Article
Chemistry, Physical
Bin Chen
Summary: A lattice-based version of the aggregation-volume-bias Monte Carlo method extends the calculation of nucleation free energies from liquid clusters to solid clusters. By using this method, the nucleation free energies of bcc and fcc clusters formed by Lennard-Jones particles were calculated, showing a crossover of thermodynamic stability from bcc to fcc structure. The obtained free energies were used to extrapolate bulk phase information, confirming the preference of bcc clusters due to lower surface tension. This work demonstrates the capability of this approach to predict the entire thermodynamic landscape, which is important for understanding crystallization and polymorphism.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Computer Science, Information Systems
Zhi Cai, Meilin Ji, Qing Mi, Bowen Yang, Xing Su, Limin Guo, Zhiming Ding
Summary: Urban rail transit stations play a crucial role in alleviating traffic pressure, but obtaining population distribution data for site selection is challenging. A method based on AP density visualization is proposed to assist decision-making in predicting the location of new rail transit stations, showing high accuracy and providing valuable data support for urban traffic development and management.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2021)
Article
Chemistry, Multidisciplinary
Xingda Yang, Zhou Qu, Sen Li, Manhua Peng, Chunxi Li, Ruimao Hua, Hongwei Fan, Juergen Caro, Hong Meng
Summary: Graphdiynes (GDYs), two-dimensional graphene-like carbon systems, are considered as potential advanced membrane material due to their unique physicochemical features. Herein, we report a simple and efficient alkynylated surface-mediated strategy to prepare hydrogen-substituted graphdiyne (HsGDY) membranes on commercial alumina tubes. The resulting membranes exhibit outstanding molecular sieving together with excellent water permeances and show a long-term durability in cross-flow nanofiltration, owing to the superhydrophilic surface and hydrophobic pore walls.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Environmental Sciences
Lei You, Xiaosa Chang, Yian Sun, Yong Pang, Yan Feng, Xinyu Song
Summary: Stem volume is an important parameter in forestry inventory and carbon storage. Existing methods for estimating stem volume often overlook the irregularity of the stem, leading to deviations from the true value. This study proposes a method for estimating stem segment volume using the tetrahedron model based on TLS data. The results demonstrate the validity of the method for stem surface reconstruction and volume estimation, with the volume based on the tetrahedron model being closer to the true value.
Article
Chemistry, Multidisciplinary
Jingting Wang, Mingying Lu, Yongxing Chen, Guolin Hao, Bin Liu, Pinghua Tang, Lian Yu, Lei Wen, Haining Ji
Summary: In this study, a machine learning Gaussian regression model was constructed to explore the growth mechanism of MoS2 materials prepared by chemical vapor deposition (CVD). The model revealed that carrier gas flow rate, molybdenum sulfur ratio, and reaction temperature had a crucial impact on the CVD growth of MoS2 materials. The optimal model was then used to predict the size of molybdenum disulfide synthesis under various experimental conditions, providing an effective solution for the preparation of large-size MoS2 materials.
Article
Agricultural Engineering
Valeriy G. Narushin, Michael N. Romanov, Darren K. Griffin
Summary: The external characteristics of chicken eggs, including volume and surface area, were accurately estimated using improved formulas based on non-destructive measurement data. The average errors in calculating volume and surface area were found to be 1.1% and 0.3%, respectively. Further improvement on these formulas may not be feasible.
BIOSYSTEMS ENGINEERING
(2021)
Article
Engineering, Marine
Langxiong Gan, Tianfu Lu, Yaqing Shu
Summary: This paper studies the diffusion of ship exhaust gas in the port area using the automatic identification system (AIS) data. The estimation of ship exhaust gas is conducted using the bottom-up method, and the diffusion of gaseous pollutants from multiple ships is calculated using a Gaussian puff model. The case study in the western area of Shenzhen Port shows that the distribution of NO2 concentration is unstable and the impact of ship exhaust gas diffusion is mainly concentrated near large ship berths at night.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Automation & Control Systems
Chen Qian, Chengying Song, Sheng Li, Qingwei Chen, Jian Guo
Summary: The study introduces the Gaussian sum technique to develop the Gaussian sum sparse grid quadrature filter for improving the filtering effect under non-Gaussian conditions. The algorithm approximates non-Gaussian probability densities and utilizes SGQF for filter updates, demonstrating better accuracy in solving nonlinear non-Gaussian filtering problems.
INTERNATIONAL JOURNAL OF CONTROL AUTOMATION AND SYSTEMS
(2021)
Article
Thermodynamics
Mahmoud Elsisi, Najmeh Bazmohammadi, Josep M. Guerrero, Mohamed A. Ebrahim
Summary: This paper proposes a hybrid control methodology based on fuzzy logic and nonlinear sliding mode control for managing the energy of distributed controllable loads in hybrid renewable energy-based multi-area power systems; by optimizing the gains of the controller, the proposed method effectively reduces deviations in system frequency and tie-line power.
Article
Mechanics
Xuan Nan, Zhihao Shen, Guodong Li, Huimei Zhang
Summary: This study developed a multi-sphere volume of fluid-discrete element method solver to investigate the dynamics of floating objects in complex terrain channels. Through rigorous validation and the ability to perform computational simulations on large-scale complex terrain models, the solver provides valuable guidance for engineering design.
Article
Automation & Control Systems
Wei Cao, Zhao Han, Ziqi Chen, Zili Jin, Jiajun Wu, Jinxiu Qu, Dong Wang
Summary: This study proposes a new physical model for wear prediction in the grinding process, based on the finite element method and numerical simulation technology. Experimental results validate the accuracy of the model. The findings are important for wear prediction and surface quality control in the grinding process.
INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Qiujie Li, Yuxi Xue
Summary: Variable-rate spraying methods using sensors have been proposed to solve the problems of pesticide waste and environmental pollution caused by traditional spraying methods. A new method based on total grid area (TGA) measured from LiDAR sensor echoes is proposed for estimating the total leaf area (TLA) of individual tree canopies. Experimental results show that the proposed method can effectively eliminate the effects of different LiDAR moving speeds and ranging distances during TLA measurements, providing a more accurate assessment.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2023)
Article
Computer Science, Interdisciplinary Applications
Zhaoyuan Wang, Frederick Stern
Summary: A geometric VOF method is implemented on static/dynamic overset grids using a new VOF interpolation algorithm. The interface is reconstructed in the fringe cells of the overset grids, and the VOF value is calculated based on the reconstructed interface. Gravity and surface tension forces are implemented using a VOF based ghost fluid method. Numerical tests and application examples demonstrate the capability and superiority of the VOF based numerical methods for predicting violent ship flows.
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS
(2022)
Article
Engineering, Mechanical
A. Jawaid, J. Seewig
Summary: Surface roughness is important in fluid dynamics and contact mechanics, and its evaluation often requires real-world or numerical experiments. This paper proposes a novel approach to simulate rough surfaces using Gaussian processes (GPs) and a noise model, allowing for a wider range of simulations compared to traditional methods. The paper introduces the theoretical similarities between GPs and auto-regressive moving-average processes, and demonstrates the use of the proposed method in modeling turned profiles and inherently periodic surfaces.
SURFACE TOPOGRAPHY-METROLOGY AND PROPERTIES
(2023)
Article
Multidisciplinary Sciences
Valeriy G. Narushin, Michael N. Romanov, Birendra Mishra, Darren K. Griffin
Summary: The development of nondestructive techniques for estimating egg parameters requires a comprehensive approach based on mathematical theory. In this study, appropriate formulae were derived for calculating the parameters of pear-shaped eggs and other naturally occurring avian egg shapes.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
H. B. Mihiri Shashikala, Arghya Chakravorty, Shailesh Kumar Panday, Emil Alexov
Summary: Ions play significant roles in biological processes, both specifically and non-specifically binding to proteins. Experimental determination of non-specifically bound ions can be challenging, but the BION-2 method provides a more accurate prediction of their positions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Gen Li, Shailesh Kumar Panday, Emil Alexov
Summary: SAAFEC-SEQ is a gradient boosting decision tree machine learning method for predicting the change of folding free energy caused by amino acid substitutions. It does not require the 3D structure of the corresponding protein, making it suitable for genome-scale investigations with sparse structural information.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Sheenam Khuttan, Solmaz Azimi, Joe Z. Wu, Emilio Gallicchio
Summary: The study introduces a family of alchemical perturbation potentials that can calculate hydration free energies of small to medium-sized molecules in a single step, instead of the usual two steps. By optimizing parameters and applying a novel soft-core function, rapid convergence of hydration free energy can be achieved in streamlined molecular dynamics simulation codes.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Joe Z. Wu, Solmaz Azimi, Sheenam Khuttan, Nanjie Deng, Emilio Gallicchio
Summary: The alchemical transfer method (ATM) is presented for calculating standard binding free energies of noncovalent molecular complexes, which is straightforward and applicable with any force field without requiring soft-core pair potentials. The method and its implementation have been validated on the SAMPL6 SAMPLing host-guest benchmark set.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Biochemical Research Methods
Gen Li, Shailesh Kumar Panday, Yunhui Peng, Emil Alexov
Summary: A new method named SAMPDI-3D has been developed to predict the change of protein-DNA binding free energy caused by mutations in both the binding protein and the bases of the corresponding DNA. Experimental results show that the method performs well in prediction and is fast, suitable for genome-scale investigations.
Article
Chemistry, Medicinal
Pierpaolo Cordone, Hari K. Namballa, Bryant Muniz, Rajat K. Pal, Emilio Gallicchio, Wayne W. Harding
Summary: In this study, the effect of rigidification of the n-butyl linker region of tetrahydroisoquinoline-containing D3R ligands by incorporating an o-xylenyl motif was investigated. Rigidification with an o-xylenyl linker group was found to decrease D3R affinity and impact selectivity versus D2R for compounds with a specific pharmacophore group, but high affinity D3R ligands with different primary pharmacophore groups were identified. The study also revealed that D3R selectivity versus sigma R-2 is influenced by the benzamide secondary pharmacophore group, particularly with 4-substituted benzamides, and identified specific compounds as high affinity D3R ligands.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Medicinal
Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu, Rajat K. Pal, Emilio Gallicchio
Summary: We propose an extension of the alchemical transfer method (ATM) called ATM-RBFE for estimating relative binding free energies of molecular complexes. The method is implemented in the OpenMM molecular simulation package and aims to provide a simpler and more generally applicable route to the calculation of relative binding free energies. The method is validated against benchmark sets and yields consistent and converged estimates in agreement with reference values and experimental measurements.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Solmaz Azimi, Joe Z. Wu, Sheenam Khuttan, Tom Kurtzman, Nanjie Deng, Emilio Gallicchio
Summary: Our participation in the SAMPL8 GDCC Blind Challenge for host-guest binding affinity predictions showed excellent quantitative agreement between two different binding free energy methods. The results were found to agree well with experimental binding affinities, demonstrating high quality and precision achieved by theory and methods.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Chemistry, Multidisciplinary
Shailesh Kumar Panday, Emil Alexov
Summary: A Gaussian-based method called f5-MM/PBSA/E is proposed for estimating protein-protein binding entropy to predict binding free energy. This method is computationally efficient and achieves similar or better performance compared to other computationally demanding approaches when tested on a dataset of 46 protein-protein binding cases.
Review
Biochemistry & Molecular Biology
Shengjie Sun, Pitambar Poudel, Emil Alexov, Lin Li
Summary: This review summarizes the role of electrostatics in computational molecular biophysics and its contribution to disease mechanisms. Electrostatic interactions play a complex role in molecular biophysics, dominating over other forces at long distances and also having pronounced effects on short-range interactions. Disruption of the electrostatic network may abolish wild-type functionality and be a dominant factor in pathogenicity. However, the plasticity of biological macromolecules may reduce the impact of amino acid mutation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Arghya Chakravorty, Samuel D. McCalpin, Bikash R. Sahoo, Ayyalusamy Ramamoorthy, Charles L. Brooks III
Summary: This study investigates the effects of neuronal ganglioside GM1 on the aggregation of Afi40 and Afi42 using experiments and simulations. The simulations show that GM1 forms stable complexes with both isoforms, and experiments support the formation of well-ordered GM1+Afi complexes. Furthermore, the study explains the binding preferences of Afi40 and Afi42 monomers to GM1-containing oligomers.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Preeti Pandey, Sanjeev Ghimire, Bohua Wu, Emil Alexov
Summary: This review provides an overview of how disease-causing mutations affect the thermodynamics of proteins. It focuses on the folding and binding free energy changes, which are crucial for structural integrity. The review highlights that complex diseases may result from mutations in multiple genes, while monogenic diseases are caused by mutations in a single gene. However, in both cases, pathogenic mutations have a greater impact on the thermodynamics compared to benign mutations. Recent studies investigating the effect of pathogenic mutations on thermodynamics, as well as structural dynamics and allosteric pathways, are discussed in the review.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Medicinal
Francesc Sabanes Zariquiey, Adria Perez, Maciej Majewski, Emilio Gallicchio, Gianni De Fabritiis
Summary: This study evaluates a relative binding free energy calculation method based on the alchemical transfer method (ATM). The results show that ATM is competitive in terms of speed and accuracy compared to traditional methods and can be applied with any potential energy function.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Joshua Buckner, Xiaorong Liu, Arghya Chakravorty, Yujin Wu, Luis F. F. Cervantes, Thanh T. T. Lai, Charles L. L. Brooks
Summary: CHARMM is a powerful program for molecular dynamics and modeling of biological macromolecules and their partners, with a wide range of methodology and functionality. The introduction of pyCHARMM, which includes Python bindings and modules, enhances access to CHARMM functionality and allows for the integration of additional tools and methods. This platform not only provides advanced modeling capabilities, but also facilitates the learning of molecular modeling methods and practices within a Python-friendly environment.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Preeti Pandey, Shailesh Kumar Panday, Prawin Rimal, Nicolas Ancona, Emil Alexov
Summary: The development of methods and algorithms for predicting the effect of mutations on protein stability and interactions is necessary for protein engineering and understanding disease mechanisms. However, most methods require training on databases that may not accurately represent the mutations seen in the human population. These methods also underestimate the energy changes and are sensitive to the chemical nature of the mutations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Michal Novotny, Matus Dubecky, Frantisek Karlicky
Summary: This paper investigates the accuracy of different DFT-based computational approaches in calculating the equilibrium lattice constants and exfoliation energy of hexagonal boron nitride (h-BN). The results are compared with experiments and reference QMC calculations to evaluate the accuracy of these computational methods.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Luigi Crisci, Federico Coppola, Alessio Petrone, Nadia Rega
Summary: The charge transfer dynamics in asymmetrically substituted indenotetracene molecules upon photo-excitation were investigated using real-time time-dependent density functional theory simulations. The study found that the electron-donating character of the substituents affects the overall electronic energy spacing and ultrafast charge transfer dynamics.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Vasilii Korotenko, Hendrik Zipse
Summary: The stability of various radicals and molecules has been studied using different theoretical methods, and good correlations between theoretical calculations and experimental results have been found. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have also been investigated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Oleg Egorov, Michael Rey, Dominika Viglaska, Andrei V. Nikitin
Summary: In this work, the rovibrational energy levels of four isotopologues of methylene were calculated using a new accurate ab initio potential energy surface. The accuracy of the calculations was improved by considering scalar relativistic effects, DBOC, and high-order electronic correlations. For the first time, all available experimental rovibrational transitions were reproduced with high accuracy, without any empirical corrections.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
