Data assimilation(DA)and uncertainty quantification(UQ)are extensively used in analysing and reducing error propagation in high-dimensional spatial-temporal dynamics.Typical applications span from computational fluid ...Data assimilation(DA)and uncertainty quantification(UQ)are extensively used in analysing and reducing error propagation in high-dimensional spatial-temporal dynamics.Typical applications span from computational fluid dynamics(CFD)to geoscience and climate systems.Recently,much effort has been given in combining DA,UQ and machine learning(ML)techniques.These research efforts seek to address some critical challenges in high-dimensional dynamical systems,including but not limited to dynamical system identification,reduced order surrogate modelling,error covariance specification and model error correction.A large number of developed techniques and methodologies exhibit a broad applicability across numerous domains,resulting in the necessity for a comprehensive guide.This paper provides the first overview of state-of-the-art researches in this interdisciplinary field,covering a wide range of applications.This review is aimed at ML scientists who attempt to apply DA and UQ techniques to improve the accuracy and the interpretability of their models,but also at DA and UQ experts who intend to integrate cutting-edge ML approaches to their systems.Therefore,this article has a special focus on how ML methods can overcome the existing limits of DA and UQ,and vice versa.Some exciting perspectives of this rapidly developing research field are also discussed.Index Terms-Data assimilation(DA),deep learning,machine learning(ML),reduced-order-modelling,uncertainty quantification(UQ).展开更多
The Nordic countries have produced famous polar explorers and researchers who have generated climate research schools at a variety of locations. The dependence of these countries with respect to the lifelihood of thei...The Nordic countries have produced famous polar explorers and researchers who have generated climate research schools at a variety of locations. The dependence of these countries with respect to the lifelihood of their societies, of their use of lands and seas, the exploitation of marine living and non-living resources have made climate research an eminent topic, and many outstanding discoveries of longand short-term climate change have been made for the first time in Scandinavia. These include early contributions to our understanding of the geological effects of continent-wide glaciations during the ice ages, the complex postglacial history of the Baltic Sea and the varved sediment sequences preserved from lakes with an extraordinary seasonality in their sediment input, as well as the detailed records of temperature, ice texture and impurities and greenhouse gas variations of the last Glacial and of the Holocene preserved in the ice cores from Greenland. Iceland with its volcanic sequences and intercalated sediment layers not only preserved the history of this subaerial segment of the mid-Atlantic Ridge, but also easily datable paleoclimate records. The fate of the Vikings, who settled during the Medieval climate optimum on Iceland and later on Greenland and who lost their habitat on Greenland at the beginning of the Little Ice Age, illustrates vividly the climate-dependent subsistence of the indigenous and non-indigenous Scandinavian populations. Modern Scandinavian climate research institutions also include sophisticated modelling groups.展开更多
The single particle energies obtained in a Kohn-Sham density functional theory(DFT) calculation are generally known to be poor approximations to electron excitation energies that are measured in transport,tunneling an...The single particle energies obtained in a Kohn-Sham density functional theory(DFT) calculation are generally known to be poor approximations to electron excitation energies that are measured in transport,tunneling and spectroscopic experiments such as photo-emission spectroscopy. The correction to these energies can be obtained from the poles of a single particle Green's function derived from a many-body perturbation theory. From a computational perspective, the accuracy and efficiency of such an approach depends on how a self energy term that properly accounts for dynamic screening of electrons is approximated. The G_0W_0 approximation is a widely used technique in which the self energy is expressed as the convolution of a noninteracting Green's function(G_0) and a screened Coulomb interaction(W_0) in the frequency domain. The computational cost associated with such a convolution is high due to the high complexity of evaluating W_0 at multiple frequencies. In this paper, we discuss how the cost of G_0W_0 calculation can be reduced by constructing a low rank approximation to the frequency dependent part of W_0. In particular, we examine the effect of such a low rank approximation on the accuracy of the G_0W_0 approximation. We also discuss how the numerical convolution of G_0 and W_0 can be evaluated efficiently and accurately by using a contour deformation technique with an appropriate choice of the contour.展开更多
Three dimensional free-decaying MHD turbulence is simulated by lattice Boltzmann methods on a spatial grid of 80003 for low and high magnetic Prandtl number.It is verified that∇·B=0 is automatically maintained to...Three dimensional free-decaying MHD turbulence is simulated by lattice Boltzmann methods on a spatial grid of 80003 for low and high magnetic Prandtl number.It is verified that∇·B=0 is automatically maintained to machine accuracy throughout the simulation.Isosurfaces of vorticity and current show the persistence of many large scale structures(both magnetic and velocity)for long times—unlike the velocity isosurfaces of Navier-Stokes turbulence.展开更多
The Pan-Eurasian Experiment Modelling Platform(PEEX-MP)is one of the key blocks of the PEEX Research Programme.The PEEX MP has more than 30 models and is directed towards seamless envir-onmental prediction.The main fo...The Pan-Eurasian Experiment Modelling Platform(PEEX-MP)is one of the key blocks of the PEEX Research Programme.The PEEX MP has more than 30 models and is directed towards seamless envir-onmental prediction.The main focus area is the Arctic-boreal regions and China.The models used in PEEX-MP cover several main components of the Earth’s system,such as the atmosphere,hydrosphere,pedosphere and biosphere,and resolve the physicalchemicalbiological processes at different spatial and temporal scales and resolutions.This paper introduces and discusses PEEX MP multi-scale modelling concept for the Earth system,online integrated,forward/inverse,and socioeconomical modelling,and other approaches with a particular focus on applications in the PEEX geographical domain.The employed high-performance com-puting facilities,capabilities,and PEEX dataflow for modelling results are described.Several virtual research platforms(PEEXView,Virtual Research Environment,Web-based Atlas)for handling PEEX modelling and observational results are introduced.The over-all approach allows us to understand better physical-chemicalbiological processes,Earth’s system interactions and feedbacks and to provide valuable information for assessment studies on evaluating risks,impact,consequences,etc.for population,envir-onment and climate in the PEEX domain.This work was also one of the last projects of Prof.Sergej Zilitinkevich,who passed away on 15 February 2021.Since the finalization took time,the paper was actually submitted in 2023 and we could not argue that the final paper text was agreed with him.展开更多
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the...The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes.This was first demonstrated on biological samples a decade ago on the giant mimivirus.Since then,a large collaboration has been pushing the limit of the smallest sample that can be imaged.The ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of macromolecules.Here we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single proteins.From the pattern,it is possible to determine the approximate orientation of the protein.Our experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.展开更多
基金the support of the Leverhulme Centre for Wildfires,Environment and Society through the Leverhulme Trust(RC-2018-023)Sibo Cheng,César Quilodran-Casas,and Rossella Arcucci acknowledge the support of the PREMIERE project(EP/T000414/1)+5 种基金the support of EPSRC grant:PURIFY(EP/V000756/1)the Fundamental Research Funds for the Central Universitiesthe support of the SASIP project(353)funded by Schmidt Futures–a philanthropic initiative that seeks to improve societal outcomes through the development of emerging science and technologiesDFG for the Heisenberg Programm Award(JA 1077/4-1)the National Natural Science Foundation of China(61976120)the Natural Science Key Foundat ion of Jiangsu Education Department(21KJA510004)。
文摘Data assimilation(DA)and uncertainty quantification(UQ)are extensively used in analysing and reducing error propagation in high-dimensional spatial-temporal dynamics.Typical applications span from computational fluid dynamics(CFD)to geoscience and climate systems.Recently,much effort has been given in combining DA,UQ and machine learning(ML)techniques.These research efforts seek to address some critical challenges in high-dimensional dynamical systems,including but not limited to dynamical system identification,reduced order surrogate modelling,error covariance specification and model error correction.A large number of developed techniques and methodologies exhibit a broad applicability across numerous domains,resulting in the necessity for a comprehensive guide.This paper provides the first overview of state-of-the-art researches in this interdisciplinary field,covering a wide range of applications.This review is aimed at ML scientists who attempt to apply DA and UQ techniques to improve the accuracy and the interpretability of their models,but also at DA and UQ experts who intend to integrate cutting-edge ML approaches to their systems.Therefore,this article has a special focus on how ML methods can overcome the existing limits of DA and UQ,and vice versa.Some exciting perspectives of this rapidly developing research field are also discussed.Index Terms-Data assimilation(DA),deep learning,machine learning(ML),reduced-order-modelling,uncertainty quantification(UQ).
文摘The Nordic countries have produced famous polar explorers and researchers who have generated climate research schools at a variety of locations. The dependence of these countries with respect to the lifelihood of their societies, of their use of lands and seas, the exploitation of marine living and non-living resources have made climate research an eminent topic, and many outstanding discoveries of longand short-term climate change have been made for the first time in Scandinavia. These include early contributions to our understanding of the geological effects of continent-wide glaciations during the ice ages, the complex postglacial history of the Baltic Sea and the varved sediment sequences preserved from lakes with an extraordinary seasonality in their sediment input, as well as the detailed records of temperature, ice texture and impurities and greenhouse gas variations of the last Glacial and of the Holocene preserved in the ice cores from Greenland. Iceland with its volcanic sequences and intercalated sediment layers not only preserved the history of this subaerial segment of the mid-Atlantic Ridge, but also easily datable paleoclimate records. The fate of the Vikings, who settled during the Medieval climate optimum on Iceland and later on Greenland and who lost their habitat on Greenland at the beginning of the Little Ice Age, illustrates vividly the climate-dependent subsistence of the indigenous and non-indigenous Scandinavian populations. Modern Scandinavian climate research institutions also include sophisticated modelling groups.
基金supported by the SciD AC Program on Excited State Phenomena in Energy Materials funded by the US Department of Energy,Office of Basic Energy Sciences and of Advanced Scientific Computing Research at Lawrence Berkeley National Laboratory(Grant No.DE-AC02-05CH11231)the Center for Applied Mathematics for Energy Research Applications funded by US Department of Energy,Office of Science,Advanced Scientific Computing Research and Basic Energy Sciences,the Alfred P.Sloan FellowshipNational Natural Science Foundation of China(Grant No.11171232)
文摘The single particle energies obtained in a Kohn-Sham density functional theory(DFT) calculation are generally known to be poor approximations to electron excitation energies that are measured in transport,tunneling and spectroscopic experiments such as photo-emission spectroscopy. The correction to these energies can be obtained from the poles of a single particle Green's function derived from a many-body perturbation theory. From a computational perspective, the accuracy and efficiency of such an approach depends on how a self energy term that properly accounts for dynamic screening of electrons is approximated. The G_0W_0 approximation is a widely used technique in which the self energy is expressed as the convolution of a noninteracting Green's function(G_0) and a screened Coulomb interaction(W_0) in the frequency domain. The computational cost associated with such a convolution is high due to the high complexity of evaluating W_0 at multiple frequencies. In this paper, we discuss how the cost of G_0W_0 calculation can be reduced by constructing a low rank approximation to the frequency dependent part of W_0. In particular, we examine the effect of such a low rank approximation on the accuracy of the G_0W_0 approximation. We also discuss how the numerical convolution of G_0 and W_0 can be evaluated efficiently and accurately by using a contour deformation technique with an appropriate choice of the contour.
基金The authors were supported by grants from DoE,AFOSR and AFRL as well as the Director,Office of Science,Office of Advanced Scientific Computing Research,Department of Energy under Contract No.DE-AC02-05CH11231.
文摘Three dimensional free-decaying MHD turbulence is simulated by lattice Boltzmann methods on a spatial grid of 80003 for low and high magnetic Prandtl number.It is verified that∇·B=0 is automatically maintained to machine accuracy throughout the simulation.Isosurfaces of vorticity and current show the persistence of many large scale structures(both magnetic and velocity)for long times—unlike the velocity isosurfaces of Navier-Stokes turbulence.
基金the last projects of Prof.Sergej Zilitinkevich(1936-2021)The financial support was/is provided through multiple projects related to the Pan-Eurasian EXperiment(PEEX)programme including Academy of Finland projects-ClimEco(grant#314798/799)+6 种基金ACCC(grant#337549)HEATCOST(grant#334798)European Union’s Horizon 2020 Programme projects-iCUPE under ERA-PLANET(grant#689443),INTAROS(grant#727890),EXHAUSTION(grant#820655),CRiceS(grant#101003826),RI-URBANS(grant#101036245)Horizon Europe project FOCI(grant#101056783)Erasmus+Programme projects-ECOIMPACT(grant#561975-EPP-1-2015-1-FI-EPPKA2-CBHE-JP),ClimEd(grant#619285-EPP-1-2020-1-FIEPPKA2-CBHE-JP)The Norwegian Research Council INTPART educational and networking project(322317/H30):URban Sustainability in Action:Multi-disciplinary Approach through Jointly Organized Research schoolsand the EEA project(Contract No.2020TO01000219):Turbulent-resolving urban modelling of air quality and thermal comfort(TURBAN).
文摘The Pan-Eurasian Experiment Modelling Platform(PEEX-MP)is one of the key blocks of the PEEX Research Programme.The PEEX MP has more than 30 models and is directed towards seamless envir-onmental prediction.The main focus area is the Arctic-boreal regions and China.The models used in PEEX-MP cover several main components of the Earth’s system,such as the atmosphere,hydrosphere,pedosphere and biosphere,and resolve the physicalchemicalbiological processes at different spatial and temporal scales and resolutions.This paper introduces and discusses PEEX MP multi-scale modelling concept for the Earth system,online integrated,forward/inverse,and socioeconomical modelling,and other approaches with a particular focus on applications in the PEEX geographical domain.The employed high-performance com-puting facilities,capabilities,and PEEX dataflow for modelling results are described.Several virtual research platforms(PEEXView,Virtual Research Environment,Web-based Atlas)for handling PEEX modelling and observational results are introduced.The over-all approach allows us to understand better physical-chemicalbiological processes,Earth’s system interactions and feedbacks and to provide valuable information for assessment studies on evaluating risks,impact,consequences,etc.for population,envir-onment and climate in the PEEX domain.This work was also one of the last projects of Prof.Sergej Zilitinkevich,who passed away on 15 February 2021.Since the finalization took time,the paper was actually submitted in 2023 and we could not argue that the final paper text was agreed with him.
基金supported by the Universität Hamburg and DFG grant numbers(INST 152/772-1|152/774-1|152/775-1|152/776-1|152/777-1 FUGG)We acknowledge the support of funding from:Cluster of Excellence‘CUI:Advanced Imaging of Matter’of the Deutsche Forschungsgemeinschaft(DFG)-EXC 2056-project ID 390715994+7 种基金ERC-2013-CoG COMOTION 614507NFR 240770Fellowship from the Joachim Herz Stiftung(P.L.X.)P.L.X.and H.N.C.acknowledge support from the Human Frontiers Science Program(RGP0010/2017)J.H.acknowledges support from the European Development Fund:Structural dynamics of biomolecular systems(ELIBIO)(CZ.02.1.01/0.0/0.0/15_003/0000447)EMBO long-term fellowship(ALTF 356-2018)awarded to L.E.F.the Röntgen-Ångström Cluster(2015-06107 and 2019-06092)the Swedish Research Council(2017-05336,2018-00234 and 2019-03935)the Swedish Foundation for Strategic Research(ITM17-0455).
文摘The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes.This was first demonstrated on biological samples a decade ago on the giant mimivirus.Since then,a large collaboration has been pushing the limit of the smallest sample that can be imaged.The ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of macromolecules.Here we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single proteins.From the pattern,it is possible to determine the approximate orientation of the protein.Our experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.
