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Frozen-density embedding (FDE) represents a versatile embedding scheme to describe the environmental effect on electron dynamics in molecular systems. The extension of the general theory of FDE to the real-time time-dependent Kohn-Sham method has previously been presented and implemented in plane waves and periodic boundary conditions [Pavanello, M.; 2015, 142, 154116]. In the current paper, we extend our recent formulation of the real-time time-dependent Kohn-Sham method based on localized basis set functions and developed within the Psi4NumPy framework to the FDE scheme. The latter has been implemented in its "uncoupled" flavor (in which the time evolution is only carried out for the active subsystem, while the environment subsystems remain at their ground state), using and adapting the FDE implementation already available in the PyEmbed module of the scripting framework PyADF. The implementation was facilitated by the fact that both Psi4NumPy and PyADF, being native Python API, provided an ideal framework of development using the Python advantages in terms of code readability and reusability. We employed this new implementation to investigate the stability of the time-propagation procedure, which is based on an efficient predictor/corrector second-order midpoint Magnus propagator employing an exact diagonalization, in combination with the FDE scheme. We demonstrate that the inclusion of the FDE potential does not introduce any numerical instability in time propagation of the density matrix of the active subsystem, and in the limit of the weak external field, the numerical results for low-lying transition energies are consistent with those obtained using the reference FDE calculations based on the linear-response TDDFT. The method is found to give stable numerical results also in the presence of a strong external field inducing nonlinear effects. Preliminary results are reported for high harmonic generation (HHG) of a water molecule embedded in a small water cluster. The effect of the embedding potential is evident in the HHG spectrum reducing the number of the well-resolved high harmonics at high energy with respect to the free water. This is consistent with a shift toward lower ionization energy passing from an isolated water molecule to a small water cluster. The computational burden for the propagation step increases approximately linearly with the size of the surrounding frozen environment. Furthermore, we have also shown that the updating frequency of the embedding potential may be significantly reduced, much less than one per time step, without jeopardizing the accuracy of the transition energies.
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http://dx.doi.org/10.1021/acs.jctc.0c00603 | DOI Listing |
ACS Sens
September 2025
School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China.
Alpha-2-macroglobulin (A2M) is a critical biomarker implicated in inflammation, immune regulation, coagulation, and various pathological conditions such as liver fibrosis, neurodegenerative diseases, and cancers. However, its precise quantification remains challenging due to complex conformational dynamics, subtle abundance fluctuations, and interference from plasma proteins. Here, we present a label-free dynamic single-molecule sensing (LFDSMS) strategy for the sensitive and specific detection of A2M.
View Article and Find Full Text PDFJ Chem Phys
September 2025
Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.
We present a self-consistent algorithm for optimal control simulations of many-body quantum systems. The algorithm features a two-step synergism that combines discrete real-time machine learning (DRTL) with Quantum Optimal Control Theory (QOCT) using the time-dependent Schrödinger equation. Specifically, in step (1), DRTL is employed to identify a compact working space (i.
View Article and Find Full Text PDFDrug Dev Res
September 2025
Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China.
Colorectal cancer (CRC) is a common malignancy often characterized by metastasis and poor prognosis. This study attempts to ascertain the anticancer impacts of theaflavin (TF) on CRC cells and examine the fundamental molecular mechanisms, focusing on the function of DDIT4 in CRC progression. This study utilized RNA sequencing for gene expression profiling, differential expression analysis, and Venn diagram analysis for overlapping genes.
View Article and Find Full Text PDFJ Mater Chem B
September 2025
Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Shenzhen Key Laboratory of Metabolic Halth, Shenzhen Metabolism and Reproductive Targeted Delivery Proof-of-Concept Center, Shenzhen Engineering Laboratory of Nano
Bacterial infections pose significant challenges in clinical diagnostics and microbiological research due to the need for rapid, sensitive, and specific detection methods. Herein, we report the development of Cy5-NO2, a novel nitro-containing fluorescent probe designed for real-time monitoring of bacterial nitroreductase (NTR) activity. Cy5-NO2 is synthesized through a streamlined, high-yield process without chromatography, yielding a stable compound confirmed by X-ray crystallography and spectroscopic methods.
View Article and Find Full Text PDFIEEE Trans Neural Syst Rehabil Eng
September 2025
Myoelectric pattern recognition systems serve as a promising predictive control approach for the lower limbs prostheses and exoskeletons. However, their actual deployment is challenged by the signal stochastic nature that could contaminate the decision stream with physiologically implausible transitions, posing safety and metabolic cost concerns on the potential user. Therefore, this study proposes a novel Physics-Informed Bayesian Fusion (PI-BF) post-processor that embeds biomechanical sequentiality constraints into the posterior probabilistic output of the classifiers to suppress unstable transitions and promote natural gait progression.
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