98%
921
2 minutes
20
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. In high-dimension PES, these reproducible failures were thought to only increase the overall computational cost, without having any effect on the methods' capacity to find all saddle points surrounding a minimum. Using activation-relaxation technique nouveau (ARTn), we characterize the nature of the PES around minima, considerably expanding on previous knowledge. We show that convex regions can lie on activation pathways and that not exploring beyond them can introduce significant bias in the saddle-point search. We introduce an efficient approach for traversing the convex regions, almost eliminating exploration failures, while multiplying by almost 10 the number of identified unique and connected saddle points as compared to the standard ARTn, thus underlining the importance of correctly handling convex regions for completeness of saddle point explorations.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1063/5.0210097 | DOI Listing |
Phys Rev Lett
August 2025
Peng Huanwu Center for Fundamental Theory, Hefei, Anhui 230026, China.
We study nonperturbative effects of torus partition function of the TT[over ¯]-deformed 2D conformal field theory (CFT) by resurgence in this Letter and a companion paper. The deformed partition function can be written as an infinite series of the deformation parameter λ. We develop highly efficient methods to compute perturbative coefficients in the λ expansion.
View Article and Find Full Text PDFACS Macro Lett
August 2025
Department of Polymer Science & Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States.
We study the thermodynamics of continuous transformations between two canonical, cubic network phases of block copolymer melts: double-gyroid, an equilibrium morphology for many systems, and double-diamond, often thought to be a close competitor. We use a strong-segregation approach to compute the free energy of double network morphologies as a function of two structural parameters that convert between two limiting cubic cases: a tetragonal stretch of the unit cell in combination with fusion of pairs of trihedal gyroid nodes into tetrahedral diamond nodes. For the simplest case of conformationally symmetric diblock melts, we find that cubic double-diamond sits at an unstable saddle point that is continuously deformable into the lower free energy gyroid, as well as a second metastable, tetragonal network composed of trihedral nodes.
View Article and Find Full Text PDFPhys Rev E
July 2025
Harbin Institute of Technology, School of Energy Science and Engineering, Harbin, Heilongjiang, People's Republic of China.
The convective and absolute instabilities in electrohydrodynamic-Poiseuille mixed convection for viscoelastic fluids with the Oldroyd-B model are examined. In the absence of Poiseuille flow, based on the stationary and oscillatory characteristics at the onset of convection, we distinguish weakly and strongly elastic fluid, dominated by viscosity effects and elasticity effects, respectively. Their borderline of the two effects in terms of the critical electric Weissenberg W_{ec} satisfies the relation W_{ec}=a/(1-β)+b where β is viscosity ratio, and the parameters a and b depend on dimensionless ion mobility.
View Article and Find Full Text PDFIEEE Trans Signal Process
July 2025
Department of Neuroscience and Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
Non-negative matrix factorization (NMF) is widely used for dimensionality reduction of large datasets and is an important feature extraction technique for source separation. However, NMF algorithms may converge to poor local minima, or to one of several minima with similar objective value but differing feature parametrizations. Here we show that some of these weaknesses may be mitigated by performing NMF in a higher-dimensional feature space and then iteratively combining components with an efficient and analytically solvable pairwise merge strategy.
View Article and Find Full Text PDFProtein Sci
September 2025
Department of Biochemistry, University of California, Riverside, California, USA.
N6-adenine (6mA) DNA methylation plays an important role in gene regulation and genome stability. The 6mA methylation in Tetrahymena thermophila is mainly mediated by the AMT complex, comprised of the AMT1, AMT7, AMTP1, and AMTP2 subunits. To date, how this complex assembles on the DNA substrate remains elusive.
View Article and Find Full Text PDF