Transformer models have emerged as pivotal tools within the realm of drug discovery,distinguished by their unique architectural features and exceptional performance in managing intricate data landscapes.Leveraging the...Transformer models have emerged as pivotal tools within the realm of drug discovery,distinguished by their unique architectural features and exceptional performance in managing intricate data landscapes.Leveraging the innate capabilities of transformer architectures to comprehend intricate hierarchical dependencies inherent in sequential data,these models showcase remarkable efficacy across various tasks,including new drug design and drug target identification.The adaptability of pre-trained trans-former-based models renders them indispensable assets for driving data-centric advancements in drug discovery,chemistry,and biology,furnishing a robust framework that expedites innovation and dis-covery within these domains.Beyond their technical prowess,the success of transformer-based models in drug discovery,chemistry,and biology extends to their interdisciplinary potential,seamlessly combining biological,physical,chemical,and pharmacological insights to bridge gaps across diverse disciplines.This integrative approach not only enhances the depth and breadth of research endeavors but also fosters synergistic collaborations and exchange of ideas among disparate fields.In our review,we elucidate the myriad applications of transformers in drug discovery,as well as chemistry and biology,spanning from protein design and protein engineering,to molecular dynamics(MD),drug target iden-tification,transformer-enabled drug virtual screening(VS),drug lead optimization,drug addiction,small data set challenges,chemical and biological image analysis,chemical language understanding,and single cell data.Finally,we conclude the survey by deliberating on promising trends in transformer models within the context of drug discovery and other sciences.展开更多
Duality analysis of time series and complex networks has been a frontier topic during the last several decades.According to some recent approaches in this direction,the intrinsic dynamics of typical nonlinear systems ...Duality analysis of time series and complex networks has been a frontier topic during the last several decades.According to some recent approaches in this direction,the intrinsic dynamics of typical nonlinear systems can be better characterized by considering the related nonlinear time series from the perspective of networks science.In this paper,the associated network family of the unified piecewise-linear(PWL)chaotic family,which can bridge the gap of the PWL chaotic Lorenz system and the PWL chaotic Chen system,was firstly constructed and analyzed.We constructed the associated network family via the original and the modified frequency-degree mapping strategy,as well as the classical visibility graph and horizontal visibility graph strategy,after removing the transient states.Typical related network characteristics,including the network fractal dimension,of the associated network family,are computed with changes of single key parameter a.These characteristic vectors of the network are also compared with the largest Lyapunov exponent(LLE)vector of the related original dynamical system.It can be found that,some network characteristics are highly correlated with LLE vector of the original nonlinear system,i.e.,there is an internal consistency between the largest Lyapunov exponents,some typical associated network characteristics,and the related network fractal dimension index.Numerical results show that the modified frequency-degree mapping strategy can demonstrate highest correlation,which means it can behave better to capture the intrinsic characteristics of the unified PWL chaotic family.展开更多
This work focuses on the evolution behaviors of ring dark solitons(RDSs) and the following vortices after the collapses of RDSs in spin-1 Bose–Einstein condensates. We find that the weighted average of the initial de...This work focuses on the evolution behaviors of ring dark solitons(RDSs) and the following vortices after the collapses of RDSs in spin-1 Bose–Einstein condensates. We find that the weighted average of the initial depths of three components determines the number and motion trajectories of vortex dipoles. For the weighted average of the initial depths below the critical depth, two vortex dipoles form and start moving along the horizontal axis.For the weighted average depth above the critical depth, two or four vortex dipoles form, and all start moving along the vertical axis. For the RDS with weighted average depth at exactly the critical point, four vortex dipoles form, half of the vortex dipoles initiate movement vertically, and the other half initiate movement horizontally.Our conclusion is applicable to the two-component system studied in earlier research, indicating its universality.展开更多
The vortex dynamics after the initial ring dark solitons in two-component ultracold Rydberg atomic systems have been investigated.The two parameters characterizing the Rydberg long-range interaction—namely,the Rydber...The vortex dynamics after the initial ring dark solitons in two-component ultracold Rydberg atomic systems have been investigated.The two parameters characterizing the Rydberg long-range interaction—namely,the Rydberg strength and the blockade radius—along with the initial depth,are identified as the main factors that affect the vortex dynamics.In the absence of Rydberg soft-core potential and spin-orbit coupling,the late vortex dipoles move along x-or y-axis first.However,this work demonstrates that,with certain Rydberg strength and blockade radius,the late vortex dipoles move towards the edge at an oblique angle to the coordinate axes,and it reveals that the Rydberg nonlocal nonlinear interaction shortens the lifetime of late vortices.When the intra-component and inter-component Rydberg strengths are different,the backgrounds of the two components gradually complement each other,and the lifetime of late vortices is significantly shortened.The presented results show that the Rydberg dressing breaks the rule that the initial average depth determines the number and paths of vortices.The motion features of vortex dipoles in the ultracold Rydberg atomic system have been ascertained,and their directions of movement can be predicted to some degree based on the rotation directions and initial positions of the vortices.展开更多
We propose a theoretical framework,based on the two-component Gross-Pitaevskii equation(GPE),for the investigation of vortex solitons(VSs)in hybrid atomic-molecular Bose-Einstein condensates under the action of the st...We propose a theoretical framework,based on the two-component Gross-Pitaevskii equation(GPE),for the investigation of vortex solitons(VSs)in hybrid atomic-molecular Bose-Einstein condensates under the action of the stimulated Raman-induced photoassociation and square-optical-lattice potential.Stationary solutions of the coupled GPE system are obtained by means of the imaginary-time integration,while the temporal dynamics are simulated using the fourth-order Runge-Kutta algorithm.The analysis reveals stable rhombus-shaped VS shapes with topological charges m=1 and 2 of the atomic component.The stability domains and spatial structure of these VSs are governed by three key parameters:the parametric-coupling strength(χ),atomicmolecular interaction strength(g_(12)),and the optical-lattice potential depth(V_(0)).By varyingχand g_(12),we demonstrate a structural transition where four-core rhombus-shaped VSs evolve into eight-core square-shaped modes,highlighting the nontrivial nonlinear dynamics of the system.This work establishes a connection between interactions of cold atoms and topologically structured matter waves in hybrid quantum systems.展开更多
The three most widely used methods for reconstructing the underlying time series via the recurrence plots （RPs） of a dynamical system are compared with each other in this paper. We aim to reconstruct a toy series, a...The three most widely used methods for reconstructing the underlying time series via the recurrence plots （RPs） of a dynamical system are compared with each other in this paper. We aim to reconstruct a toy series, a periodical series, a random series, and a chaotic series to compare the effectiveness of the most widely used typical methods in terms of signal correlation analysis. The application of the most effective algorithm to the typical chaotic Lorenz system verifies the correctness of such an effective algorithm. It is verified that, based on the unthresholded RPs, one can reconstruct the original attractor by choosing different RP thresholds based on the Hirata algorithm. It is shown that, in real applications, it is possible to reconstruct the underlying dynamics by using quite little information from observations of real dynamical systems. Moreover, rules of the threshold chosen in the algorithm are also suggested.展开更多
The effect of laser microbeam trapping the bioparticles has been appfied widely in the biology .However the micromechanism of the acting that realizes the laser-microbeam trapping bioparticles is still lacking. In thi...The effect of laser microbeam trapping the bioparticles has been appfied widely in the biology .However the micromechanism of the acting that realizes the laser-microbeam trapping bioparticles is still lacking. In this paper ,the act microchenism of the gradiant force of laser microbeam for the bioparticles is analysed by means of quantum theory ,The result accords with our experiment.展开更多
In this article, we study the preservation properties of （Silov） boundary of mul-tiplieative subgroups in C（X） spaces for non-surjective norm-preserving multiplieative maps.We also show a sufficient condition for ...In this article, we study the preservation properties of （Silov） boundary of mul-tiplieative subgroups in C（X） spaces for non-surjective norm-preserving multiplieative maps.We also show a sufficient condition for surjective maps between groups of positive continuousfunctions to be a composition operator.展开更多
This work focuses on chirped solitons in a higher-order nonlinear Schrodinger equation,including cubic-quinticseptic nonlinearity,weak nonlocal nonlinearity,self-frequency shift,and self-steepening effect.For the firs...This work focuses on chirped solitons in a higher-order nonlinear Schrodinger equation,including cubic-quinticseptic nonlinearity,weak nonlocal nonlinearity,self-frequency shift,and self-steepening effect.For the first time,analytical bright and kink solitons,as well as their corresponding chirping,are obtained.The influence of septic nonlinearity and weak nonlocality on the dynamical behaviors of those nonlinearly chirped solitons is thoroughly addressed.The findings of the study give an experimental basis for nonlinear-managed solitons in optical fibers.展开更多
We present a computer model of diffusion limited aggregation with linear seed. The clusters with varying linear seed lengths are simulated, and their pattern structure, fractal dimension and multifractal spectrum are ...We present a computer model of diffusion limited aggregation with linear seed. The clusters with varying linear seed lengths are simulated, and their pattern structure, fractal dimension and multifractal spectrum are obtained. The simulation results show that the linear seed length has little effect on the pattern structure of the aggregation clusters if its length is comparatively shorter. With its increasing, the linear seed length has stronger effects on the pattern structure, while the dimension D f decreases. When the linear seed length is larger, the corresponding pattern structure is cross alike. The larger the linear seed length is, the more obvious the cross-like structure with more particles clustering at the two ends of the linear seed and along the vertical direction to the centre of the linear seed. Furthermore, the multifractal spectra curve becomes lower and the range of singularity narrower. The longer the length of a linear seed is, the less irregular and nonuniform the pattern becomes.展开更多
We present a novel approach for generating stable three-dimensional(3D)spatiotemporal solitons(SSs)within a rotating Bose–Einstein condensate,incorporating spin–orbit coupling(SOC),a weakly anharmonic potential and ...We present a novel approach for generating stable three-dimensional(3D)spatiotemporal solitons(SSs)within a rotating Bose–Einstein condensate,incorporating spin–orbit coupling(SOC),a weakly anharmonic potential and cold Rydberg atoms.This intricate system facilitates the emergence of quasi-stable 3D SSs with topological charges|m|≤3 in two spinor components,potentially exhibiting diverse spatial configurations.Our findings reveal that the Rydberg long-range interaction,spin–orbit coupling,and rotational angular frequency exert significant influence on the domains of existence and stability of these solitons.Notably,the Rydberg interaction contributes to a reduction in the norm of topological solitons,while the SOC plays a key role in stabilizing the SSs with finite topological charges.This research of SSs exhibits potential applications in precision measurement,quantum information processing,and other advanced technologies.展开更多
Knowledge of RNA 3-dimensional(3 D) structures is critical to understand the important biological functions of RNAs, and various models have been developed to predict RNA 3 D structures in silico. However, there is st...Knowledge of RNA 3-dimensional(3 D) structures is critical to understand the important biological functions of RNAs, and various models have been developed to predict RNA 3 D structures in silico. However, there is still lack of a reliable and efficient statistical potential for RNA 3 D structure evaluation. For this purpose, we developed a statistical potential based on a minimal coarse-grained representation and residue separation, where every nucleotide is represented by C4’ atom for backbone and N1(or N9) atom for base. In analogy to the newly developed all-atom rsRNASP, cgRNASP-CN is composed of short-ranged and long-ranged potentials, and the short-ranged one was involved more subtly. The examination indicates that the performance of cgRNASP-CN is close to that of the all-atom rsRNASP and is superior to other top all-atom traditional statistical potentials and scoring functions trained from neural networks, for two realistic test datasets including the RNA-Puzzles dataset. Very importantly,cgRNASP-CN is about 100 times more efficient than existing all-atom statistical potentials/scoring functions including rsRNASP. cgRNASP-CN is available at website: https://github.com/Tan-group/cgRNASP-CN.展开更多
Ribonucleic acids(RNAs)play a vital role in biology,and knowledge of their three-dimensional(3D)structure is required to understand their biological functions.Recently structural prediction methods have been developed...Ribonucleic acids(RNAs)play a vital role in biology,and knowledge of their three-dimensional(3D)structure is required to understand their biological functions.Recently structural prediction methods have been developed to address this issue,but a series of RNA 3D structures are generally predicted by most existing methods.Therefore,the evaluation of the predicted structures is generally indispensable.Although several methods have been proposed to assess RNA 3D structures,the existing methods are not precise enough.In this work,a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures.The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism.Based on extensive test sets generated from independent methods,the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best.Furthermore,the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing.Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation.展开更多
This article deals with an averaging principle for Caputo fractional stochastic differential equations with compensated Poisson random measure.The main contribution of this article is impose some new averaging conditi...This article deals with an averaging principle for Caputo fractional stochastic differential equations with compensated Poisson random measure.The main contribution of this article is impose some new averaging conditions to deal with the averaging principle for Caputo fractional stochastic differential equations.Under these conditions,the solution to a Caputo fractional stochastic differential system can be approximated by that of a corresponding averaging equation in the sense ofmean square.展开更多
基金supported in part by National Institute of Health(NIH),USA(Grant Nos.:R01GM126189,R01AI164266,and R35GM148196)the National Science Foundation,USA(Grant Nos.DMS2052983,DMS-1761320,and IIS-1900473)+3 种基金National Aero-nautics and Space Administration(NASA),USA(Grant No.:80NSSC21M0023)Michigan State University(MSU)Foundation,USA,Bristol-Myers Squibb(Grant No.:65109)USA,and Pfizer,USAsupported by the National Natural Science Foundation of China(Grant Nos.:11971367,12271416,and 11972266).
文摘Transformer models have emerged as pivotal tools within the realm of drug discovery,distinguished by their unique architectural features and exceptional performance in managing intricate data landscapes.Leveraging the innate capabilities of transformer architectures to comprehend intricate hierarchical dependencies inherent in sequential data,these models showcase remarkable efficacy across various tasks,including new drug design and drug target identification.The adaptability of pre-trained trans-former-based models renders them indispensable assets for driving data-centric advancements in drug discovery,chemistry,and biology,furnishing a robust framework that expedites innovation and dis-covery within these domains.Beyond their technical prowess,the success of transformer-based models in drug discovery,chemistry,and biology extends to their interdisciplinary potential,seamlessly combining biological,physical,chemical,and pharmacological insights to bridge gaps across diverse disciplines.This integrative approach not only enhances the depth and breadth of research endeavors but also fosters synergistic collaborations and exchange of ideas among disparate fields.In our review,we elucidate the myriad applications of transformers in drug discovery,as well as chemistry and biology,spanning from protein design and protein engineering,to molecular dynamics(MD),drug target iden-tification,transformer-enabled drug virtual screening(VS),drug lead optimization,drug addiction,small data set challenges,chemical and biological image analysis,chemical language understanding,and single cell data.Finally,we conclude the survey by deliberating on promising trends in transformer models within the context of drug discovery and other sciences.
文摘Duality analysis of time series and complex networks has been a frontier topic during the last several decades.According to some recent approaches in this direction,the intrinsic dynamics of typical nonlinear systems can be better characterized by considering the related nonlinear time series from the perspective of networks science.In this paper,the associated network family of the unified piecewise-linear(PWL)chaotic family,which can bridge the gap of the PWL chaotic Lorenz system and the PWL chaotic Chen system,was firstly constructed and analyzed.We constructed the associated network family via the original and the modified frequency-degree mapping strategy,as well as the classical visibility graph and horizontal visibility graph strategy,after removing the transient states.Typical related network characteristics,including the network fractal dimension,of the associated network family,are computed with changes of single key parameter a.These characteristic vectors of the network are also compared with the largest Lyapunov exponent(LLE)vector of the related original dynamical system.It can be found that,some network characteristics are highly correlated with LLE vector of the original nonlinear system,i.e.,there is an internal consistency between the largest Lyapunov exponents,some typical associated network characteristics,and the related network fractal dimension index.Numerical results show that the modified frequency-degree mapping strategy can demonstrate highest correlation,which means it can behave better to capture the intrinsic characteristics of the unified PWL chaotic family.
基金supported by the National Natural Science Foundation of China (Grant Nos.12261131495,11975172,and 12381240286)。
文摘This work focuses on the evolution behaviors of ring dark solitons(RDSs) and the following vortices after the collapses of RDSs in spin-1 Bose–Einstein condensates. We find that the weighted average of the initial depths of three components determines the number and motion trajectories of vortex dipoles. For the weighted average of the initial depths below the critical depth, two vortex dipoles form and start moving along the horizontal axis.For the weighted average depth above the critical depth, two or four vortex dipoles form, and all start moving along the vertical axis. For the RDS with weighted average depth at exactly the critical point, four vortex dipoles form, half of the vortex dipoles initiate movement vertically, and the other half initiate movement horizontally.Our conclusion is applicable to the two-component system studied in earlier research, indicating its universality.
基金supported by the Natural Science Foundation of Hubei Province of China(Grant No.2025AFB370)。
文摘The vortex dynamics after the initial ring dark solitons in two-component ultracold Rydberg atomic systems have been investigated.The two parameters characterizing the Rydberg long-range interaction—namely,the Rydberg strength and the blockade radius—along with the initial depth,are identified as the main factors that affect the vortex dynamics.In the absence of Rydberg soft-core potential and spin-orbit coupling,the late vortex dipoles move along x-or y-axis first.However,this work demonstrates that,with certain Rydberg strength and blockade radius,the late vortex dipoles move towards the edge at an oblique angle to the coordinate axes,and it reveals that the Rydberg nonlocal nonlinear interaction shortens the lifetime of late vortices.When the intra-component and inter-component Rydberg strengths are different,the backgrounds of the two components gradually complement each other,and the lifetime of late vortices is significantly shortened.The presented results show that the Rydberg dressing breaks the rule that the initial average depth determines the number and paths of vortices.The motion features of vortex dipoles in the ultracold Rydberg atomic system have been ascertained,and their directions of movement can be predicted to some degree based on the rotation directions and initial positions of the vortices.
基金supported by the National Natural Science Foundation of China(Grant No.62275075)the Natural Science Foundation of Hubei Soliton Research Association(Grant No.2025HBSRA09)+1 种基金joint supported by Hubei Provincial Natural Science Foundation and Xianning of China(Grant Nos.2025AFD401 and 2025AFD405)Israel Science Foundation(Grant No.1695/22).
文摘We propose a theoretical framework,based on the two-component Gross-Pitaevskii equation(GPE),for the investigation of vortex solitons(VSs)in hybrid atomic-molecular Bose-Einstein condensates under the action of the stimulated Raman-induced photoassociation and square-optical-lattice potential.Stationary solutions of the coupled GPE system are obtained by means of the imaginary-time integration,while the temporal dynamics are simulated using the fourth-order Runge-Kutta algorithm.The analysis reveals stable rhombus-shaped VS shapes with topological charges m=1 and 2 of the atomic component.The stability domains and spatial structure of these VSs are governed by three key parameters:the parametric-coupling strength(χ),atomicmolecular interaction strength(g_(12)),and the optical-lattice potential depth(V_(0)).By varyingχand g_(12),we demonstrate a structural transition where four-core rhombus-shaped VSs evolve into eight-core square-shaped modes,highlighting the nontrivial nonlinear dynamics of the system.This work establishes a connection between interactions of cold atoms and topologically structured matter waves in hybrid quantum systems.
基金Project supported by the Key Project of Ministry of Education of China (Grant No. 2010141)the National Natural Science Foundation of China (Grant No. 61203159)
文摘The three most widely used methods for reconstructing the underlying time series via the recurrence plots （RPs） of a dynamical system are compared with each other in this paper. We aim to reconstruct a toy series, a periodical series, a random series, and a chaotic series to compare the effectiveness of the most widely used typical methods in terms of signal correlation analysis. The application of the most effective algorithm to the typical chaotic Lorenz system verifies the correctness of such an effective algorithm. It is verified that, based on the unthresholded RPs, one can reconstruct the original attractor by choosing different RP thresholds based on the Hirata algorithm. It is shown that, in real applications, it is possible to reconstruct the underlying dynamics by using quite little information from observations of real dynamical systems. Moreover, rules of the threshold chosen in the algorithm are also suggested.
基金the Natural Science Foundation of Yunnan Province(2000A0021M and 2006E0091M)the National Science Foundation of China(60068001)+1 种基金the Natural science Foundation of Education department of Yunnan Province in China(07Y40499)the Science Foundation of Honghe College (KSS06021)
文摘The effect of laser microbeam trapping the bioparticles has been appfied widely in the biology .However the micromechanism of the acting that realizes the laser-microbeam trapping bioparticles is still lacking. In this paper ,the act microchenism of the gradiant force of laser microbeam for the bioparticles is analysed by means of quantum theory ,The result accords with our experiment.
基金supported in part by the NSFC(11671314)the Foundation of Hubei Provincial Department of Education(Q20161602)+1 种基金supported in part by the NSF-DMS(1200370)the NSFC(11628102)
文摘In this article, we study the preservation properties of （Silov） boundary of mul-tiplieative subgroups in C（X） spaces for non-surjective norm-preserving multiplieative maps.We also show a sufficient condition for surjective maps between groups of positive continuousfunctions to be a composition operator.
基金supported by the National Natural Science Foundation of China(Grant No.11975172)the Science and Technology Plan of Shenzhen City(Grant Nos.JCYJ20180306173235924 and JCYJ20180305164708625)。
文摘This work focuses on chirped solitons in a higher-order nonlinear Schrodinger equation,including cubic-quinticseptic nonlinearity,weak nonlocal nonlinearity,self-frequency shift,and self-steepening effect.For the first time,analytical bright and kink solitons,as well as their corresponding chirping,are obtained.The influence of septic nonlinearity and weak nonlocality on the dynamical behaviors of those nonlinearly chirped solitons is thoroughly addressed.The findings of the study give an experimental basis for nonlinear-managed solitons in optical fibers.
基金Supported by the Natural Science Foundation of Wuhan University of Science and Engineering under Grant No 20063133, and the Natural Science Foundation of Hubei Province under Grant No 2003ABA057.
文摘We present a computer model of diffusion limited aggregation with linear seed. The clusters with varying linear seed lengths are simulated, and their pattern structure, fractal dimension and multifractal spectrum are obtained. The simulation results show that the linear seed length has little effect on the pattern structure of the aggregation clusters if its length is comparatively shorter. With its increasing, the linear seed length has stronger effects on the pattern structure, while the dimension D f decreases. When the linear seed length is larger, the corresponding pattern structure is cross alike. The larger the linear seed length is, the more obvious the cross-like structure with more particles clustering at the two ends of the linear seed and along the vertical direction to the centre of the linear seed. Furthermore, the multifractal spectra curve becomes lower and the range of singularity narrower. The longer the length of a linear seed is, the less irregular and nonuniform the pattern becomes.
基金supported by the National Natural Science Foundation of China(Grant Nos.62275075 and 11975172)the Sci-ence and Technology Research Program of Education De-partment of Hubei Province(Grant No.B2022188)+1 种基金the Natural Science Foundation of Hubei Province(Grant No.2023AFC042)the Training Program of Innova-tion and Entrepreneurship for Undergraduates of Hubei Province(Grant No.S202210927003).
文摘We present a novel approach for generating stable three-dimensional(3D)spatiotemporal solitons(SSs)within a rotating Bose–Einstein condensate,incorporating spin–orbit coupling(SOC),a weakly anharmonic potential and cold Rydberg atoms.This intricate system facilitates the emergence of quasi-stable 3D SSs with topological charges|m|≤3 in two spinor components,potentially exhibiting diverse spatial configurations.Our findings reveal that the Rydberg long-range interaction,spin–orbit coupling,and rotational angular frequency exert significant influence on the domains of existence and stability of these solitons.Notably,the Rydberg interaction contributes to a reduction in the norm of topological solitons,while the SOC plays a key role in stabilizing the SSs with finite topological charges.This research of SSs exhibits potential applications in precision measurement,quantum information processing,and other advanced technologies.
基金supported by grants from the National Science Foundation of China(12075171,11774272)。
文摘Knowledge of RNA 3-dimensional(3 D) structures is critical to understand the important biological functions of RNAs, and various models have been developed to predict RNA 3 D structures in silico. However, there is still lack of a reliable and efficient statistical potential for RNA 3 D structure evaluation. For this purpose, we developed a statistical potential based on a minimal coarse-grained representation and residue separation, where every nucleotide is represented by C4’ atom for backbone and N1(or N9) atom for base. In analogy to the newly developed all-atom rsRNASP, cgRNASP-CN is composed of short-ranged and long-ranged potentials, and the short-ranged one was involved more subtly. The examination indicates that the performance of cgRNASP-CN is close to that of the all-atom rsRNASP and is superior to other top all-atom traditional statistical potentials and scoring functions trained from neural networks, for two realistic test datasets including the RNA-Puzzles dataset. Very importantly,cgRNASP-CN is about 100 times more efficient than existing all-atom statistical potentials/scoring functions including rsRNASP. cgRNASP-CN is available at website: https://github.com/Tan-group/cgRNASP-CN.
基金Project supported by the National Science Foundation of China(Grants Nos.11605125,11105054,11274124,and 11401448)
文摘Ribonucleic acids(RNAs)play a vital role in biology,and knowledge of their three-dimensional(3D)structure is required to understand their biological functions.Recently structural prediction methods have been developed to address this issue,but a series of RNA 3D structures are generally predicted by most existing methods.Therefore,the evaluation of the predicted structures is generally indispensable.Although several methods have been proposed to assess RNA 3D structures,the existing methods are not precise enough.In this work,a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures.The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism.Based on extensive test sets generated from independent methods,the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best.Furthermore,the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing.Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation.
基金Zhongkai Guo supported by NSF of China(Nos.11526196,11801575)the Fundamental Research Funds for the Central Universities,South-Central University for Nationalities(Grant Number:CZY20014)+1 种基金Hongbo Fu is supported by NSF of China(Nos.11826209,11301403)Natural Science Foundation of Hubei Province(No.2018CFB688).
文摘This article deals with an averaging principle for Caputo fractional stochastic differential equations with compensated Poisson random measure.The main contribution of this article is impose some new averaging conditions to deal with the averaging principle for Caputo fractional stochastic differential equations.Under these conditions,the solution to a Caputo fractional stochastic differential system can be approximated by that of a corresponding averaging equation in the sense ofmean square.
