Chemical concepts such as structure,bonding,reactivity,etc.have been widely used in the literature and text books to appreciate molecular properties and chemical transformations.Even though modern theoretical and comp...Chemical concepts such as structure,bonding,reactivity,etc.have been widely used in the literature and text books to appreciate molecular properties and chemical transformations.Even though modern theoretical and computational chemistry is well established from the perspective of accuracy and complexity,how to quantify these concepts is a still unresolved task.Conceptual density functional theory and its related recent developments provide unique opportunities to tackle this problem.In this Special Issue,27 contributions from top investigators over the world are collected to highlight the state-of-art research on this topic,which not only showcases the status of where we are now but also unveils a number to possible future directions to be pursued.展开更多
The Hohenberg-Kohn theorem in density functional theory,as originally formulated,states that if an electron density,ρ_0(r),is the nondegenerate ground state density of an N-electron system with external potential v_0...The Hohenberg-Kohn theorem in density functional theory,as originally formulated,states that if an electron density,ρ_0(r),is the nondegenerate ground state density of an N-electron system with external potential v_0(r),where N is a展开更多
A novel satellite technique for air temperature mapping with a spatial resolution of~100 m was proposed for the town of Apatity,the Kola Peninsula(Russia),taken as a case study.The main idea behind this novel techniqu...A novel satellite technique for air temperature mapping with a spatial resolution of~100 m was proposed for the town of Apatity,the Kola Peninsula(Russia),taken as a case study.The main idea behind this novel technique is to find the statistical relationships between the land surface temperatures in each point of the study area,observed by multiple infrared thermal satellite imagery,and the time series of air temperatures recorded by World Meteorological Organization(WMO)weather station.Fourteen scenes of infrared thermal spectral band of the Landsat satellites for the period 2014–2019 were used,as well as the long-term time series of air temperature from the weather station and the results of air temperature observations carried out by the network of loggers.For calm weather conditions,according to the ground truth,the error of air temperature mapping wasσ=1.5°C,and the precision was estimated asδ=1.0°C.An analysis of the compiled air temperature map showed that,under polar night conditions,the air temperature on the hilltops was by 10–18°C higher than in the lowlands.It was concluded that,for economic reasons,as well as for the reasons of population health protection in the Arctic,it would be advisable to plan the placement of new cities on the hills.Each of these new areas should be designed in a“semi-isolated”manner in order to minimize the time needed by the local people for crossing the lowlands between the nearby districts.A characteristic feature of modern megalopolises is their internal structure formed by the growing primary settlements that can be considered as nuclei interlinked by transportation routes.Thus,the new Arctic cities can be called“Arctic megalopolises”because of their internal structure that is specific to megalopolises.展开更多
Several decades ago Ghosh,Berkowitz and Parr^1 rewrote the ground-state density functional theory(DFT)into a local thermodynamics.They obtained a phase–space
The martensitic-type phase transformation paths from the rutile to theα-PbO2 phase of TiO2 are studied with linear interpolation and NEB/G-SSNEB methods based on first-principles calculations.Its potential energy sur...The martensitic-type phase transformation paths from the rutile to theα-PbO2 phase of TiO2 are studied with linear interpolation and NEB/G-SSNEB methods based on first-principles calculations.Its potential energy surface and the lowest energy path are revealed.Our results indicate that the titanium atoms of the rutile phase shuffle along the[0-11]rut crystal direction to form theα-PbO2 phase.During the phase transition,the oxygen atoms are dragged by the heavier titanium atoms and then reach their new equilibrium positions.The barrier of phase transition from nudged elastic band theory is about 231 meV,which is qualitatively consistent with previous theoretical calculations from the monoclinic phase to the tetragonal phase for ZrO2 and HfO2.Debye model can also be successfully used to predict the pressure and temperature of the phase transformation.展开更多
An approach for studying the influence of nano-particles on the structural properties of deposited thin films is proposed. It is based on the molecular dynamic modeling of the deposition process in the presence of con...An approach for studying the influence of nano-particles on the structural properties of deposited thin films is proposed. It is based on the molecular dynamic modeling of the deposition process in the presence of contaminating nano-particles. The nano-particle is assumed to be immobile and its interaction with film atoms is described by a spherically symmetric potential. The approach is applied to the investigation of properties of silicon dioxide films. Visualization tools are used to investigate the porosity associated with nano-particles. The structure of the film near the nano-particle is studied using the radial distribution function. It is found that fluctuations of film density near the nano-particles are essentially different in the cases of low-energy and high-energy deposition processes.展开更多
Quantitative correlation of several theoretical electrophilicity measures over different families of organic compounds are examined relative to the experimental values of Mayr et al.Notably,the ability to predict thes...Quantitative correlation of several theoretical electrophilicity measures over different families of organic compounds are examined relative to the experimental values of Mayr et al.Notably,the ability to predict these values accurately will help to elucidate the reactivity and selectivity trends observed in charge-transfer reactions.A crucial advantage of this theoretical approach is that itprovides this information without the need of experiments,which are often demanding and time-consuming.Here,two different types of electrophilicity measures were analyzed.First,models derived from conceptual density functional theory(c-DFT),including Parr's original proposal and further generalizations of this index,are investigated.For instance,the approaches of Gázquez et al.and Chamorro et al.are considered,whereby it is possible to distinguish between processes in which a molecule gains or loses electrons.Further,we also explored two novel electrophilicity definitions.On one hand,the potential of environmental perturbations to affect electron incorporation into a system is analyzed in terms of recent developments in c-DFT.These studies highlight the importance of considering the molecular surroundings when a consistent description of chemical reactivity is needed.On the other hand,we test a new definition of electrophilicity that is free from inconsistencies(so-called thermodynamic electrophilicity).This approach is based on Parr's pioneering insights,though it corrects issues present in the standard working expression for the calculation of electrophilicity.Additionally,we use machine-learning tools(i.e.,symbolic regression)to identify the models that best fit the experimental values.In this way,the best possible description of the electrophilicity values in terms of different electronic structure quantities is obtained.Overall,this straightforward approach enables one to obtain good correlations between the theoretical and experimental quantities by using the simple,yet powerful,interpretative advantage of c-DFT methods.In general,we observed that the correlations found at the HF/6-31 G(d)level of theory are of semi-quantitative value.To obtain more accurate results,we showed that working with families of compounds with similar functional groups is indispensable.展开更多
With the increased frequency of natural hazards and disasters and consequent losses,it is imperative to develop efficient and timely strategies for emergency response and relief operations.In this paper,we propose a c...With the increased frequency of natural hazards and disasters and consequent losses,it is imperative to develop efficient and timely strategies for emergency response and relief operations.In this paper,we propose a cyberGIS-enabled multi-criteria spatial decision support system for supporting rapid decision making during emergency management.It combines a high-performance computing environment(cyberGIS-Jupyter)and multi-criteria decision analysis models(Weighted Sum Model(WSM)and Technique for Order Preference by Similarity to Ideal Solution Model(TOPSIS))with various types of social vulnerability indicators to solve decision problems that contain conflicting evaluation criteria in a flood emergency situation.Social media data(e.g.Twitter data)was used as an additional tool to support the decision-making process.Our case study involves two decision goals generated based on a past flood event in the city of Austin,Texas,U.S.A.As our result shows,WSM produces more diverse values and higher output category estimations than the TOPSIS model.Finally,the model was validated using an innovative questionnaire.This cyberGIS-enabled spatial decision support system allows collaborative problem solving and efficient knowledge transformation between decision makers,where different emergency responders can formulate their decision objectives,select relevant evaluation criteria,and perform interactive weighting and sensitivity analyses.展开更多
Molecular simulations are an important tool for research in physics,chemistry,and biology.The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that pe...Molecular simulations are an important tool for research in physics,chemistry,and biology.The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes.In this sense,software that can be seamlessly adapted to a broad range of complex systems is essential.Building on past efforts to provide open-source community-supported software for advanced sampling,we introduce PySAGES,a Python implementation of the Software Suite for Advanced General Ensemble Simulations(SSAGES)that provides full GPU support for massively parallel applications of enhanced sampling methods such as adaptive biasing forces,harmonic bias,or forward flux sampling in the context of molecular dynamics simulations.By providing an intuitive interface that facilitates the management of a system’s configuration,the inclusion of new collective variables,and the implementation of sophisticated free energy-based sampling methods,the PySAGES library serves as a general platform for the development and implementation of emerging simulation techniques.The capabilities,core features,and computational performance of this tool are demonstrated with clear and concise examples pertaining to different classes of molecular systems.We anticipate that PySAGES will provide the scientific community with a robust and easily accessible platform to accelerate simulations,improve sampling,and enable facile estimation of free energies for a wide range of materials and processes.展开更多
基金supported by the National Natural Science Foundation of China(21503076)Aid Program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province,China(Xiang Jiao Tong[2012]318)~~
基金supported by the Aid Program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province,China(Xiang Tong Jiao[2012]318)Hunan Provincial Natural Science Foundation,China(12JJ2029)+2 种基金Aid Program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province,China(12K030)Scientific Research Fund of Changde Municipal Science and Technology Bureau,Hunan Province,China(2014JF15)Provincial Science and Technology Project,China(2013FJ4220)~~
基金supported by the‘XiaoXiang Scholar’Talents Foundation of Hunan Normal University,China (23040609)Hunan Provincial Innovation Foundation for Postgraduate,China (CX2012B223)+1 种基金Aid Program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province,ChinaThe Hundred Talents Foundation of Hunan Province is gratefully acknowledged for the financial support to S. J. and S. R. K.~~
基金‘XiaoXiang Scholar’Talents Foundation of Hunan Normal University,China(23040609)Hunan Provincial Innovation Foundation for Postgraduate,China(CX2012B223)Aid Program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province,China~~
基金We are immensely indebted to the Editor-in-Chief as well as the entire crew of the Editorial Office of Acta Physico-Chimica Sinica for making the Special Issue possible. I am in particular grateful to Dr. Xiaojuan Zhang, the Managing Editor, and Dr. Ying
文摘Chemical concepts such as structure,bonding,reactivity,etc.have been widely used in the literature and text books to appreciate molecular properties and chemical transformations.Even though modern theoretical and computational chemistry is well established from the perspective of accuracy and complexity,how to quantify these concepts is a still unresolved task.Conceptual density functional theory and its related recent developments provide unique opportunities to tackle this problem.In this Special Issue,27 contributions from top investigators over the world are collected to highlight the state-of-art research on this topic,which not only showcases the status of where we are now but also unveils a number to possible future directions to be pursued.
文摘The Hohenberg-Kohn theorem in density functional theory,as originally formulated,states that if an electron density,ρ_0(r),is the nondegenerate ground state density of an N-electron system with external potential v_0(r),where N is a
基金supported by SRCES RAS,by the project TRAKT 2018,by Belmont Forum project SERUS,and RFBR project no.20-55-71004Pre-processing of in-situ observations in Apatity performed by Mikhail Varentsov and Pavel Konstantinov was supported by Russian Science Foundation,project no.19-05-50112Results of this research are promoted through the activities of the PanEurasian EXperiment(PEEX)programme.We are grateful to Dr.Igor Esau for insightful discussions.
文摘A novel satellite technique for air temperature mapping with a spatial resolution of~100 m was proposed for the town of Apatity,the Kola Peninsula(Russia),taken as a case study.The main idea behind this novel technique is to find the statistical relationships between the land surface temperatures in each point of the study area,observed by multiple infrared thermal satellite imagery,and the time series of air temperatures recorded by World Meteorological Organization(WMO)weather station.Fourteen scenes of infrared thermal spectral band of the Landsat satellites for the period 2014–2019 were used,as well as the long-term time series of air temperature from the weather station and the results of air temperature observations carried out by the network of loggers.For calm weather conditions,according to the ground truth,the error of air temperature mapping wasσ=1.5°C,and the precision was estimated asδ=1.0°C.An analysis of the compiled air temperature map showed that,under polar night conditions,the air temperature on the hilltops was by 10–18°C higher than in the lowlands.It was concluded that,for economic reasons,as well as for the reasons of population health protection in the Arctic,it would be advisable to plan the placement of new cities on the hills.Each of these new areas should be designed in a“semi-isolated”manner in order to minimize the time needed by the local people for crossing the lowlands between the nearby districts.A characteristic feature of modern megalopolises is their internal structure formed by the growing primary settlements that can be considered as nuclei interlinked by transportation routes.Thus,the new Arctic cities can be called“Arctic megalopolises”because of their internal structure that is specific to megalopolises.
文摘Several decades ago Ghosh,Berkowitz and Parr^1 rewrote the ground-state density functional theory(DFT)into a local thermodynamics.They obtained a phase–space
基金Project supported by the National Natural Science Foundation of China(Grant Nos.51872227,51572219,and 11447030).
文摘The martensitic-type phase transformation paths from the rutile to theα-PbO2 phase of TiO2 are studied with linear interpolation and NEB/G-SSNEB methods based on first-principles calculations.Its potential energy surface and the lowest energy path are revealed.Our results indicate that the titanium atoms of the rutile phase shuffle along the[0-11]rut crystal direction to form theα-PbO2 phase.During the phase transition,the oxygen atoms are dragged by the heavier titanium atoms and then reach their new equilibrium positions.The barrier of phase transition from nudged elastic band theory is about 231 meV,which is qualitatively consistent with previous theoretical calculations from the monoclinic phase to the tetragonal phase for ZrO2 and HfO2.Debye model can also be successfully used to predict the pressure and temperature of the phase transformation.
基金Supported by the RFBR under Grant No 17-57-53091the National Natural Science Foundation of China under Grant No11611530687
文摘An approach for studying the influence of nano-particles on the structural properties of deposited thin films is proposed. It is based on the molecular dynamic modeling of the deposition process in the presence of contaminating nano-particles. The nano-particle is assumed to be immobile and its interaction with film atoms is described by a spherically symmetric potential. The approach is applied to the investigation of properties of silicon dioxide films. Visualization tools are used to investigate the porosity associated with nano-particles. The structure of the film near the nano-particle is studied using the radial distribution function. It is found that fluctuations of film density near the nano-particles are essentially different in the cases of low-energy and high-energy deposition processes.
基金support by FONDECYT(1140313)Financiamiento Basal para Centros Cientificos y Tecnoldgicos de Excelencia-FB0807project RC-130006 CILLIS,Chile
文摘Quantitative correlation of several theoretical electrophilicity measures over different families of organic compounds are examined relative to the experimental values of Mayr et al.Notably,the ability to predict these values accurately will help to elucidate the reactivity and selectivity trends observed in charge-transfer reactions.A crucial advantage of this theoretical approach is that itprovides this information without the need of experiments,which are often demanding and time-consuming.Here,two different types of electrophilicity measures were analyzed.First,models derived from conceptual density functional theory(c-DFT),including Parr's original proposal and further generalizations of this index,are investigated.For instance,the approaches of Gázquez et al.and Chamorro et al.are considered,whereby it is possible to distinguish between processes in which a molecule gains or loses electrons.Further,we also explored two novel electrophilicity definitions.On one hand,the potential of environmental perturbations to affect electron incorporation into a system is analyzed in terms of recent developments in c-DFT.These studies highlight the importance of considering the molecular surroundings when a consistent description of chemical reactivity is needed.On the other hand,we test a new definition of electrophilicity that is free from inconsistencies(so-called thermodynamic electrophilicity).This approach is based on Parr's pioneering insights,though it corrects issues present in the standard working expression for the calculation of electrophilicity.Additionally,we use machine-learning tools(i.e.,symbolic regression)to identify the models that best fit the experimental values.In this way,the best possible description of the electrophilicity values in terms of different electronic structure quantities is obtained.Overall,this straightforward approach enables one to obtain good correlations between the theoretical and experimental quantities by using the simple,yet powerful,interpretative advantage of c-DFT methods.In general,we observed that the correlations found at the HF/6-31 G(d)level of theory are of semi-quantitative value.To obtain more accurate results,we showed that working with families of compounds with similar functional groups is indispensable.
基金supported by the U.S.National Science Foundation under[grant numbers:1047916,1429699,1443080,1551492,and 1664119].
文摘With the increased frequency of natural hazards and disasters and consequent losses,it is imperative to develop efficient and timely strategies for emergency response and relief operations.In this paper,we propose a cyberGIS-enabled multi-criteria spatial decision support system for supporting rapid decision making during emergency management.It combines a high-performance computing environment(cyberGIS-Jupyter)and multi-criteria decision analysis models(Weighted Sum Model(WSM)and Technique for Order Preference by Similarity to Ideal Solution Model(TOPSIS))with various types of social vulnerability indicators to solve decision problems that contain conflicting evaluation criteria in a flood emergency situation.Social media data(e.g.Twitter data)was used as an additional tool to support the decision-making process.Our case study involves two decision goals generated based on a past flood event in the city of Austin,Texas,U.S.A.As our result shows,WSM produces more diverse values and higher output category estimations than the TOPSIS model.Finally,the model was validated using an innovative questionnaire.This cyberGIS-enabled spatial decision support system allows collaborative problem solving and efficient knowledge transformation between decision makers,where different emergency responders can formulate their decision objectives,select relevant evaluation criteria,and perform interactive weighting and sensitivity analyses.
基金supported by the Department of Energy,Basic Energy Sciences,Materials Science and Engineering Division,through the Midwest Integrated Center for Computational Materials(MICCoM)supported by the Dutch Research Council(NWO Rubicon 019.202EN.028)supported by the U.S.Department of Energy,Office of Science,Office of Advanced Scientific Computing Research,Department of Energy Computational Science Graduate Fellowship under Award Number DE-SC0022158.
文摘Molecular simulations are an important tool for research in physics,chemistry,and biology.The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes.In this sense,software that can be seamlessly adapted to a broad range of complex systems is essential.Building on past efforts to provide open-source community-supported software for advanced sampling,we introduce PySAGES,a Python implementation of the Software Suite for Advanced General Ensemble Simulations(SSAGES)that provides full GPU support for massively parallel applications of enhanced sampling methods such as adaptive biasing forces,harmonic bias,or forward flux sampling in the context of molecular dynamics simulations.By providing an intuitive interface that facilitates the management of a system’s configuration,the inclusion of new collective variables,and the implementation of sophisticated free energy-based sampling methods,the PySAGES library serves as a general platform for the development and implementation of emerging simulation techniques.The capabilities,core features,and computational performance of this tool are demonstrated with clear and concise examples pertaining to different classes of molecular systems.We anticipate that PySAGES will provide the scientific community with a robust and easily accessible platform to accelerate simulations,improve sampling,and enable facile estimation of free energies for a wide range of materials and processes.
