DNA-based hydrogels are exceptional materials for biological applications because of their numerous advantages such as biodegradability,biocompatibility,hydrophilicity,super absorbency,porosity,and swelling.Among thes...DNA-based hydrogels are exceptional materials for biological applications because of their numerous advantages such as biodegradability,biocompatibility,hydrophilicity,super absorbency,porosity,and swelling.Among these advantages,the ability of DNA-based hydrogels to respond to specific physical and chemical triggers and undergo reversible phase transitions has garnered significant attention in the fields of disease diagnosis(biosensors)and treatment(drug delivery).This article focuses on the recent advancements in the research of DNA-based hydrogels and discusses the different types of these hydrogels,the synthetic methods,their unique properties,and their applications in biosensors and drug delivery.The types of DNA hydrogels are categorized based on their building blocks,and the process of synthesis as well as the unique characteristics of DNA-based hydrogels are described.Then,DNA-based responsive hydrogels utilized as intelligent materials for the development of biosensors are reviewed.Furthermore,this article also presents the current status of DNA-based responsive hydrogels in drug delivery for cancer treatment,wound healing,and other therapeutic applications.Ultimately,this paper discusses the current challenges in expanding the practical application of DNA-based hydrogels.展开更多
The Dynamical Density Functional Theory(DDFT)algorithm,derived by associating classical Density Functional Theory(DFT)with the fundamental Smoluchowski dynamical equation,describes the evolution of inhomo-geneous flui...The Dynamical Density Functional Theory(DDFT)algorithm,derived by associating classical Density Functional Theory(DFT)with the fundamental Smoluchowski dynamical equation,describes the evolution of inhomo-geneous fluid density distributions over time.It plays a significant role in studying the evolution of density distributions over time in inhomogeneous systems.The Sunway Bluelight II supercomputer,as a new generation of China’s developed supercomputer,possesses powerful computational capabilities.Porting and optimizing industrial software on this platform holds significant importance.For the optimization of the DDFT algorithm,based on the Sunway Bluelight II supercomputer and the unique hardware architecture of the SW39000 processor,this work proposes three acceleration strategies to enhance computational efficiency and performance,including direct parallel optimization,local-memory constrained optimization for CPEs,and multi-core groups collaboration and communication optimization.This method combines the characteristics of the program’s algorithm with the unique hardware architecture of the Sunway Bluelight II supercomputer,optimizing the storage and transmission structures to achieve a closer integration of software and hardware.For the first time,this paper presents Sunway-Dynamical Density Functional Theory(SW-DDFT).Experimental results show that SW-DDFT achieves a speedup of 6.67 times within a single-core group compared to the original DDFT implementation,with six core groups(a total of 384 CPEs),the maximum speedup can reach 28.64 times,and parallel efficiency can reach 71%,demonstrating excellent acceleration performance.展开更多
Multiple endocrine neoplasia type 2A （MEN2A）, a subtype of MEN2, is characterized by medullary thyroid cancer, pheochromocytoma, and primary hyperparathyroidism. A Han Chinese pedigree with MEN2A was investigated fo...Multiple endocrine neoplasia type 2A （MEN2A）, a subtype of MEN2, is characterized by medullary thyroid cancer, pheochromocytoma, and primary hyperparathyroidism. A Han Chinese pedigree with MEN2A was investigated following confirmation of the proband＇s diagnosis by pathological findings and DNA/biochemical screening. DNA samples from 4 other family members were collected and exon 5, 8, 10, 11, 13, 16 and 18 of the RET proto-oncogene were sequenced and then analyzed. A missense mutation of TGG （Trp） to TGC （Cys） at codon 634 （the classic MEN2A mutation） in exon 11 of the RET gene was detected in 3 family members, including the proband. Sequencing data were compared with the human gene mutation database. Elevated serum calcitonin level was detected initially; medullary thyroid carcinoma was revealed in the 3 cases and adrenal pheochromocytoma was also found in the proband. Elective operations were successfully performed on the adrenal and thyroid glands because of pheochromocytoma and medullary thyroid carcinoma. Our case study confirms that integrated DNA-based/biochemical screening is crucial for early diagnosis of MEN2A and is helpful in the screening of their relatives. In addition, DNA-based screening may occasionally uncover a previously unknown RET sequence.展开更多
An electrochemical sensor incorporating a signal enhancement for the determination of lead （II） ions （Pb2＋） was designed on the basis of the thrombin-binding aptamer （TBA） as a molecular recog- nition element a...An electrochemical sensor incorporating a signal enhancement for the determination of lead （II） ions （Pb2＋） was designed on the basis of the thrombin-binding aptamer （TBA） as a molecular recog- nition element and ionic liquid supported cerium oxide （CeO2） nanoparticles-carbon nanotubes compo- site modification. The composite comprises nanoparticles CeO2, multi-waU carbon nanotubes （MWNTs） and hydrophobic room temperature ionic liquid （RTIL） 1-ethyl-3-methylimidazolium tetrafluoroborate （EMIMBF4）. The electrochemical sensors were fabricated by immersing the CeOa-MWNTs-EMIMBF4 modified glassy carbon electrode （GCE） into the solution of TBA probe. In the presence of Pb2＋, the TBA probe could form stable G-quartet structure by the specific binding interactions between Pb2＋ and TBA. The TBA-bound Pb2＋ can be electrochemically reduced, which provides a readout signal for quantitative detection of Pb2＋. The reduction peak current is linearly related to the concentration of Pb2＋ from 1.0 ＊ 10-8 M to 1.0 ＊ 105 M with a detection limit of 5 ＊ 109 M. This work demonstrates that the CeOz-MWNTs-EMIMBF4 nanocomposite modified GCE provides a promising platform for immobi- lizing the TBA probe and enhancing the sensitivity of the DNA-based sensors.展开更多
In this paper,a typical experiment is carried out based on a high-resolution air-sea coupled model,namely,the coupled ocean-atmosphere-wave-sediment transport(COAWST)model,on both heterogeneous many-core(SW)and homoge...In this paper,a typical experiment is carried out based on a high-resolution air-sea coupled model,namely,the coupled ocean-atmosphere-wave-sediment transport(COAWST)model,on both heterogeneous many-core(SW)and homogenous multicore(Intel)supercomputing platforms.We construct a hindcast of Typhoon Lekima on both the SW and Intel platforms,compare the simulation results between these two platforms and compare the key elements of the atmospheric and ocean modules to reanalysis data.The comparative experiment in this typhoon case indicates that the domestic many-core computing platform and general cluster yield almost no differences in the simulated typhoon path and intensity,and the differences in surface pressure(PSFC)in the WRF model and sea surface temperature(SST)in the short-range forecast are very small,whereas a major difference can be identified at high latitudes after the first 10 days.Further heat budget analysis verifies that the differences in SST after 10 days are mainly caused by shortwave radiation variations,as influenced by subsequently generated typhoons in the system.These typhoons generated in the hindcast after the first 10 days attain obviously different trajectories between the two platforms.展开更多
This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA ...This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA molecules are used as the storage structure of the queue, and the basic bio-operations over the queue are described. Furthermore, the comparison between the queue of the electronic computer and that of DNA-based computer are elucidated. To prove the feasibility of our work, nucleotide encodings for an instance of queue are given out. All the biological technology mentioned in this paper can be practically implemented in the laboratory. Based on this work, other data structures could be developed in DNA-based computer.展开更多
随着高性能计算体系结构的发展,软件与硬件都具有多层的并行结构。当不同纵向层级与横向分组的计算任务被划分到不同节点的不同处理器时,存在非常多的分配方式。这些分配方式一般在运行时由用户输入的多个并行参数来确定,并对计算效率...随着高性能计算体系结构的发展,软件与硬件都具有多层的并行结构。当不同纵向层级与横向分组的计算任务被划分到不同节点的不同处理器时,存在非常多的分配方式。这些分配方式一般在运行时由用户输入的多个并行参数来确定,并对计算效率影响很大。随着计算规模与复杂度的提升,多个并行参数的可配置空间越来越大,用户越来越难以确定最佳的并行参数值。这类运行时优化问题在科学计算应用中较为普遍,但相关的研究与解决方法比较少见。以VASP(Vienna Ab initio Simulation Package)应用为例,首先分析了该应用的多层并行结构,展示了不同并行参数配置引发的巨大运行速度差异。然后提出了一个基于约化并行效率指标的全自动运行优化方法,其不仅可以帮助用户简单快捷地确定最佳应用并行参数,而且可以帮助用户确定最佳的计算资源使用量,使应用可以高效率地扩展到大规模的并行计算中。最后将该优化方法与计算集群作业调度系统相融合应用于用户提交的真实VASP计算作业。统计结果表明,该方法显著提升了作业运行速度与超算资源的使用效率,具有很好的工程应用前景。展开更多
Monitoring and analyzing expression levels of multiple biomarkers in biological samples can improve disease risk prediction and guide precision medicine but suffers from high cost and being time-consuming.Here,we cons...Monitoring and analyzing expression levels of multiple biomarkers in biological samples can improve disease risk prediction and guide precision medicine but suffers from high cost and being time-consuming.Here,we construct a fast molecular classifier based on freeze-thaw cycling that implements an in silico support vector machine(SVM)classifier model at the molecular level with a panel of disease-related biomarkers expression patterns for rapid disease diagnosis.The molecular classifier employs DNA reaction networks as the computing module and repeated dehydration and concentration process as the driving force to implement a set of simplified mathematical operations(such as multiplication,summation and subtraction)for efficient classification of complex input patterns.We demonstrate that the fast DNA-based molecular classifier enables precise cancer diagnosis within a short turnaround time in synthetic samples compared to those of free diffusion classifiers.We envision that this all-in-one molecular classifier will create more opportunities for inexpensive,accurate,and rapid disease diagnosis,prognosis and therapy,particularly in emergency departments or the point of care.展开更多
基金financially supported by the National Natural Science Foundation of China(No.21804014)the Natural Science Foundation of Chongqing Science&Technology Commission(No.2023jcyjA3529)+1 种基金the Science and Technology Research Program of Chongqing Municipal Education Commission(No.KJQN202200832)Construction of Graduate Joint Training Base of Chongqing Municipal Education Commission(No.yjd223005)。
文摘DNA-based hydrogels are exceptional materials for biological applications because of their numerous advantages such as biodegradability,biocompatibility,hydrophilicity,super absorbency,porosity,and swelling.Among these advantages,the ability of DNA-based hydrogels to respond to specific physical and chemical triggers and undergo reversible phase transitions has garnered significant attention in the fields of disease diagnosis(biosensors)and treatment(drug delivery).This article focuses on the recent advancements in the research of DNA-based hydrogels and discusses the different types of these hydrogels,the synthetic methods,their unique properties,and their applications in biosensors and drug delivery.The types of DNA hydrogels are categorized based on their building blocks,and the process of synthesis as well as the unique characteristics of DNA-based hydrogels are described.Then,DNA-based responsive hydrogels utilized as intelligent materials for the development of biosensors are reviewed.Furthermore,this article also presents the current status of DNA-based responsive hydrogels in drug delivery for cancer treatment,wound healing,and other therapeutic applications.Ultimately,this paper discusses the current challenges in expanding the practical application of DNA-based hydrogels.
基金supported by National Key Research and Development Program of China under Grant 2024YFE0210800National Natural Science Foundation of China under Grant 62495062Beijing Natural Science Foundation under Grant L242017.
文摘The Dynamical Density Functional Theory(DDFT)algorithm,derived by associating classical Density Functional Theory(DFT)with the fundamental Smoluchowski dynamical equation,describes the evolution of inhomo-geneous fluid density distributions over time.It plays a significant role in studying the evolution of density distributions over time in inhomogeneous systems.The Sunway Bluelight II supercomputer,as a new generation of China’s developed supercomputer,possesses powerful computational capabilities.Porting and optimizing industrial software on this platform holds significant importance.For the optimization of the DDFT algorithm,based on the Sunway Bluelight II supercomputer and the unique hardware architecture of the SW39000 processor,this work proposes three acceleration strategies to enhance computational efficiency and performance,including direct parallel optimization,local-memory constrained optimization for CPEs,and multi-core groups collaboration and communication optimization.This method combines the characteristics of the program’s algorithm with the unique hardware architecture of the Sunway Bluelight II supercomputer,optimizing the storage and transmission structures to achieve a closer integration of software and hardware.For the first time,this paper presents Sunway-Dynamical Density Functional Theory(SW-DDFT).Experimental results show that SW-DDFT achieves a speedup of 6.67 times within a single-core group compared to the original DDFT implementation,with six core groups(a total of 384 CPEs),the maximum speedup can reach 28.64 times,and parallel efficiency can reach 71%,demonstrating excellent acceleration performance.
基金supported by grant 81170747 from the National Natural Sciences Foundation of Chinagrant H201106 from Health Promotion Foundation of Jiangsu Provincegrant from the Office of Human Resources and Social Security of Jiangsu Province (Peak of the Six Personnel in Jiangsu Province) to Hongwen Zhou
文摘Multiple endocrine neoplasia type 2A （MEN2A）, a subtype of MEN2, is characterized by medullary thyroid cancer, pheochromocytoma, and primary hyperparathyroidism. A Han Chinese pedigree with MEN2A was investigated following confirmation of the proband＇s diagnosis by pathological findings and DNA/biochemical screening. DNA samples from 4 other family members were collected and exon 5, 8, 10, 11, 13, 16 and 18 of the RET proto-oncogene were sequenced and then analyzed. A missense mutation of TGG （Trp） to TGC （Cys） at codon 634 （the classic MEN2A mutation） in exon 11 of the RET gene was detected in 3 family members, including the proband. Sequencing data were compared with the human gene mutation database. Elevated serum calcitonin level was detected initially; medullary thyroid carcinoma was revealed in the 3 cases and adrenal pheochromocytoma was also found in the proband. Elective operations were successfully performed on the adrenal and thyroid glands because of pheochromocytoma and medullary thyroid carcinoma. Our case study confirms that integrated DNA-based/biochemical screening is crucial for early diagnosis of MEN2A and is helpful in the screening of their relatives. In addition, DNA-based screening may occasionally uncover a previously unknown RET sequence.
基金supports from the National Science Foundations of China (Nos. 20875076 and 21005061)the Specialized Research Fund for the Doctoral Program of Higher Education of China (No. 20096101120011)+2 种基金the Natural Science Basic Research Plan in Shaanxi Province of China (No.2010JQ2013)the Education Department of Shaanxi Province,China (No. 09JK759)the NWU Graduate Innovation and Creativity Funds (No. 09YSY04)
文摘An electrochemical sensor incorporating a signal enhancement for the determination of lead （II） ions （Pb2＋） was designed on the basis of the thrombin-binding aptamer （TBA） as a molecular recog- nition element and ionic liquid supported cerium oxide （CeO2） nanoparticles-carbon nanotubes compo- site modification. The composite comprises nanoparticles CeO2, multi-waU carbon nanotubes （MWNTs） and hydrophobic room temperature ionic liquid （RTIL） 1-ethyl-3-methylimidazolium tetrafluoroborate （EMIMBF4）. The electrochemical sensors were fabricated by immersing the CeOa-MWNTs-EMIMBF4 modified glassy carbon electrode （GCE） into the solution of TBA probe. In the presence of Pb2＋, the TBA probe could form stable G-quartet structure by the specific binding interactions between Pb2＋ and TBA. The TBA-bound Pb2＋ can be electrochemically reduced, which provides a readout signal for quantitative detection of Pb2＋. The reduction peak current is linearly related to the concentration of Pb2＋ from 1.0 ＊ 10-8 M to 1.0 ＊ 105 M with a detection limit of 5 ＊ 109 M. This work demonstrates that the CeOz-MWNTs-EMIMBF4 nanocomposite modified GCE provides a promising platform for immobi- lizing the TBA probe and enhancing the sensitivity of the DNA-based sensors.
基金This work is supported by the National Key Research and Development Plan program of the Ministry of Science and Technology of China(No.2016YFB0201100)Additionally,this work is supported by the National Laboratory for Marine Science and Technology(Qingdao)Major Project of the Aoshan Science and Technology Innovation Program(No.2018ASKJ01-04)the Open Fundation of Key Laboratory of Marine Science and Numerical Simulation,Ministry of Natural Resources(No.2021-YB-02).
文摘In this paper,a typical experiment is carried out based on a high-resolution air-sea coupled model,namely,the coupled ocean-atmosphere-wave-sediment transport(COAWST)model,on both heterogeneous many-core(SW)and homogenous multicore(Intel)supercomputing platforms.We construct a hindcast of Typhoon Lekima on both the SW and Intel platforms,compare the simulation results between these two platforms and compare the key elements of the atmospheric and ocean modules to reanalysis data.The comparative experiment in this typhoon case indicates that the domestic many-core computing platform and general cluster yield almost no differences in the simulated typhoon path and intensity,and the differences in surface pressure(PSFC)in the WRF model and sea surface temperature(SST)in the short-range forecast are very small,whereas a major difference can be identified at high latitudes after the first 10 days.Further heat budget analysis verifies that the differences in SST after 10 days are mainly caused by shortwave radiation variations,as influenced by subsequently generated typhoons in the system.These typhoons generated in the hindcast after the first 10 days attain obviously different trajectories between the two platforms.
基金This work was supportedin part by the National Nature Science Foundation of China (No.60474037and60004006) Programfor NewCentury Excellent Talents in University (NCET04 415) +1 种基金Specialized Research Fund for the Doctoral Programof Higher Educationfrom Educational Committee of China (No.20030255009) the Youth Foundation fromEducational Committee of Anhui Province(No.2005jql043) .
文摘This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA molecules are used as the storage structure of the queue, and the basic bio-operations over the queue are described. Furthermore, the comparison between the queue of the electronic computer and that of DNA-based computer are elucidated. To prove the feasibility of our work, nucleotide encodings for an instance of queue are given out. All the biological technology mentioned in this paper can be practically implemented in the laboratory. Based on this work, other data structures could be developed in DNA-based computer.
文摘随着高性能计算体系结构的发展,软件与硬件都具有多层的并行结构。当不同纵向层级与横向分组的计算任务被划分到不同节点的不同处理器时,存在非常多的分配方式。这些分配方式一般在运行时由用户输入的多个并行参数来确定,并对计算效率影响很大。随着计算规模与复杂度的提升,多个并行参数的可配置空间越来越大,用户越来越难以确定最佳的并行参数值。这类运行时优化问题在科学计算应用中较为普遍,但相关的研究与解决方法比较少见。以VASP(Vienna Ab initio Simulation Package)应用为例,首先分析了该应用的多层并行结构,展示了不同并行参数配置引发的巨大运行速度差异。然后提出了一个基于约化并行效率指标的全自动运行优化方法,其不仅可以帮助用户简单快捷地确定最佳应用并行参数,而且可以帮助用户确定最佳的计算资源使用量,使应用可以高效率地扩展到大规模的并行计算中。最后将该优化方法与计算集群作业调度系统相融合应用于用户提交的真实VASP计算作业。统计结果表明,该方法显著提升了作业运行速度与超算资源的使用效率,具有很好的工程应用前景。
基金supported by the National Science Foundation of China(Grant Nos.21991134,22074041)the Shanghai Science and Technology Committee(STCSM)(23ZR1479600).
文摘Monitoring and analyzing expression levels of multiple biomarkers in biological samples can improve disease risk prediction and guide precision medicine but suffers from high cost and being time-consuming.Here,we construct a fast molecular classifier based on freeze-thaw cycling that implements an in silico support vector machine(SVM)classifier model at the molecular level with a panel of disease-related biomarkers expression patterns for rapid disease diagnosis.The molecular classifier employs DNA reaction networks as the computing module and repeated dehydration and concentration process as the driving force to implement a set of simplified mathematical operations(such as multiplication,summation and subtraction)for efficient classification of complex input patterns.We demonstrate that the fast DNA-based molecular classifier enables precise cancer diagnosis within a short turnaround time in synthetic samples compared to those of free diffusion classifiers.We envision that this all-in-one molecular classifier will create more opportunities for inexpensive,accurate,and rapid disease diagnosis,prognosis and therapy,particularly in emergency departments or the point of care.
