Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C(20) clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1063/1.3609924 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Modified Activation-Relaxation Technique (ARTn) Method Tuned for Efficient Identification of Transition States in Surface Reactions.
J Chem Theory Comput
September 2024
Department of Material Science and Engineering, Seoul National University, Seoul 08826, Korea.
Exploring potential energy surfaces (PES) is essential for unraveling the underlying mechanisms of chemical reactions and material properties. While the activation-relaxation technique (ARTn) is a state-of-the-art method for identifying saddle points on PES, it often faces challenges in complex energy landscapes, especially on surfaces. In this study, we introduce iso-ARTn, an enhanced ARTn method that incorporates constraints on an orthogonal hyperplane and employs an adaptive active volume.
View Article and Find Full Text PDFDiffusion mechanisms for spinel ferrite NiFe2O4 by using kinetic activation-relaxation technique.
J Chem Phys
September 2024
Département de physique, Regroupement québécois sur les matériaux de pointe, and Institut Courtois, Université de Montréal, Case Postale 6128, Succursale Centre-Ville, Montréal, Quebec H3C 3J7, Canada.
Mass transport in bulk spinel ferrites NiFe2O4 is studied computationally using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo algorithm. Diffusion mechanisms-difficult to observe with molecular dynamics-are described by k-ART. Point defects are assumed to be responsible for ionic diffusion; thus, both cation and anion defects are investigated.
View Article and Find Full Text PDFExploring potential energy surfaces to reach saddle points above convex regions.
J Chem Phys
June 2024
LAAS-CNRS, Université de Toulouse, CNRS, 7 Avenue Du Colonel Roche, 31000 Toulouse, France.
Saddle points on high-dimensional potential energy surfaces (PES) play a determining role in the activated dynamics of molecules and materials. Building on approaches dating back more than 50 years, many open-ended transition-state search methods have been developed to follow the direction of negative curvature from a local minimum to an adjacent first-order saddle point. Despite the mathematical justification, these methods can display a high failure rate: using small deformation steps, up to 80% of the explorations can end up in a convex region of the PES, where all directions of negative curvature vanish, while if the deformation is aggressive, a similar fraction of attempts lead to saddle points that are not directly connected to the initial minimum.
View Article and Find Full Text PDFMeasuring the Contractile Kinetics of Isolated Myofibrils from Human-Induced Pluripotent Stem Cell Derived Cardiomyocyte (hiPSC-CM) Models of Cardiomyopathy.
Methods Mol Biol
December 2023
Department of Bioengineering, University of Washington, Seattle, WA, USA.
Isolated myofibrils provide biomechanical data at the contractile organelle level that are independent of cellular calcium handling and signaling pathways. These myofibrils can be harvested from animal tissue, human muscle biopsies, or stem cell-derived striated muscle. Here we present our myofibril isolation and rapid solution switching protocols, which allow for precise measurements of activation (kinetics and tension generation) and a biphasic relaxation relationship (initial slow isometric relaxation followed by a fast exponential decay in tension).
View Article and Find Full Text PDFEvaluating approaches for on-the-fly machine learning interatomic potentials for activated mechanisms sampling with the activation-relaxation technique nouveau.
J Chem Phys
June 2023
Département de physique and Regroupement québécois sur les matériaux de pointe, Université de Montréal, Case Postale 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada.
In the last few years, much effort has gone into developing general machine-learning potentials capable of describing interactions for a wide range of structures and phases. Yet, as attention turns to more complex materials, including alloys and disordered and heterogeneous systems, the challenge of providing reliable descriptions for all possible environments becomes ever more costly. In this work, we evaluate the benefits of using specific vs general potentials for the study of activated mechanisms in solid-state materials.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!