To dynamically update the shape of orebody according to the knowledge of a structural geologist’s insight,an approach of orebody implicit modeling from raw drillhole data using the generalized radial basis function i...To dynamically update the shape of orebody according to the knowledge of a structural geologist’s insight,an approach of orebody implicit modeling from raw drillhole data using the generalized radial basis function interpolant was presented.A variety of constraint rules,including geology trend line,geology constraint line,geology trend surface,geology constraint surface and anisotropy,which can be converted into interpolation constraints,were developed to dynamically control the geology trends.Combined with the interactive tools of constraint rules,this method can avoid the shortcomings of the explicit modeling method based on the contour stitching,such as poor model quality,and is difficult to update dynamically,and simplify the modeling process of orebody.The results of numerical experiments show that the 3D ore body model can be reconstructed quickly,accurately and dynamically by the implicit modeling method.展开更多
Surface-based geometric modeling has many advantages in terms of visualization and traditional subtractive manufacturing using computer-numerical-control cutting-machine tools.However,it is not an ideal solution for a...Surface-based geometric modeling has many advantages in terms of visualization and traditional subtractive manufacturing using computer-numerical-control cutting-machine tools.However,it is not an ideal solution for additive manufacturing because to digitally print a surface-represented geometric object using a certain additive manufacturing technology,the object has to be converted into a solid representation.However,converting a known surface-based geometric representation into a printable representation is essentially a redesign process,and this is especially the case,when its interior material structure needs to be considered.To specify a 3D geometric object that is ready to be digitally manufactured,its representation has to be in a certain volumetric form.In this research,we show how some of the difficulties experienced in additive manufacturing can be easily solved by using implicitly represented geometric objects.Like surface-based geometric representation is subtractive manufacturing-friendly,implicitly described geometric objects are additive manufacturing-friendly:implicit shapes are 3D printing ready.The implicit geometric representation allows to combine a geometric shape,material colors,an interior material structure,and other required attributes in one single description as a set of implicit functions,and no conversion is needed.In addition,as implicit objects are typically specified procedurally,very little data is used in their specifications,which makes them particularly useful for design and visualization with modern cloud-based mobile devices,which usually do not have very big storage spaces.Finally,implicit modeling is a design procedure that is parallel computing-friendly,as the design of a complex geometric object can be divided into a set of simple shape-designing tasks,owing to the availability of shape-preserving implicit blending operations.展开更多
We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, a...We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide foldinz landscapes.展开更多
To enhance the stability of helicopter maneuvers during task execution,a composite trajectory tracking controller design based on the implicit model(IM)and linear active disturbance rejection control(LADRC)is proposed...To enhance the stability of helicopter maneuvers during task execution,a composite trajectory tracking controller design based on the implicit model(IM)and linear active disturbance rejection control(LADRC)is proposed.Initially,aerodynamic models of the main and tail rotor are created using the blade element theory and the uniform inflow assumption.Subsequently,a comprehensive flight dynamic model of the helicopter is established through fitting aerodynamic force fitting.Subsequently,for precise helicopter maneuvering,including the spiral,spiral up,and Ranversman maneuver,a regular trim is undertaken,followed by minor perturbation linearization at the trim point.Utilizing the linearized model,controllers are created for the IM attitude inner loop and LADRC position outer loop of the helicopter.Ultimately,a comparison is made between the maneuver trajectory tracking results of the IM‑LADRC and the conventional proportional-integral-derivative(PID)control method is performed.Experimental results demonstrate that utilizing the post-trim minor perturbation linearized model in combination with the IM‑LADRC method can achieve higher precision in tracking results,thus enhancing the accuracy of helicopter maneuver execution.展开更多
Accurate three-dimensional （3D） target positioning is of great importance in many industrial applications. Although various methods for reconstructing 3D information from a set of images have been available in the l...Accurate three-dimensional （3D） target positioning is of great importance in many industrial applications. Although various methods for reconstructing 3D information from a set of images have been available in the literature, few of them pay enough attention to the indispensable procedures, such as target extraction from images and image correction having strong influences upon the 3D positioning accuracy. This article puts forward a high-precision ellipse center （target point） extraction method and a new image correction approach which has been integrated into the 3D reconstruction pipeline with a concise implicit model to accurately compensates for the image distortion. The methods are applied to a copyright-reserved close range photogrammetric system. Real measuring experiments and industrial applications have evidenced the proposed methods, which can significantly improve the 3D positioning accuracy.展开更多
Fast high-precision patient-specific vascular tissue and geometric structure reconstruction is an essential task for vascular tissue engineering and computer-aided minimally invasive vascular disease diagnosis and sur...Fast high-precision patient-specific vascular tissue and geometric structure reconstruction is an essential task for vascular tissue engineering and computer-aided minimally invasive vascular disease diagnosis and surgery.In this paper,we present an effective vascular geometry reconstruction technique by representing a highly complicated geometric structure of a vascular system as an implicit function.By implicit geometric modelling,we are able to reduce the complexity and level of difficulty of this geometric reconstruction task and turn it into a parallel process of reconstructing a set of simple short tubular-like vascular sections,thanks to the easy-blending nature of implicit geometries on combining implicitly modelled geometric forms.The basic idea behind our technique is to consider this extremely difficult task as a process of team exploration of an unknown environment like a cave.Based on this idea,we developed a parallel vascular modelling technique,called Skeleton Marching,for fast vascular geometric reconstruction.With the proposed technique,we first extract the vascular skeleton system from a given volumetric medical image.A set of sub-regions of a volumetric image containing a vascular segment is then identified by marching along the extracted skeleton tree.A localised segmentation method is then applied to each of these sub-image blocks to extract a point cloud from the surface of the short simple blood vessel segment contained in the image block.These small point clouds are then fitted with a set of implicit surfaces in a parallel manner.A high-precision geometric vascular tree is then reconstructed by blending together these simple tubular-shaped implicit surfaces using the shape-preserving blending operations.Experimental results show the time required for reconstructing a vascular system can be greatly reduced by the proposed parallel technique.展开更多
We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures,...We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.展开更多
In this work, an enhanced treatment of the solid boundaries is proposed for smoothed particle hydrodynamics with implicit time integration scheme （Implicit SPH）. Three types of virtual particles, i.e., boundary part...In this work, an enhanced treatment of the solid boundaries is proposed for smoothed particle hydrodynamics with implicit time integration scheme （Implicit SPH）. Three types of virtual particles, i.e., boundary particles, image particles and mirror particles, are used to impose boundary conditions. Boundary particles are fixed on the solid boundary, and each boundary particle is associated with two fixed image particles inside the fluid domain and two fixed mirror particles outside the fluid domain. The image particles take the flow properties through fluid particles with moving least squares （MLS） interpolation and the properties of mirror particles can be obtained by the corresponding image particles. A repulsive force is also applied for boundary particles to prevent fluid particles from unphysical penetra- tion through solid boundaries. The new boundary treatment method has been validated with five numerical examples. All the numerical results show that Implicit SPH with this new boundary-treatment method can obtain accurate results for non-Newtonian fluids as well as Newtonian fluids, and this method is suitable for complex solid boundaries and can be easily extended to 3D problems.展开更多
Graphene-based frameworks suffer from a low quantum capacitance due to graphene’s Dirac point at the Fermi level.This theoretical study investigated the effect structural defects,nitrogen and boron doping,and surface...Graphene-based frameworks suffer from a low quantum capacitance due to graphene’s Dirac point at the Fermi level.This theoretical study investigated the effect structural defects,nitrogen and boron doping,and surface epoxy/hydroxy groups have on the electronic structure and capacitance of graphene.Density functional theory calculations reveal that the lowest energy configurations for nitrogen or boron substitutional doping occur when the dopant atoms are segregated.This elucidates why the magnetic transition for nitrogen doping is experimentally only observed at higher doping levels.We also highlight that the lowest energy configuration for a single vacancy defect is magnetic.Joint density functional theory calculations show that the fixed band approximation becomes increasingly inaccurate for electrolytes with lower dielectric constants.The introduction of structural defects rather than nitrogen or boron substitutional doping,or the introduction of adatoms leads to the largest increase in density of states and capacitance around graphene’s Dirac point.However,the presence of adatoms or substitutional doping leads to a larger shift of the potential of zero charge away from graphene’s Dirac point.展开更多
An implicit solvent coarse-grained （CG） lipid model using three beads to reflect the basically molecular structure of two-tailed lipid is developed. In this model, the nonbonded interaction employs a variant MIE pot...An implicit solvent coarse-grained （CG） lipid model using three beads to reflect the basically molecular structure of two-tailed lipid is developed. In this model, the nonbonded interaction employs a variant MIE potential and the bonded interaction utilizes a Harmonic potential form. The CG force field parameters are achieved by matching the structural and mechan-ical properties of dipalmitoylphosphatidylcholine （DPPC） bilayers. The model successfully reproduces the formation of lipid bilayer from a random initial state and the spontaneous vesiculation of lipid bilayer from a disk-like structure. After that, the model is used to sys-tematically study the vesiculation processes of spherical and cylindrical lipid droplets. The results show that the present CG model can effectively simulate the formation and evolution of mesoscale complex vesicles.展开更多
This paper deals with the use of optimal control techniques in large-scale water distribution networks. According to the network characteristics and actual state of the water supply system in China, the implicit model...This paper deals with the use of optimal control techniques in large-scale water distribution networks. According to the network characteristics and actual state of the water supply system in China, the implicit model, which may be solved by utilizing the hierarchical optimization method, is established. In special, based on the analyses of the water supply system containing variable-speed pumps, a software tool has been developed successfully. The application of this model to the city of Shenyang (China) is compared to experiential strategy. The results of this study show that the developed model is a very promising optimization method to control the large-scale water supply systems.展开更多
Generally, predicting whether an item will be liked or disliked by active users, and how much an item will be liked, is a main task of collaborative filtering systems or recommender systems. Recently, predicting most ...Generally, predicting whether an item will be liked or disliked by active users, and how much an item will be liked, is a main task of collaborative filtering systems or recommender systems. Recently, predicting most likely bought items for a target user, which is a subproblem of the rank problem of collaborative filtering, became an important task in collaborative filtering. Traditionally, the prediction uses the user item co-occurrence data based on users' buying behaviors. However, it is challenging to achieve good prediction performance using traditional methods based on single domain information due to the extreme sparsity of the buying matrix. In this paper, we propose a novel method called the preference transfer model for effective cross-domain collaborative filtering. Based on the preference transfer model, a common basis item-factor matrix and different user-factor matrices are factorized.Each user-factor matrix can be viewed as user preference in terms of browsing behavior or buying behavior. Then,two factor-user matrices can be used to construct a so-called ‘preference dictionary' that can discover in advance the consistent preference of users, from their browsing behaviors to their buying behaviors. Experimental results demonstrate that the proposed preference transfer model outperforms the other methods on the Alibaba Tmall data set provided by the Alibaba Group.展开更多
We present a multi-level partition of unity algebraic set surfaces （MPU-APSS） for surface reconstruction which can be represented by either a projection or in an implicit form. An algebraic point set surface （APSS...We present a multi-level partition of unity algebraic set surfaces （MPU-APSS） for surface reconstruction which can be represented by either a projection or in an implicit form. An algebraic point set surface （APSS） defines a smooth surface from a set of unorganized points using local moving least-squares （MLS） fitting of algebraic spheres. However, due to the local nature, APSS does not work well for geometry editing and modeling. Instead, our method builds an implicit approximation function for the scattered point set based on the partition of unity approach. By using an octree subdivision strategy, we first adaptively construct local algebraic spheres for the point set, and then apply weighting functions to blend together these local shape functions. Finally, we compute an error-controlled approximation of the signed distance function from the surface. In addition, we present an efficient projection operator which makes our representation suitable for point set filtering and dynamic point resampling. We demonstrate the effectiveness of our unified approach for both surface reconstruction and geometry modeling such as surface completion.展开更多
It is now over half a century since Keulegan conducted his open channel flow experiments. Over the past decades, many empirical formulae were proposed based on his results, however, there is still not a combined expre...It is now over half a century since Keulegan conducted his open channel flow experiments. Over the past decades, many empirical formulae were proposed based on his results, however, there is still not a combined expression to describe the effects of friction over all hydraulic regions in open channel flows. Therefore, in this letter, based on the analysis of the implicit model and the logarithmic matching method, the results of Keulegan （for authentic experiment data are no longer available, here we adopt the analytical solutions given by Dou） are rescaled into one monotone curve by combining the Reynolds number and the relative roughness of the river bed. A united expression that could cover the entire turbulence regions and be validated with Dou＇s analytical solutions is suggested to estimate the friction factor throughout the turbulent region in open channel flows, with higher accuracy than that of the previous formulas.展开更多
This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity ...This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity will contain the solute and some explicit solvent molecules,and an intermediate buffer layer and an exterior layer contain the bulk solvent.A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer.The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion.Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions.Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects.In particular,the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent.Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.展开更多
A popular explicit analytic Borowy 2C PV module model is proposed for power generation prediction.The maximum power point and the open-circuit point which are calculated in this model cannot be equal to the data given...A popular explicit analytic Borowy 2C PV module model is proposed for power generation prediction.The maximum power point and the open-circuit point which are calculated in this model cannot be equal to the data given by manufacturers under standard test condition(STC).The derivation of this model has never been mentioned in any literatures.The parameter forms of 2C model in this paper are more simplified,and the model is decomposed into a STC sub-model and an incremental sub-model.The STC model is derived successfully from an ideal single-diode circuit model.Relative error estimations are developed to do the conformity error measurements.The analysis results showed that though the biases at those critical points are very small,the conformity will depend on both of the two ratio values I_(m)/I_(sc) and V_(m)/V_(oc),which can be used to verify whether 2C model is applicable for the PV module produced by a particular manufacturer.展开更多
We review in this article our recent simulation works on modeling peptide T-jump and thermal unfolding Fourier transform infrared spectroscopy(FTIR) and two-dimensional infrared(2DIR) spectra. The theoretical and comp...We review in this article our recent simulation works on modeling peptide T-jump and thermal unfolding Fourier transform infrared spectroscopy(FTIR) and two-dimensional infrared(2DIR) spectra. The theoretical and computational techniques used,including Markov state model(MSM), integrated tempering sampling(ITS) and nonlinear exciton propagation(NEP), are first briefly introduced. The protocols for simulating the thermal unfolding as well as T-jump unfolding are then summarized in details. The simulated spectral features, such as the intensity and ellipticity, are demonstrated to agree well with the experimental observations.展开更多
Electrochemical NO reduction reaction(NORR)to NH3 emerges as a fascinating approach to achieve both the migration of NO pollutant and the green synthesis of NH3.In this contribution,within the framework of computation...Electrochemical NO reduction reaction(NORR)to NH3 emerges as a fascinating approach to achieve both the migration of NO pollutant and the green synthesis of NH3.In this contribution,within the framework of computational hydrogen model and constant-potential implicit solvent model,the NORR electrocatalyzed by a novel transition-metal-anchored SnOSe armchair nanotube(TM@SnOSe_ANT)was investigated using density functional theory calculations.Through the checking in terms of stability,activity,and selectivity,Sc-and Y@SnOSe_ANTs were screened out from the twenty-five candidates.Considering the effects of pH,solvent environment,as well as applied potential,only Sc@SnOSe_ANT is found to be most promising.The predicted surface area normalized capacitance is 11.4μF/cm^(2),and the highest NORR performance can be achieved at the U_(RHE) of-0.58 V in the acid environment.The high activity originates from the mediate adsorption strength of OH.These findings add a new perspective that the nanotube can be served as a highly promising electrocatalyst towards NORR.展开更多
文摘To dynamically update the shape of orebody according to the knowledge of a structural geologist’s insight,an approach of orebody implicit modeling from raw drillhole data using the generalized radial basis function interpolant was presented.A variety of constraint rules,including geology trend line,geology constraint line,geology trend surface,geology constraint surface and anisotropy,which can be converted into interpolation constraints,were developed to dynamically control the geology trends.Combined with the interactive tools of constraint rules,this method can avoid the shortcomings of the explicit modeling method based on the contour stitching,such as poor model quality,and is difficult to update dynamically,and simplify the modeling process of orebody.The results of numerical experiments show that the 3D ore body model can be reconstructed quickly,accurately and dynamically by the implicit modeling method.
基金supported by the National Natural Science Foundation of China(Grant No.61502402 and 61379080)the Natural Science Foundation of Fujian Province of China(Grant No.2015J05129).
文摘Surface-based geometric modeling has many advantages in terms of visualization and traditional subtractive manufacturing using computer-numerical-control cutting-machine tools.However,it is not an ideal solution for additive manufacturing because to digitally print a surface-represented geometric object using a certain additive manufacturing technology,the object has to be converted into a solid representation.However,converting a known surface-based geometric representation into a printable representation is essentially a redesign process,and this is especially the case,when its interior material structure needs to be considered.To specify a 3D geometric object that is ready to be digitally manufactured,its representation has to be in a certain volumetric form.In this research,we show how some of the difficulties experienced in additive manufacturing can be easily solved by using implicitly represented geometric objects.Like surface-based geometric representation is subtractive manufacturing-friendly,implicitly described geometric objects are additive manufacturing-friendly:implicit shapes are 3D printing ready.The implicit geometric representation allows to combine a geometric shape,material colors,an interior material structure,and other required attributes in one single description as a set of implicit functions,and no conversion is needed.In addition,as implicit objects are typically specified procedurally,very little data is used in their specifications,which makes them particularly useful for design and visualization with modern cloud-based mobile devices,which usually do not have very big storage spaces.Finally,implicit modeling is a design procedure that is parallel computing-friendly,as the design of a complex geometric object can be divided into a set of simple shape-designing tasks,owing to the availability of shape-preserving implicit blending operations.
基金supported by the National Natural Science Foundation of China(Grant No.21203178)the National Natural Science Foundation of China(Grant No.21373201)+2 种基金the National Natural Science Foundation of China(Grant No.21433014)the Science and Technological Ministry of China(Grant No.2011YQ09000505)“Strategic Priority Research Program”of the Chinese Academy of Sciences(Grant Nos.XDB10040304 and XDB100202002)
文摘We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide foldinz landscapes.
基金supported in part by the National Natural Science Foundation of China(No.12032012)the Key Discipline Construction Project of Colleges and Universities in Jiangsu Province.
文摘To enhance the stability of helicopter maneuvers during task execution,a composite trajectory tracking controller design based on the implicit model(IM)and linear active disturbance rejection control(LADRC)is proposed.Initially,aerodynamic models of the main and tail rotor are created using the blade element theory and the uniform inflow assumption.Subsequently,a comprehensive flight dynamic model of the helicopter is established through fitting aerodynamic force fitting.Subsequently,for precise helicopter maneuvering,including the spiral,spiral up,and Ranversman maneuver,a regular trim is undertaken,followed by minor perturbation linearization at the trim point.Utilizing the linearized model,controllers are created for the IM attitude inner loop and LADRC position outer loop of the helicopter.Ultimately,a comparison is made between the maneuver trajectory tracking results of the IM‑LADRC and the conventional proportional-integral-derivative(PID)control method is performed.Experimental results demonstrate that utilizing the post-trim minor perturbation linearized model in combination with the IM‑LADRC method can achieve higher precision in tracking results,thus enhancing the accuracy of helicopter maneuver execution.
基金National Natural Science Foundation of China （50875 130） Doctoral Discipline Foundation of China （200802870016） Science Foundation of Jiangsu, China （BE2008136）
文摘Accurate three-dimensional （3D） target positioning is of great importance in many industrial applications. Although various methods for reconstructing 3D information from a set of images have been available in the literature, few of them pay enough attention to the indispensable procedures, such as target extraction from images and image correction having strong influences upon the 3D positioning accuracy. This article puts forward a high-precision ellipse center （target point） extraction method and a new image correction approach which has been integrated into the 3D reconstruction pipeline with a concise implicit model to accurately compensates for the image distortion. The methods are applied to a copyright-reserved close range photogrammetric system. Real measuring experiments and industrial applications have evidenced the proposed methods, which can significantly improve the 3D positioning accuracy.
基金partly supported by National Natural Science Foundation of China (No. 61502402)the Fundamental Research Funds for the Central Universities (No. 20720180073)
文摘Fast high-precision patient-specific vascular tissue and geometric structure reconstruction is an essential task for vascular tissue engineering and computer-aided minimally invasive vascular disease diagnosis and surgery.In this paper,we present an effective vascular geometry reconstruction technique by representing a highly complicated geometric structure of a vascular system as an implicit function.By implicit geometric modelling,we are able to reduce the complexity and level of difficulty of this geometric reconstruction task and turn it into a parallel process of reconstructing a set of simple short tubular-like vascular sections,thanks to the easy-blending nature of implicit geometries on combining implicitly modelled geometric forms.The basic idea behind our technique is to consider this extremely difficult task as a process of team exploration of an unknown environment like a cave.Based on this idea,we developed a parallel vascular modelling technique,called Skeleton Marching,for fast vascular geometric reconstruction.With the proposed technique,we first extract the vascular skeleton system from a given volumetric medical image.A set of sub-regions of a volumetric image containing a vascular segment is then identified by marching along the extracted skeleton tree.A localised segmentation method is then applied to each of these sub-image blocks to extract a point cloud from the surface of the short simple blood vessel segment contained in the image block.These small point clouds are then fitted with a set of implicit surfaces in a parallel manner.A high-precision geometric vascular tree is then reconstructed by blending together these simple tubular-shaped implicit surfaces using the shape-preserving blending operations.Experimental results show the time required for reconstructing a vascular system can be greatly reduced by the proposed parallel technique.
基金Supported by the National Natural Science Foundation of China under Grant Nos 31200545,11274206 and 11574184
文摘We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.
基金supported by the National Natural Science Foundation of China(51276192)
文摘In this work, an enhanced treatment of the solid boundaries is proposed for smoothed particle hydrodynamics with implicit time integration scheme （Implicit SPH）. Three types of virtual particles, i.e., boundary particles, image particles and mirror particles, are used to impose boundary conditions. Boundary particles are fixed on the solid boundary, and each boundary particle is associated with two fixed image particles inside the fluid domain and two fixed mirror particles outside the fluid domain. The image particles take the flow properties through fluid particles with moving least squares （MLS） interpolation and the properties of mirror particles can be obtained by the corresponding image particles. A repulsive force is also applied for boundary particles to prevent fluid particles from unphysical penetra- tion through solid boundaries. The new boundary treatment method has been validated with five numerical examples. All the numerical results show that Implicit SPH with this new boundary-treatment method can obtain accurate results for non-Newtonian fluids as well as Newtonian fluids, and this method is suitable for complex solid boundaries and can be easily extended to 3D problems.
基金supported partially by JST SICORP(Grant No.JPMJSC2112)JST Adaptable and Seamless Technology Transfer Program through Target-driven R&D(A-STEP)(Grant No.JPMJTR22T6),and JSPS KAKENHI(Grant No.22K14757)+1 种基金Calculations were performed using the U.K.National Supercomputing Facility ARCHER2(http://www.archer2.ac.uk)via our membership of the U.K.’s HEC Materials Chemistry Consortium,which is funded by the EPSRC(Grant Nos.EP/L000202 and EP/R029431)the Molecular Modelling Hub for computational resources,MMM Hub,which is partially funded by EPSRC(Grant No.EP/P020194/1).This research has also utilized Queen Mary’s Apocrita HPC facility,supported by QMUL Research-IT.
文摘Graphene-based frameworks suffer from a low quantum capacitance due to graphene’s Dirac point at the Fermi level.This theoretical study investigated the effect structural defects,nitrogen and boron doping,and surface epoxy/hydroxy groups have on the electronic structure and capacitance of graphene.Density functional theory calculations reveal that the lowest energy configurations for nitrogen or boron substitutional doping occur when the dopant atoms are segregated.This elucidates why the magnetic transition for nitrogen doping is experimentally only observed at higher doping levels.We also highlight that the lowest energy configuration for a single vacancy defect is magnetic.Joint density functional theory calculations show that the fixed band approximation becomes increasingly inaccurate for electrolytes with lower dielectric constants.The introduction of structural defects rather than nitrogen or boron substitutional doping,or the introduction of adatoms leads to the largest increase in density of states and capacitance around graphene’s Dirac point.However,the presence of adatoms or substitutional doping leads to a larger shift of the potential of zero charge away from graphene’s Dirac point.
基金We thank Professor Dr. Markus Deserno （Department of Physics, Carnegie Mellon University）, Jemal Guven （Institute of Nuclear Science, Universidad Nacional Autonoma de Mexico）, and Zhan-chun Tu （Department of Physics, Beijing Normal University） for their valuable advice. This work is supported by the National Natural Science Foundation of China （No.20974078, No.21274107, and No.91127046）. The computation and simulation are partly carried out in High Performance Computing Center of Tianjin University.
文摘An implicit solvent coarse-grained （CG） lipid model using three beads to reflect the basically molecular structure of two-tailed lipid is developed. In this model, the nonbonded interaction employs a variant MIE potential and the bonded interaction utilizes a Harmonic potential form. The CG force field parameters are achieved by matching the structural and mechan-ical properties of dipalmitoylphosphatidylcholine （DPPC） bilayers. The model successfully reproduces the formation of lipid bilayer from a random initial state and the spontaneous vesiculation of lipid bilayer from a disk-like structure. After that, the model is used to sys-tematically study the vesiculation processes of spherical and cylindrical lipid droplets. The results show that the present CG model can effectively simulate the formation and evolution of mesoscale complex vesicles.
基金This work has been partly funded by the National Natural Science Foundation of China(No.50078048).
文摘This paper deals with the use of optimal control techniques in large-scale water distribution networks. According to the network characteristics and actual state of the water supply system in China, the implicit model, which may be solved by utilizing the hierarchical optimization method, is established. In special, based on the analyses of the water supply system containing variable-speed pumps, a software tool has been developed successfully. The application of this model to the city of Shenyang (China) is compared to experiential strategy. The results of this study show that the developed model is a very promising optimization method to control the large-scale water supply systems.
基金supported by the National Basic Research Program(973)of China(No.2012CB316400)the National Natural Science Foundation of China(No.61571393)
文摘Generally, predicting whether an item will be liked or disliked by active users, and how much an item will be liked, is a main task of collaborative filtering systems or recommender systems. Recently, predicting most likely bought items for a target user, which is a subproblem of the rank problem of collaborative filtering, became an important task in collaborative filtering. Traditionally, the prediction uses the user item co-occurrence data based on users' buying behaviors. However, it is challenging to achieve good prediction performance using traditional methods based on single domain information due to the extreme sparsity of the buying matrix. In this paper, we propose a novel method called the preference transfer model for effective cross-domain collaborative filtering. Based on the preference transfer model, a common basis item-factor matrix and different user-factor matrices are factorized.Each user-factor matrix can be viewed as user preference in terms of browsing behavior or buying behavior. Then,two factor-user matrices can be used to construct a so-called ‘preference dictionary' that can discover in advance the consistent preference of users, from their browsing behaviors to their buying behaviors. Experimental results demonstrate that the proposed preference transfer model outperforms the other methods on the Alibaba Tmall data set provided by the Alibaba Group.
基金supported by the National Natural Science Foundation of China under Grant Nos. 60803081,61070081the National High Technology Research and Development 863 Program of China under Grant No. 2008AA121603+1 种基金the Fundamental Research Funds for the Central Universities under Grant No. 6081005the National Research Foundation for the Doctoral Program of Higher Education of China under Grant No. 200804861038
文摘We present a multi-level partition of unity algebraic set surfaces （MPU-APSS） for surface reconstruction which can be represented by either a projection or in an implicit form. An algebraic point set surface （APSS） defines a smooth surface from a set of unorganized points using local moving least-squares （MLS） fitting of algebraic spheres. However, due to the local nature, APSS does not work well for geometry editing and modeling. Instead, our method builds an implicit approximation function for the scattered point set based on the partition of unity approach. By using an octree subdivision strategy, we first adaptively construct local algebraic spheres for the point set, and then apply weighting functions to blend together these local shape functions. Finally, we compute an error-controlled approximation of the signed distance function from the surface. In addition, we present an efficient projection operator which makes our representation suitable for point set filtering and dynamic point resampling. We demonstrate the effectiveness of our unified approach for both surface reconstruction and geometry modeling such as surface completion.
基金supported by the National Natural Science Foun-dation of China(Grant Nos.51479007,11172218 and 11372232)the Specialized Research Fund for the Doctoral Program of Higher Education(Grant No.20130141110016)
文摘It is now over half a century since Keulegan conducted his open channel flow experiments. Over the past decades, many empirical formulae were proposed based on his results, however, there is still not a combined expression to describe the effects of friction over all hydraulic regions in open channel flows. Therefore, in this letter, based on the analysis of the implicit model and the logarithmic matching method, the results of Keulegan （for authentic experiment data are no longer available, here we adopt the analytical solutions given by Dou） are rescaled into one monotone curve by combining the Reynolds number and the relative roughness of the river bed. A united expression that could cover the entire turbulence regions and be validated with Dou＇s analytical solutions is suggested to estimate the friction factor throughout the turbulent region in open channel flows, with higher accuracy than that of the previous formulas.
基金The authors would like to thank the financial support provided by the National Institutes of Health(Grant No.1R01GM083600-02)Z.Xu is also partially supported by the Charlotte Research Institute through a Duke Postdoctoral FellowshipW.Cai and Z.Xu are also partially supported by the Department of Energy(Grant No.DEFG0205ER25678).
文摘This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity will contain the solute and some explicit solvent molecules,and an intermediate buffer layer and an exterior layer contain the bulk solvent.A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer.The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion.Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions.Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects.In particular,the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent.Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.
基金This work was partially supported by Key Science,Technology Project of Zhejiang Province(LZ12E07001)National Natural Science Foundation of China(51307038).
文摘A popular explicit analytic Borowy 2C PV module model is proposed for power generation prediction.The maximum power point and the open-circuit point which are calculated in this model cannot be equal to the data given by manufacturers under standard test condition(STC).The derivation of this model has never been mentioned in any literatures.The parameter forms of 2C model in this paper are more simplified,and the model is decomposed into a STC sub-model and an incremental sub-model.The STC model is derived successfully from an ideal single-diode circuit model.Relative error estimations are developed to do the conformity error measurements.The analysis results showed that though the biases at those critical points are very small,the conformity will depend on both of the two ratio values I_(m)/I_(sc) and V_(m)/V_(oc),which can be used to verify whether 2C model is applicable for the PV module produced by a particular manufacturer.
基金supported by the National Natural Science Foundation of China(21373201,21433014)the“Strategic Priority Research Program”of the Chinese Academy of Sciences(XDB10040304,XDB20010000)
文摘We review in this article our recent simulation works on modeling peptide T-jump and thermal unfolding Fourier transform infrared spectroscopy(FTIR) and two-dimensional infrared(2DIR) spectra. The theoretical and computational techniques used,including Markov state model(MSM), integrated tempering sampling(ITS) and nonlinear exciton propagation(NEP), are first briefly introduced. The protocols for simulating the thermal unfolding as well as T-jump unfolding are then summarized in details. The simulated spectral features, such as the intensity and ellipticity, are demonstrated to agree well with the experimental observations.
基金This study was supported by the National Natural Science Foundation of China(No.21573002)Natural Science Funds for Distinguished Young Scholar of Anhui Province(No.1908085J08)the University Annual Scientific Research Plan of Anhui Province(Nos.2022AH050209 and 2022AH010013).
文摘Electrochemical NO reduction reaction(NORR)to NH3 emerges as a fascinating approach to achieve both the migration of NO pollutant and the green synthesis of NH3.In this contribution,within the framework of computational hydrogen model and constant-potential implicit solvent model,the NORR electrocatalyzed by a novel transition-metal-anchored SnOSe armchair nanotube(TM@SnOSe_ANT)was investigated using density functional theory calculations.Through the checking in terms of stability,activity,and selectivity,Sc-and Y@SnOSe_ANTs were screened out from the twenty-five candidates.Considering the effects of pH,solvent environment,as well as applied potential,only Sc@SnOSe_ANT is found to be most promising.The predicted surface area normalized capacitance is 11.4μF/cm^(2),and the highest NORR performance can be achieved at the U_(RHE) of-0.58 V in the acid environment.The high activity originates from the mediate adsorption strength of OH.These findings add a new perspective that the nanotube can be served as a highly promising electrocatalyst towards NORR.
