In recent years, the time-dependent variational principle (TDVP) method based on the matrix product state (MPS) wave function formulation has shown its great power in performing large-scale quantum dynamics simulations for realistic chemical systems with strong electron-vibration interactions. In this work, we propose a stochastic adaptive single-site TDVP (SA-1TDVP) scheme to evolve the bond-dimension adaptively, which can integrate the traditional advantages of both the high efficiency of the single-site TDVP (1TDVP) variant and the high accuracy of the two-site TDVP (2TDVP) variant. Based on the assumption that the level statistics of entanglement Hamiltonians, which originate from the reduced density matrices of the MPS method, follows a Poisson or Wigner distribution, as generically predicted by random-matrix theory, additional random singular values are generated to expand the bond-dimension automatically. Tests on simulating the vibrationally resolved quantum dynamics and absorption spectra in the pyrazine molecule and perylene bisimide (PBI) J-aggregate trimer as well as a spin-1/2 Heisenberg chain show that it can be automatic and as accurate as 2TDVP but reduce the computational time remarkably.
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http://dx.doi.org/10.1021/jacsau.1c00474 | DOI Listing |
Nat Commun
January 2025
Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India.
Single-point mutations are pivotal in molecular zoology, shaping functions and influencing genetic diversity and evolution. Here we study three such genetic variants of a mechano-responsive protein, cadherin-23, that uphold the structural integrity of the protein, but showcase distinct genotypes and phenotypes. The variants exhibit subtle differences in transient intra-domain interactions, which in turn affect the anti-correlated motions among the constituent β-strands.
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January 2025
School of Reliability and Systems Engineering, Beihang University, Beijing 100191, China.
Accurately predicting the remaining useful life (RUL) of critical mechanical components is a central challenge in reliability engineering. Stochastic processes, which are capable of modeling uncertainties, are widely used in RUL prediction. However, conventional stochastic process models face two major limitations: (1) the reliance on strict assumptions during model formulation, restricting their applicability to a narrow range of degradation processes, and (2) the inability to account for potential variations in the degradation mechanism during modeling and prediction.
View Article and Find Full Text PDFMicroorganisms
January 2025
State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China.
As transitional ecosystems between land and sea, estuaries are characterized by a unique environment that supports complex and diverse microbial communities. A comprehensive analysis of microbial diversity and ecological processes at different trophic levels is crucial for understanding the ecological functions of estuarine ecosystems. In this study, we systematically analyzed the diversity patterns, community assembly, and environmental adaptability of bacterial and protist communities using high-throughput sequencing techniques.
View Article and Find Full Text PDFBiomolecules
December 2024
Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
Microorganisms, including bacteria, fungi, and protists, are key drivers in aquatic ecosystems, maintaining ecological balance and normal material circulation, playing vital roles in ecosystem functions and biogeochemical processes. To evaluate the environmental impact of different river crab polyculture practices, we set up two different river crab () polyculture practices: one where river crabs were cultured with mandarin fish (), silver carp (), and freshwater fish stone moroko (), and another where river crabs were cultured just with mandarin fish and silver carp. These two polyculture practices were referred to as PC and MC, respectively.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Mathematics, Konkuk University, Seoul, Republic of Korea.
Mathematical and statistical methods are invaluable in epidemiological investigations, enhancing our understanding of disease transmission dynamics and informing effective control measures. In this study, we presented a method to estimate transmissibility using patient-level data, with application to the 2015 MERS outbreak at Pyeongtaek St. Mary's Hospital, the Republic of Korea.
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