Article
Biochemistry & Molecular Biology
Negin Forouzesh, Nikita Mishra
Summary: The study introduces a new flavor of the generalized Born model for calculating binding affinity in protein-ligand complexes. It presents an efficient computational protocol and evaluates two options for representing dielectric boundaries, showing quantitative agreement with experimental values. Additionally, efficient entropy calculation strategies are proposed.
Article
Biochemistry & Molecular Biology
Sahar Cain, Ali Risheh, Negin Forouzesh
Summary: This research explores the application of Theory-Guided Data Science in studying protein-ligand binding. A hybrid model, integrating a data-driven model with a physics-based model, is proposed to improve the accuracy and interpretability of the pure data-driven model. The proposed model is tested on experimental datasets, demonstrating improved accuracy and interpretability compared to the purely data-driven model.
Article
Chemistry, Physical
Jia Wang, Chaonan Cui, Xinli Zhu, Hua Wang, Qingfeng Ge
Summary: Water is often treated as an implicit solvent in modeling electrochemical reactions, but this may not be sufficient as water molecules can play important roles in the reactions. In this study, the effect of explicit water molecules on the stability of hydrogenation intermediates in the electrochemical hydrogenation of CO2 is investigated using density functional theory method. The results show that including six water molecules is necessary to account for the local interaction between intermediates and the water solvent. The presence of explicit water molecules also alters the prediction of the potential-limiting step and increases selectivity towards methane.
Article
Chemistry, Physical
Sebastian Spicher, Christoph Plett, Philipp Pracht, Andreas Hansen, Stefan Grimme
Summary: An automated and broadly applicable workflow, called quantum cluster growth (QCG), is introduced for the explicit description of solvation effects. This method is based on semiempirical GFN2-xTB/GFN-FF methods and provides efficient geometry optimizations and MD simulations. QCG with GFN2-xTB yields realistic solution geometries and reasonable solvation free energies for various systems without introducing many empirical parameters.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Rajarshi Roy, Sayan Poddar, Parimal Kar
Summary: All-atom MD simulations provide atomic details of glycan structures, but extensive sampling is required for simulating conformational transitions. In the case of carbohydrate modeling, the glycosidic linkages are often well sampled on the sub-mu s time scale. Simulating large glycans or glycoconjugates in aqueous environments at the atomistic level is challenging due to a high number of water molecules that slow down conformational sampling. A multiscale simulation approach, where the glycan is represented at the all-atom level while the solvent is treated implicitly, offers an alternative to the all-atom approach. This study compares the implicit solvent model with the commonly used explicit model using Gaussian accelerated molecular dynamics (GaMD). The results show similar monosaccharide conformations in both solvent models, with minor differences in global conformation and a significant increase in inter-residue hydrogen bonds in the explicit solvent model. The analysis of structural parameters reveals a balanced trade-off between computational speed and accuracy for studying long-chain glycan molecules in an implicit solvent.
CARBOHYDRATE RESEARCH
(2022)
Article
Computer Science, Interdisciplinary Applications
Praveen K. Maurya, Vivek S. Yadav, Bikash Mahato, Naveen Ganta, Manoj K. Rajpoot, Yogesh G. Bhumkar
Summary: This paper presents a new class of optimized implicit-explicit Runge-Kutta methods for the numerical solution of dispersive and non-dispersive hyperbolic systems, which have better stability and dispersion properties and lower computational costs compared to existing methods.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Mathematics, Applied
Andrew Cleary, Jacob Page
Summary: This paper presents a new method for systematically exploring the free-energy landscape in the study of superfluids. It discovers new equilibrium states and evaluates the likelihood of observing certain states in experiments. Additionally, it investigates the dynamics near the minimizing state.
Article
Chemistry, Multidisciplinary
Myung Keun Cho, Song-Ho Chong, Sihyun Ham, Seokmin Shin
Summary: Understanding protein stability requires thermodynamic analysis of folding, which is often done through molecular simulations using explicit or implicit water models. However, it is unclear how reliable results from different solvation models are at the molecular level. This study quantifies the influence of solvation models on folding stability at both backbone and side chain resolutions for beta-sheet and helical proteins. The results show that the discrepancies mostly come from charged side chains and under-stabilized hydrophobic ones in implicit solvent simulations. Backbone residues contribute similarly in both explicit and implicit water models. This study lays the foundation for assessing solvation models in protein simulations.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Computer Science, Artificial Intelligence
Valentina Fietta, Francesca Zecchinato, Brigida Di Stasi, Mirko Polato, Merylin Monaro
Summary: The latest developments in artificial intelligence (AI) have raised many ethical and socio-economic issues. While most participants explicitly express a positive attitude towards AI, their implicit responses appear to be in the opposite direction. Females tend to show more negative attitudes than males, and those working in the AI field are more positive towards AI.
IEEE TRANSACTIONS ON HUMAN-MACHINE SYSTEMS
(2022)
Article
Multidisciplinary Sciences
Korak Kumar Ray, Colin D. Kinz-Thompson, Jingyi Fei, Bin Wang, Qiao Lin, Ruben L. Gonzalez
Summary: Biomolecular machines utilize thermal and chemical energy to perform cellular processes, and they require dynamic rearrangements of structural components. The physical and structural mechanisms through which ligands achieve repurposing of these dynamics remain unknown.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Materials Science, Ceramics
T. Odagaki, Y. Saruyama, T. Ishida
Summary: The free energy landscape is reorganized with temperature modulation, impacting the relaxation process and physical properties. The relaxation time of dielectric response depends on the relaxation of the FEL, converging to equilibrium in the long term. In temperature modulation spectroscopy, the dynamics are influenced by the relaxation time of FEL.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Article
Chemistry, Multidisciplinary
Benjamin W. J. Chen, Xinglong Zhang, Jia Zhang
Summary: Machine learning interatomic potentials, combined with active learning, enable fast and accurate modelling of solvents in catalytic reactions. This approach accelerates molecular dynamics simulations and accurately predicts key catalytic quantities, opening up possibilities for studying solvated catalysts.
Article
Psychology, Multidisciplinary
Wanyu Zhang, Jilin Zou, Tong Yue
Summary: This study aims to investigate the explicit and implicit attitudes of Chinese university students towards genetic modification (GM), and examine the role of education level. The results show that the explicit attitudes of university students are generally positive, while the implicit attitudes are generally negative. Education level has a significant impact on explicit attitudes, but not on implicit attitudes.
FRONTIERS IN PSYCHOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Badrut Tamam Ibnu Ali, Nurul Widiastuti, Yuly Kusumawati, Atthar Luqman Ivansyah, Juhana Jaafar
Summary: The selection of solvent greatly influences the characteristics of membrane preparation. Using a computational approach, solvents can be selected based on the solvation energy value, providing the advantage of no organic waste generation. In this study, the optimization of PET structure was conducted using a computational approach, and the PET obtained from plastic bottle waste was validated against experimental results. The best solvent for dissolving PET waste was determined using a conductor-like polarizable continuum model. The results showed that the computational and experimental spectra were not significantly different, and phenol was found to be the most effective solvent for PET plastic bottle waste dissolution.
MATERIALS RESEARCH EXPRESS
(2022)
Article
Computer Science, Interdisciplinary Applications
Shuang Liu, Zirui Zhang, Hsiao-Bing Cheng, Li-Tien Cheng, Bo Li
Summary: Coarse-grained modeling and efficient computer simulations are crucial for studying complex molecular processes. In this study, the variational implicit-solvent model (VISM) is extended to include solute mechanical interactions, and fast algorithms and GPU implementation for molecular simulations are developed. Numerical tests demonstrate the accuracy, stability, and efficiency of the methods, suggesting their potential for simulating large molecular systems.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Esther Carrasco, Patricia Gomez-Gutierrez, Pedro M. Campos, Miguel Vega, Angel Messeguer, Juan Jesus Perez
Summary: In this study, we have identified a series of di-substituted analogs of [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[3,4-b]pyrazine) as potent inhibitors of p38 MAP kinase, shown by their ability to inhibit IL-10 secretion in human monocyte-derived macrophages.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Maria Guadalupe Herrera-Hernandez, Neda Razzaghi, Pol Fernandez-Gonzalez, Laia Bosch-Presegue, Guillem Vila-Julia, Juan Jesus Perez, Pere Garriga
Summary: This article introduces the impact of two rhodopsin mutations, Y102H and I307N, on retinal degeneration, compares them with the previously studied G90V mutation, and provides a theoretical basis for studying retinal degeneration. It is found that these mutations alter the inactive-active equilibrium of the receptor and have a profound effect on the signal transduction process.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Chemistry, Analytical
Gloria. Ebube. Uwaya, Yangping Wen, Krishna. Bisetty
Summary: This study presents a sensor based on nickel oxide nanoparticles and polyaniline that shows good sensitivity and selectivity for the detection of epinephrine. The sensor has been experimentally investigated and theoretically modeled, and its performance has been evaluated in different solutions. Monte Carlo and molecular dynamics simulations were used to assess the binding affinity between the sensor and epinephrine. Density functional theory calculations confirmed the chemical reactivity and stability of the sensor with epinephrine.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Khethiwe Mthiyane, Gloria Ebube Uwaya, Maryam Amra Jordaan, Suvardhan Kanchi, Krishna Bisetty
Summary: A new hybrid sensor was developed using titanium oxide nanoparticles and nafion as an anchor agent on a glassy carbon electrode for efavirenz detection. The sensor demonstrated good selectivity and practicality, with excellent recovery rates for the drug.
Article
Chemistry, Analytical
Kwanele Kunene, Syreina Sayegh, Matthieu Weber, Myalowenkosi Sabela, Damien Voiry, Igor Iatsunskyi, Emerson Coy, Suvardhan Kanchi, Krishna Bisetty, Mikhael Bechelany
Summary: This study presents a method for fabricating an electrochemical immunosensor for aflatoxin detection. The sensor showed good analytical performance with a large linear range, low detection limit, and long-term stability. It was successfully applied to detect aflatoxin in wine samples.
Article
Chemistry, Medicinal
Guillem Vila-Julia, Juan J. Perez, Jaime Rubio-Martinez
Summary: Bak, a member of the Bcl-2 family, plays a key role in apoptosis and its activation triggers mitochondrial outer membrane permeabilization. The deregulation of this process is associated with cancer and neurodegenerative disorders. The 3D structure of Bak poses a challenge for selective drug discovery due to the similarity in binding sites between pro and anti-apoptotic proteins. This study aims to identify potential allosteric sites in Bak, which could guide future docking studies and drug development efforts.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Analytical
Lyndon Naidoo, Gloria Ebube Uwaya, Florian Meier, Krishna Bisetty
Summary: This study investigates the impact of PEGylated Fe3O4 nanoparticles intercalated with carboxylic acid-functionalized multi-walled carbon nanotubes on the design of an electrochemical sensor for zearalenone (ZEN) analysis. The nanocomposite-enhanced electrode exhibits a strong cathodic redox response of ZEN and provides significantly low limits of detection and quantification. Spike recoveries for real samples of rice and corn flour are excellent. The incorporation of the nanocomposite-enhanced electrode shows potential in preventing ZEN mycotoxin exposure.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2023)
Article
Materials Science, Multidisciplinary
Gloria. Ebube Uwaya, Krishna Bisetty
Summary: This study presents an electrochemical sensor for the detection of epicatechin (EC) in food samples, which utilizes cobalt oxide (Co3O4) synthesized from Carica papaya peel extract combined with multiwalled carbon nanotubes (MWCNTs). The sensor exhibited excellent electron transport properties and electrocatalytic activity towards EC, with a lower resistance value than that of the bare electrode. The designed sensor demonstrated good repeatability, stability, reproducibility, selectivity, and excellent recoveries for the detection of EC in food samples. Furthermore, the study also analyzed the energy band gap, absolute hardness, and adsorption energy of the sensor, providing insights into its chemical reactivity and potential applications in the food industry.
Article
Chemistry, Medicinal
Patricia Gomez-Gutierrez, Jaime Rubio-Martinez, Juan J. Perez
Summary: Mutants of Ras are oncogenic drivers in human tumors. Computational methods have been used to characterize potential allosteric pockets in K-Ras and identify molecules with inhibitory capability. These findings open new avenues for cancer treatment.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Analytical
Gloria Ebube Uwaya, Krishna Bisetty
Summary: This study introduces an innovative sensing platform designed for the detection of sunset yellow (SY), which showed enhanced electrochemical sensing behaviour for SY oxidation. The platform employs a composite electrode material comprising of a zeolitic imidazole framework (ZIF-67) and multiwalled carbon nanotubes (MWCNTs) on a glassy carbon electrode (GCE). The experimental results demonstrate high precision and reliability.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Giulia Sormani, Aruna Korde, Alex Rodriguez, Melissa Denecke, Ali Hassanali
Summary: In recent years, the use of Zirconium-89 (Zr-89) as a radionuclide in nuclear medicine for cancer diagnostic imaging and drug discovery has increased. Our research reveals a different coordination structure of the Zr-DFO complex, which is contrary to the conventional belief. Through molecular dynamics simulations and free energy calculations, we find that thermal fluctuations lead to an open hexadentate chelate structure of the Zr-DFO complex, while a stable and closely packed structure is formed by binding with 4HMS.
Article
Chemistry, Multidisciplinary
Mesfin Diro Chaka, Chernet Amente Geffe, Alex Rodriguez, Nicola Seriani, Qin Wu, Yedilfana Setarge Mekonnen
Summary: Redox flow batteries (RFBs) are a promising option for large-scale energy storage due to their high energy density, low cost, and environmental benefits. However, identifying organic compounds with the desired properties for RFB technology is a challenging task. In this study, a graph neural network-based model called MolGAT was developed to predict the redox potential of organic molecules using their molecular structures, atomic properties, and bond attributes.
Article
Chemistry, Physical
Gloria Ebube Uwaya, Lyndon Naidoo, Krishna Bisetty
Summary: This research study focuses on the interaction between efavirenz (EFV) and TiO2 NPs using complementary analytical techniques. The results indicate that EFV is encapsulated around TiO2 NPs, as evidenced by increased UV absorbance and a larger mean radius of the EFV-TiO2 complex. Additionally, EIS measurements reveal reduced impedance in the complex, suggesting polarization due to increased ion presence. Understanding the physiochemical behavior of EFV and TiO2 NPs in aqueous medium is crucial for research on the physiological interactions of drugs with nanoparticles.
SURFACES AND INTERFACES
(2023)
Article
Chemistry, Analytical
Gloria Ebube Uwaya, Salvador Sagrado, Krishna Bisetty
Summary: A novel sensor using Au nanoparticles derived from Callistemon viminalis leaf extract and multiwalled carbon nanotubes doped onto glassy carbon electrode was developed for detecting xylitol in sugar free chewing gum. The sensor showed significantly enhanced electrochemical response to xylitol and achieved a low detection limit. Machine learning and molecular dynamics simulations were used to study the electrochemical reaction and interaction of xylitol on the electrode surfaces. This study demonstrates a new strategy for rapid detection of xylitol.
Article
Chemistry, Physical
Patricia Gomez-Gutierrez, Jaime Rubio-Martinez, Juan J. Perez
Summary: This study investigates the conformational profile of Balaram's peptide in different solvents using computational methods. The results reveal the significant influence of solvents on the peptide's conformation, supporting previous experimental findings and providing further insights.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
