The great learning ability of deep learning facilitates us to comprehend the real physical world, making learning to simulate complicated particle systems a promising endeavour both in academia and industry. However, the complex laws of the physical world pose significant challenges to the learning based simulations, such as the varying spatial dependencies between interacting particles and varying temporal dependencies between particle system states in different time stamps, which dominate particles' interacting behavior and the physical systems' evolution patterns. Existing learning based methods fail to fully account for the complexities, making them unable to yield satisfactory simulations. To better comprehend the complex physical laws, we propose a novel model - Graph Networks with Spatial-Temporal neural Ordinary Differential Equations (GNSTODE) - that characterizes the varying spatial and temporal dependencies in particle systems using a united end-to-end framework. Through training with real-world particle-particle interaction observations, GNSTODE can simulate any possible particle systems with high precisions. We empirically evaluate GNSTODE's simulation performance on two real-world particle systems, Gravity and Coulomb, with varying levels of spatial and temporal dependencies. The results show that GNSTODE yields better simulations than state-of-the-art methods, showing that GNSTODE can serve as an effective tool for particle simulation in real-world applications. Our code is made available at https://github.com/Guangsi-Shi/AI-for-physics-GNSTODE.
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http://dx.doi.org/10.1016/j.neunet.2024.106341 | DOI Listing |
J Chem Theory Comput
January 2025
Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
Self-diffusion coefficients, *, are routinely estimated from molecular dynamics simulations by fitting a linear model to the observed mean squared displacements (MSDs) of mobile species. MSDs derived from simulations exhibit statistical noise that causes uncertainty in the resulting estimate of *. An optimal scheme for estimating * minimizes this uncertainty, i.
View Article and Find Full Text PDFActa Pharm Sin B
December 2024
Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China.
The respiratory tract is susceptible to various infections and can be affected by many serious diseases. Vaccination is one of the most promising ways that prevent infectious diseases and treatment of some diseases such as malignancy. Direct delivery of vaccines to the respiratory tract could mimic the natural process of infection and shorten the delivery path, therefore unique mucosal immunity at the first line might be induced and the efficiency of delivery can be high.
View Article and Find Full Text PDFActa Pharm Sin B
December 2024
School of Pharmacy, Institute of Hepatology and Metabolic Diseases, Department of Hepatology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China.
Specific tumor-targeted gene delivery remains an unsolved therapeutic issue due to aberrant vascularization in tumor microenvironment (TME). Some bacteria exhibit spontaneous chemotaxis toward the anaerobic and immune-suppressive TME, which makes them ideal natural vehicles for cancer gene therapy. Here, we conjugated ZIF-8 metal-organic frameworks encapsulating eukaryotic murine interleukin 2 () expression plasmid onto the surface of VNP20009, an attenuated strain with well-documented anti-cancer activity, and constructed a TME-targeted delivery system named /ZIF-8@.
View Article and Find Full Text PDFMath Biosci Eng
December 2024
Department of Engineering and Natural Sciences, University of Applied Sciences Merseburg, Eberhard-Leibnitz-Str. 2, D-06217 Merseburg, Germany.
In this article, we reconsider the classical target cell limited dynamical within-host HIV model, solely taking into account the interaction between $ {\rm{CD}}4^{+} $ T cells and virus particles. First, we summarize some analytical results regarding the corresponding dynamical system. For that purpose, we proved some analytical results regarding the system of differential equations as our first main contribution.
View Article and Find Full Text PDFEnviron Sci Pollut Res Int
January 2025
Research Centre for Energy, Environment and Technology (CIEMAT), Avda. Complutense, 40, 28040, Madrid, Spain.
As tailpipe emissions have decreased, there is a growing focus on the relative contribution of non-exhaust sources of vehicle emissions. Addressing these emissions is key to better evaluating and reducing vehicles' impact on air quality and public health. Tailoring solutions for different non-exhaust sources, including brake emissions, is essential for achieving sustainable mobility.
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