-TOF MS) data using normal-exponential-Bernoulli (NEB) and mixture probability…
Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
Analyzing the physical and chemical properties of single DNA based molecular machines such as polymerases and helicases often necessitates to track stepping motion on the length scale of base pairs. Although high resolution instruments have…