Yang Pu

Shuo Wang, Yang Pu, Layne Watson et al.

Stochastic effect in cellular systems has been an important topic in systems biology. Stochastic modeling and simulation methods are important tools to study stochastic effect. Given the low efficiency of stochastic simulation algorithms, the hybrid method, which combines an ordinary differential equation (ODE) system with a stochastic chemically reacting system, shows its unique advantages in the modeling and simulation of biochemical systems. The efficiency of hybrid method is usually limited by reactions in the stochastic subsystem, which are modeled and simulated using Gillespie's framework and frequently interrupt the integration of the ODE subsystem. In this paper we develop an efficient implementation approach for the hybrid method coupled with traditional ODE solvers. We also compare the efficiency of hybrid methods with three widely used ODE solvers RADAU5, DASSL, and DLSODAR. Numerical experiments with three biochemical models are presented. A detailed discussion is presented for the performances of three ODE solvers.

Yang Pu, Zhiyuan Dai, Yifan Zhou et al.

Machine learning (ML) has been extensively employed in planar perovskite photovoltaics to screen effective organic molecular additives, while encountering predictive biases for novel materials due to small datasets and reliance on predefined descriptors. Present work thus proposes an effective approach, Co-Pilot for Perovskite Additive Screener (Co-PAS), an ML-driven framework designed to accelerate additive screening for perovskite solar cells (PSCs). Co-PAS overcomes predictive biases by integrating the Molecular Scaffold Classifier (MSC) for scaffold-based pre-screening and utilizing Junction Tree Variational Autoencoder (JTVAE) latent vectors to enhance molecular structure representation, thereby enhancing the accuracy of power conversion efficiency (PCE) predictions. Leveraging Co-PAS, we integrate domain knowledge to screen an extensive dataset of 250,000 molecules from PubChem, prioritizing candidates based on predicted PCE values and key molecular properties such as donor number, dipole moment, and hydrogen bond acceptor count. This workflow leads to the identification of several promising passivating molecules, including the novel Boc-L-threonine N-hydroxysuccinimide ester (BTN), which, to our knowledge, has not been explored as an additive in PSCs and achieves a device PCE of 25.20%. Our results underscore the potential of Co-PAS in advancing additive discovery for high-performance PSCs.