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 energy path for typical potential energy surfaces encountered in molecular simulation. We propose a preconditioning scheme which, combined with a new adaptive time step selection algorithm, substantially reduces the computational cost of transition path finding algorithms. We demonstrate the improved performance of our approach in a range of examples including vacancy and dislocation migration modeled with both interatomic potentials and density functional theory.
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http://dx.doi.org/10.1063/1.5064465 | DOI Listing |
Basic Res Cardiol
December 2024
Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
Numerous cardioprotective interventions have been reported to reduce myocardial infarct size (IS) in pre-clinical studies. However, their translation for the benefit of patients with acute myocardial infarction (AMI) has been largely disappointing. One reason for the lack of translation is the lack of rigor and reproducibility in pre-clinical studies.
View Article and Find Full Text PDFAdv Mater
October 2024
School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
Bioactive hydrogels have emerged as promising artificial niches for enhancing stem cell-mediated tendon repair. However, a substantial knowledge gap remains regarding the optimal combination of niche features for targeted cellular responses, which often leads to lengthy development cycles and uncontrolled healing outcomes. To address this critical gap, an innovative, data-driven materiomics strategy is developed.
View Article and Find Full Text PDFBIT Numer Math
September 2024
Mekelweg 6, 2628 CD Delft, The Netherlands.
A preconditioner is proposed for Laplace exterior boundary value problems on multi-screens. To achieve this, the quotient-space boundary element method and operator preconditioning are combined. For a fairly general subclass of multi-screens, it is shown that this approach paves the way for block diagonal Calderón preconditioners which achieve a spectral condition number that grows only logarithmically with decreasing mesh size, just as in the case of simple screens.
View Article and Find Full Text PDFJ Sci Comput
August 2024
Section of Mathematics, University of Geneva, Geneva, Switzerland.
We propose two implicit numerical schemes for the low-rank time integration of stiff nonlinear partial differential equations. Our approach uses the preconditioned Riemannian trust-region method of Absil, Baker, and Gallivan, 2007. We demonstrate the efficiency of our method for solving the Allen-Cahn and the Fisher-KPP equations on the manifold of fixed-rank matrices.
View Article and Find Full Text PDFJ Nanobiotechnology
May 2024
Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China.
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