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Examining the Accuracy of DNA Parentage Tests Using Computer Simulations and Known Pedigrees

Wang et al. | Jul 13, 2020

Examining the Accuracy of DNA Parentage Tests Using Computer Simulations and Known Pedigrees

How accurate are DNA parentage tests? In this study, the authors hypothesized that current parentage tests are reliable if the analysis involves only one or a few families of yellow perch fish Perca flavescens. Their results suggest that DNA parentage tests are reliable as long as the right methods are used, since these tests involve only one family in most cases, and that the results from parentage analyses of large populations can only be used as a reference.

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Computational Structure-Activity Relationship (SAR) of Berberine Analogs in Double-Stranded and G-Quadruplex DNA Binding Reveals Both Position and Target Dependence

Sun et al. | Dec 18, 2020

Computational Structure-Activity Relationship (SAR) of Berberine Analogs in Double-Stranded and G-Quadruplex DNA Binding Reveals Both Position and Target Dependence

Berberine, a natural product alkaloid, and its analogs have a wide range of medicinal properties, including antibacterial and anticancer effects. Here, the authors explored a library of alkyl or aryl berberine analogs to probe binding to double-stranded and G-quadruplex DNA. They determined that the nature of the substituent, the position of the substituent, and the nucleic acid target affect the free energy of binding of berberine analogs to DNA and G-quadruplex DNA, however berberine analogs did not result in net stabilization of G-quadruplex DNA.

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Modelling effects of alkylamines on sea salt aerosols using the Extended Aerosols and Inorganics Model

Chang et al. | Apr 29, 2022

Modelling effects of alkylamines on sea salt aerosols using the Extended Aerosols and Inorganics Model

With monitoring of climate change and the evolving properties of the atmosphere more critical than ever, the authors of this study take sea salt aerosols into consideration. These sea salt aerosols, sourced from the bubbles found at the surface of the sea, serve as cloud condensation nuclei (CCN) and are effective for the formation of clouds, light scattering in the atmosphere, and cooling of the climate. With amines being involved in the process of CCN formation, the authors explore the effects of alkylamines on the properties of sea salt aerosols and their potential relevance to climate change.

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Prediction of molecular energy using Coulomb matrix and Graph Neural Network

Hazra et al. | Feb 01, 2022

Prediction of molecular energy using Coulomb matrix and Graph Neural Network

With molecular energy being an integral element to the study of molecules and molecular interactions, computational methods to determine molecular energy are used for the preservation of time and resources. However, these computational methods have high demand for computer resources, limiting their widespread feasibility. The authors of this study employed machine learning to address this disadvantage, utilizing neural networks trained on different representations of molecules to predict molecular properties without the requirement of computationally-intensive processing. In their findings, the authors determined the Feedforward Neural Network, trained by two separate models, as capable of predicting molecular energy with limited prediction error.

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Tomato disease identification with shallow convolutional neural networks

Trinh et al. | Mar 03, 2023

Tomato disease identification with shallow convolutional neural networks

Plant diseases can cause up to 50% crop yield loss for the popular tomato plant. A mobile device-based method to identify diseases from photos of symptomatic leaves via computer vision can be more effective due to its convenience and accessibility. To enable a practical mobile solution, a “shallow” convolutional neural networks (CNNs) with few layers, and thus low computational requirement but with high accuracy similar to the deep CNNs is needed. In this work, we explored if such a model was possible.

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Impact of carbon number and atom number on cc-pVTZ Hartree-Fock Energy and program runtime of alkanes

Pan et al. | Mar 06, 2024

Impact of carbon number and atom number on cc-pVTZ Hartree-Fock Energy and program runtime of alkanes
Image credit: The authors

It's time-consuming to complete the calculations that are used to study nuclear reactions and energy. To uncover which computational chemistry tools are useful for this challenge, Pan, Vaiyakarnam, Li, and McMahan investigated whether the Python-based Simulations of Chemistry Framework’s Hartree-Fock (PySCF) method is an efficient and accurate way to assess alkane molecules.

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An efficient approach to automated geometry diagram parsing

Date et al. | Oct 02, 2022

An efficient approach to automated geometry diagram parsing

Here, beginning from an initial interest in the possibility to use a computer to automatically solve a geometry diagram parser, the authors developed their own Fast Geometry Diagram Parser (FastGDP) that uses clustering and corner information. They compared their own methods to a more widely available, method, GeoSolver, finding their own to be an order of magnitude faster in most cases that they considered.

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Do elders care about eHealth? A correlational study between eHealth consumption and literacy

Liang et al. | Jul 19, 2023

Do elders care about eHealth? A correlational study between eHealth consumption and literacy
Image credit: Liang and Sposa

As digital tools become more prevalent in medicine, the ability for individuals to understand and take actions based on what they read on the internet is crucial. eHealth literacy is defined as as the ability to seek, find, understand, and evaluate health information from electronic sources and apply the knowledge gained to addressing or solving a health problem. In general, Americans have low eHealth literacy rates. However, limited research has been conducted to understand the eHealth literacy level among older Chinese adult immigrants in the U.S. To determine the eHealth literacy of elderly Chinese immigrants, we sent out an eHealth survey and relevant computer skills survey using a modified version of the eHEALS (eHealth Literacy Scale) health literacy test. We hypothesized that elders who consumed more electronic health content would have a higher eHealth literacy score. The results of this survey showed that there was a positive correlation between the frequency of electronic health information consumption and the participant's eHealth literacy rate. In addition, the results of our computer literacy test show that the frequency of consumption and computer literacy are positively correlated as well. There is a strong positive correlation between the level of computer skills and eHealth literacy of participants. These results reveal possible steps individuals can take to reduce health misinformation and improve their own health by attaining, understanding, and taking action on health material on the internet.

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The Effect of Varying Training on Neural Network Weights and Visualizations

Fountain et al. | Dec 04, 2019

The Effect of Varying Training on Neural Network Weights and Visualizations

Neural networks are used throughout modern society to solve many problems commonly thought of as impossible for computers. Fountain and Rasmus designed a convolutional neural network and ran it with varying levels of training to see if consistent, accurate, and precise changes or patterns could be observed. They found that training introduced and strengthened patterns in the weights and visualizations, the patterns observed may not be consistent between all neural networks.

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Modeling Hartree-Fock approximations of the Schrödinger Equation for multielectron atoms from Helium to Xenon using STO-nG basis sets

Gangal et al. | Oct 05, 2023

Modeling Hartree-Fock approximations of the Schrödinger Equation for multielectron atoms from Helium to Xenon using STO-nG basis sets

The energy of an atom is extremely useful in nuclear physics and reaction mechanism pathway determination but is challenging to compute. This work aimed to synthesize regression models for Pople Gaussian expansions of Slater-type Orbitals (STO-nG) atomic energy vs. atomic number scatter plots to allow for easy approximation of atomic energies without using computational chemistry methods. The data indicated that of the regressions, sinusoidal regressions most aptly modeled the scatter plots.

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