Charge scaling, also denoted as the electronic continuum correction, has proven to be an efficient method for effectively including electronic polarization in force field molecular dynamics simulations without additional computational costs. However, scaling charges in existing force fields, fitted at least in part to experimental data, lead to inconsistencies, such as overscaling. We have, therefore, recently developed a four-site water model consistent with charge scaling, i.e., possessing the correct low-frequency dielectric constant of 45. Here, we build on top of this water model to develop charge-scaled models of biologically relevant Li+, Na+, K+, Ca2+, and Mg2+ cations as well as Cl-, Br-, and I- anions, employing machine learning to streamline and speed up the parametrization process. On the one hand, we show that the present model outperforms the best existing charge scaled model of aqueous ions. On the other hand, the present work points to a future need for consistently and simultaneously improving the water and ion models within the electronic continuum correction framework.
29 March 2024 in Journal of Chemical Theory and Computation
Vegetation classifications on large geographic scales are necessary to inform conservation decisions and monitor keystone, invasive, and endangered species. These classifications are often effectively achieved by applying models to imaging spectroscopy, a type of remote sensing data, but such undertakings are often limited in spatial extent. Here we provide accurate, high-resolution spatial data on the keystone species Metrosideros polymorpha, a highly polymorphic tree species distributed across bioclimatic zones and environmental gradients on Hawai’i Island using airborne imaging spectroscopy and LiDAR. We compare two tree species classification techniques, the support vector machine (SVM) and spectral mixture analysis (SMA), to assess their ability to map M. polymorpha over 28,000 square kilometers where differences in topography, background vegetation, sun angle relative to the aircraft, and day of data collection, among others, challenge accurate classification. To capture spatial variability in model performance, we applied Gaussian process classification (GPC) to estimate the spatial probability density of M. polymorpha occurrence using only training sample locations. We found that while SVM and SMA models exhibit similar raw score accuracy over the test set (96.0% and 93.4%, respectively), SVM better reproduces the spatial distribution of M. polymorpha than SMA. We developed a final 2 m × 2 m M. polymorpha presence dataset and a 30 m × 30 m M. polymorpha density dataset using SVM classifications that have been made publicly available for use in conservation applications. Accurate, large-scale species classifications are achievable, but metrics for model performance assessments must account for spatial variation of model accuracy.
16 December 2024 in The Journal of Physical Chemistry Letters
Vegetation classifications on large geographic scales are necessary to inform conservation decisions and monitor keystone, invasive, and endangered species. These classifications are often effectively achieved by applying models to imaging spectroscopy, a type of remote sensing, data, but such undertakings are often limited in spatial extent. Here we provide accurate, high-resolution spatial data on the keystone species Metrosideros polymorpha, a highly polymorphic tree species distributed across bioclimatic zones and environmental gradients on Hawai'i island, using airborne imaging spectroscopy and LiDAR. We compare two tree species classification techniques, support vector machine (SVM) and spectral mixture analysis (SMA), to assess their ability to map M. polymorpha over 28,000 square kilometers where differences in topography, background vegetation, sun angle relative to the aircraft, and day of data collection, among others, challenge accurate classification. To capture spatial variability in model performance, we applied gaussian process classification (GPC) to estimate the spatial probability density of M. polymorpha occurrence using only training sample locations. We found that, while SVM and SMA models exhibit similar raw score accuracy over the test set (96.0% and 93.4%, respectively), SVM better reproduces the spatial distribution of M. polymorpha than SMA. We developed a final 2 m x 2 m M. polymorpha presence dataset and a 30 m x 30 m M. polymorpha density dataset using SVM classifications that have been made publicly available for use in conservation applications. Accurate, large-scale species classifications are achievable, but metrics for model performance assessments must account for spatial variation of model accuracy.
19 February 2026 in Journal of Chemical Theory and Computation