Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based me...Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction.However,traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules.Similarly,graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information.To address these limitations,we propose a novel fingerprint-enhanced hierarchical graph neural network(FH-GNN)for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints.The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks(D-MPNN)on a hierarchical molecular graph that integrates atomic-level,motif-level,and graph-level information along with their relationships.Addi-tionally,we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features,creating a comprehensive molecular embedding that integrated hierarchical mo-lecular structures with domain knowledge.Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction,validating its capability to comprehensively capture molecular informa-tion.By integrating molecular structure and chemical knowledge,FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates.展开更多
Colorectal cancer(CRC)ranks among the top causes of cancer-related fatalities globally.Recent progress in genomics,proteomics,and bioinformatics has greatly improved our comprehension of the molecular underpinnings of...Colorectal cancer(CRC)ranks among the top causes of cancer-related fatalities globally.Recent progress in genomics,proteomics,and bioinformatics has greatly improved our comprehension of the molecular underpinnings of CRC,paving the way for targeted therapies and immunotherapies.Nonetheless,obstacles such as tumor heterogeneity and drug resistance persist,hindering advancements in treatment efficacy.In this context,the integration of artificial intelligence(AI)and organoid technology presents promising new avenues.AI can analyze genetic and clinical data to forecast disease risk,prognosis,and treatment responses,thereby expediting drug development and tailoring treatment plans.Organoids replicate the genetic traits and biological behaviors of tumors,acting as platforms for drug testing and the formulation of personalized treatment approaches.Despite notable strides in CRC research and treatment-from genetic insights to therapeutic innovations-numerous challenges endure,including the intricate tumor microen-vironment,tumor heterogeneity,adverse effects of immunotherapies,issues related to AI data quality and privacy,and the need for standardization in organoid culture.Future initiatives should concentrate on clarifying the pathogenesis of CRC,refining AI algorithms and organoid models,and creating more effective therapeutic strategies to alleviate the global impact of CRC.展开更多
Pancreatic cancer, particularly pancreatic ductal adenocarcinoma(PDAC), is one of the most lethal malignancies,which is characterized by a complex tumor microenvironment(TME) that fosters immune evasion and treatment ...Pancreatic cancer, particularly pancreatic ductal adenocarcinoma(PDAC), is one of the most lethal malignancies,which is characterized by a complex tumor microenvironment(TME) that fosters immune evasion and treatment resistance. Recent genomic advancements have unveiled diverse molecular subtypes of PDAC, providing insights into targeted therapies and precision medicine. This review synthesizes the current understanding of PDAC's molecular characterization and immunosuppressive TME, as well as emerging therapeutic strategies, including innovative approaches targeting key molecular pathways such as kirsten rat sarcoma viral oncogene homolog(KRAS), epidermal growth factor receptor(EGFR), and immune checkpoints. Despite advances, challenges remain in overcoming treatment resistance and inherent heterogeneity of pancreatic cancer subtypes. We highlight the need for multidisciplinary collaboration to enhance early diagnosis and develop individualized therapeutic protocols, paving the way for improving the outcomes of this aggressive cancer. This integrated perspective underscores the urgency of transforming the innovative research into pancreatic cancer management.展开更多
Advancements in molecular approaches have been utilized to breed crops with a wide range of economically valuable traits to develop superior cultivars.This review provides a concise overview of modern breakthroughs in...Advancements in molecular approaches have been utilized to breed crops with a wide range of economically valuable traits to develop superior cultivars.This review provides a concise overview of modern breakthroughs in molecular plant production.Genotyping and high-throughput phenotyping methods for predictive plant breeding are briefly discussed.In this study,we explore contemporary molecular breeding techniques for producing desirable crop varieties.These techniques include cisgenesis,clustered regularly interspaced short palindromic repeat(CRISPR/Cas9)gene editing,haploid induction,and de novo domestication.We examine the speed breeding approach-a strategy for cultivating plants under controlled conditions.We further highlight the significance of modern breeding technologies in efficiently utilizing agricultural resources for crop production in urban areas.The deciphering of crop genomes has led to the development of extensive DNA markers,quantitative trait loci(QTLs),and pangenomes associated with various desirable crop traits.This shift to the genotypic selection of crops considerably expedites the plant breeding process.Based on the plant population used,the connection between genotypic and phenotypic data provides several genetic elements,including genes,markers,and alleles that can be used in genomic breeding and gene editing.The integration of speed breeding with genomic-assisted breeding and cutting-edge genome editing tools has made it feasible to rapidly manipulate and generate multiple crop cycles and accelerate the plant breeding process.Breakthroughs in molecular techniques have led to substantial improvements in modern breeding methods.展开更多
Recently,diffusion models have emerged as a promising paradigm for molecular design and optimization.However,most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geom-etries,with limited ...Recently,diffusion models have emerged as a promising paradigm for molecular design and optimization.However,most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geom-etries,with limited research on molecular sequence diffusion models.The International Union of Pure and Applied Chemistry(IUPAC)names are more akin to chemical natural language than the simplified molecular input line entry system(SMILES)for organic compounds.In this work,we apply an IUPAC-guided conditional diffusion model to facilitate molecular editing from chemical natural language to chemical language(SMILES)and explore whether the pre-trained generative performance of diffusion models can be transferred to chemical natural language.We propose DiffIUPAC,a controllable molecular editing diffusion model that converts IUPAC names to SMILES strings.Evaluation results demonstrate that our model out-performs existing methods and successfully captures the semantic rules of both chemical languages.Chemical space and scaffold analysis show that the model can generate similar compounds with diverse scaffolds within the specified constraints.Additionally,to illustrate the model’s applicability in drug design,we conducted case studies in functional group editing,analogue design and linker design.展开更多
Aqueous zinc-ion batteries(AZIBs)have regained interest due to their inherent safety and costeffectiveness.However,the zinc anode is notorious for side reactions and dendrite growth,which plague the practical applicat...Aqueous zinc-ion batteries(AZIBs)have regained interest due to their inherent safety and costeffectiveness.However,the zinc anode is notorious for side reactions and dendrite growth,which plague the practical application of AZIBs.Adjusting the interfacial pH to reduce the by-products has been proven to be effective in protecting the zinc anode.Nevertheless,the dynamic regulation of the inherently unstable zinc interface during prolonged cycling remains a significant challenge.Herein,zwitterionic N-tris(hydroxymethyl)methylglycine(TMG)integrated with negative-COO^(-)and positive NH_(2)^(+)groups is proposed to stabilize the Zn anode and extend the lifespan as a self-regulating interfacial additive.The anionic portion serves as a trapping site to balance the interfacial pH and thus mitigate the unintended side reactions.Simultaneously,the NH_(2)^(+)cations are anchored on the zinc surface,forming a water-shielding,zincophilic molecular layer that guides three-dimensional diffusion and promotes uniform electro-deposition.Thus,an average plating efficiency of 99.74%over 3300 cycles at a current density of2 mA cm^(-2)is achieved.Notably,the TMG additive actualizes ultralong life in Zn‖Zn symmetrical cells(5500 h,exceeding 229 days,1 mA cm^(-2)/1 mA h cm^(-2)),and enables the Zn‖I_(2)cells to reach capacity retention rate of 89.4%after 1000 cycles at 1 A g^(-1).展开更多
Guided by molecular networking,nine novel curvularin derivatives(1-9)and 16 known analogs(10-25)were isolated from the hydrothermal vent sediment fungus Penicillium sp.HL-50.Notably,compounds 5-7 represented a hybrid ...Guided by molecular networking,nine novel curvularin derivatives(1-9)and 16 known analogs(10-25)were isolated from the hydrothermal vent sediment fungus Penicillium sp.HL-50.Notably,compounds 5-7 represented a hybrid of curvularin and purine.The structures and absolute configurations of compounds 1-9 were elucidated via nuclear magnetic resonance(NMR)spectroscopy,X-ray diffraction,electronic circular dichroism(ECD)calculations,^(13)C NMR calculation,modified Mosher's method,and chemical derivatization.Investigation of anti-inflammatory activities revealed that compounds 7-9,11,12,14,15,and 18 exhibited significant suppressive effects against lipopolysaccharide(LPS)-induced nitric oxide(NO)production in murine macrophage RAW264.7 cells,with IC_(50)values ranging from 0.44 to 4.40μmol·L^(-1).Furthermore,these bioactive compounds were found to suppress the expression of inflammation-related proteins,including inducible NO synthase(i NOS),cyclooxygenase-2(COX-2),NLR family pyrin domain-containing protein 3(NLRP3),and nuclear factor kappa-B(NF-κB).Additional studies demonstrated that the novel compound 7 possessed potent antiinflammatory activity by inhibiting the transcription of inflammation-related genes,downregulating the expression of inflammation-related proteins,and inhibiting the release of inflammatory cytokines,indicating its potential application in the treatment of inflammatory diseases.展开更多
The global energy demand is increasing rapidly,and it is imperative to develop shale hydrocarbon re-sources vigorously.The prerequisite for enhancing the exploitation efficiency of shale reservoirs is the systematic e...The global energy demand is increasing rapidly,and it is imperative to develop shale hydrocarbon re-sources vigorously.The prerequisite for enhancing the exploitation efficiency of shale reservoirs is the systematic elucidation of the occurrence characteristics,flow behavior,and enhanced oil recovery(EOR)mechanisms of shale oil within commonly developed nanopores.Molecular dynamics(MD)technique can simulate the occurrence,flow,and extraction processes of shale oil at the nanoscale,and then quantitatively characterize various fluid properties,flow characteristics,and action mechanisms under different reservoir conditions by calculating and analyzing a series of MD parameters.However,the existing review on the application of MD simulation in shale oil reservoirs is not systematic enough and lacks a summary of technical challenges and solutions.Therefore,recent MD studies on shale oil res-ervoirs were summarized and analyzed.Firstly,the applicability of force fields and ensembles of MD in shale reservoirs with different reservoir conditions and fluid properties was discussed.Subsequently,the calculation methods and application examples of MD parameters characterizing various properties of fluids at the microscale were summarized.Then,the application of MD simulation in the study of shale oil occurrence characteristics,flow behavior,and EOR mechanisms was reviewed,along with the elucidation of corresponding micro-mechanisms.Moreover,influencing factors of pore structure,wall properties,reservoir conditions,fluid components,injection/production parameters,formation water,and inorganic salt ions were analyzed,and some new conclusions were obtained.Finally,the main challenges associated with the application of MD simulations to shale oil reservoirs were discussed,and reasonable prospects for future MD research directions were proposed.The purpose of this review is to provide theoretical basis and methodological support for applying MD simulation to study shale oil reservoirs.展开更多
This study identified castor oil and phosphate ester as effective retarders through setting time,tensile,and flexural tests,and determined their optimal dosages.The mechanism by which phosphate ester affects the setti...This study identified castor oil and phosphate ester as effective retarders through setting time,tensile,and flexural tests,and determined their optimal dosages.The mechanism by which phosphate ester affects the setting time of polyurethane was further investigated using molecular dynamics simulations.Fourier transform infrared spectroscopy was also employed to systematically study the physical and chemical interactions between phosphate esters and polyurethane materials.The results demonstrate that a 1%concentration of phosphate ester provides the most effective retarding effect with minimal impact on the strength of polyurethane.When phosphate ester is added to the B component of the two-component polyurethane system,its interaction energy with component A decreases,as do the diffusion coefficient and aggregation degree of component B on the surface of component A.This reduction in interaction slows the setting time.Additionally,the addition of phosphate ester to polyurethane leads to the disappearance or weakening of functional groups,indicating competitive interactions within the phosphate ester components that inhibit the reaction rate.展开更多
Carbon capture is an important strategy and is implemented to achieve the goals of CO_(2)reduction and carbon neutrality.As a high energy-efficient technology,membrane-based separation plays a crucial role in CO_(2)ca...Carbon capture is an important strategy and is implemented to achieve the goals of CO_(2)reduction and carbon neutrality.As a high energy-efficient technology,membrane-based separation plays a crucial role in CO_(2)capture.It is urgently needed for membrane-based CO_(2)capture to develop the high-performance membrane materials with high permeability,selectivity,and stability.Herein,ultrapermeable carbon molecular sieve(CMS)membranes are fabricated by py roly zing a finely-engineered benzoxazole-containing copolyimide precursor for efficient CO_(2)capture.The microstructure of CMS membrane has been optimized by initially engineering the precursor-chemistry and subsequently tuning the pyrolysis process.Deep insights into the structure-property relationship of CMSs are provided in detail by a combination of experimental characterization and molecular simulations.We demonstrate that the intrinsically high free volume environment of the precursor,coupled with the steric hindrance of thermostable contorted fragments,promotes the formation of loosely packed and ultramicroporous carbon structures within the resultant CMS membrane,thereby enabling efficient CO_(2)discrimination via size sieving and affinity.The membrane achieves an ultrahigh CO_(2)permeability,good selectivity,and excellent stability.After one month of long-term operation,the CO_(2)permeability in the mixed gas is maintained at 11,800 Barrer,with a CO_(2)/N_(2)selectivity exceeding 60.This study provides insights into the relationship between precursor-chemistry and CMS performance,and our ultrapermeable CMS membrane,which is scalable using thin film manufacturing,holds great potential for industrial CO_(2)capture.展开更多
The pre-wetting of aggregate surface is a means to improve the interface performance of SBS modified asphalt and aggregate.The effect of pre-wetting technology on the interaction between SBS modified asphalt and aggre...The pre-wetting of aggregate surface is a means to improve the interface performance of SBS modified asphalt and aggregate.The effect of pre-wetting technology on the interaction between SBS modified asphalt and aggregate was analyzed by molecular dynamics simulation.The diffusion coefficient and concentration distribution of SBS modified asphalt on aggregate surface are included.The simulation results show that the diffusion coefficient of the aggregate surface of SBS modified asphalt is increased by 47.6%and 70.5%respectively after 110#asphalt and 130#asphalt are pre-wetted.The concentration distribution of SBS modified asphalt on the aggregate surface after pre-wetting is more uniform.According to the results of interface energy calculation,the interface energy of SBS modified bitumen and aggregate can be increased by about 5%after pre-wetting.According to the results of molecular dynamics simulation,the pre-wetting technology can effectively improve the interface workability of SBS modified bitumen and aggregate,so as to improve the interface performance.展开更多
Layer-structured Ruddlesden–Popper(RP)perovskites(RPPs)with decent stability have captured the imagination of the photovoltaic research community and bring hope for boosting the development of perovskite solar cell(P...Layer-structured Ruddlesden–Popper(RP)perovskites(RPPs)with decent stability have captured the imagination of the photovoltaic research community and bring hope for boosting the development of perovskite solar cell(PSC)technology.However,two-dimensional(2D)or quasi-2D RP PSCs are encountered with some challenges of the large exciton binding energy,blocked charge transport and poor film quality,which restrict their photovoltaic performance.Fortunately,these issues can be readily resolved by rationally designing spacer cations of RPPs.This review mainly focuses on how to design the molecular structures of organic spacers and aims to endow RPPs with outstanding photovoltaic applications.We firstly elucidated the important roles of organic spacers in impacting crystallization kinetics,charge transporting ability and stability of RPPs.Then we brought three aspects to attention for designing organic spacers.Finally,we presented the specific molecular structure design strategies for organic spacers of RPPs aiming to improve photovoltaic performance of RP PSCs.These proposed strategies in this review will provide new avenues to develop novel organic spacers for RPPs and advance the development of RPP photovoltaic technology for future applications.展开更多
The complex morphological,anatomical,physiological,and chemical mechanisms within the aging brain have been the hot topic of research for centuries.The aging process alters the brain structure that affects functions a...The complex morphological,anatomical,physiological,and chemical mechanisms within the aging brain have been the hot topic of research for centuries.The aging process alters the brain structure that affects functions and cognitions,but the worsening of such processes contributes to the pathogenesis of neurodegenerative disorders,such as Alzheimer's disease.Beyond these observable,mild morphological shifts,significant functional modifications in neurotransmission and neuronal activity critically influence the aging brain.Understanding these changes is important for maintaining cognitive health,especially given the increasing prevalence of age-related conditions that affect cognition.This review aims to explore the age-induced changes in brain plasticity and molecular processes,differentiating normal aging from the pathogenesis of Alzheimer's disease,thereby providing insights into predicting the risk of dementia,particularly Alzheimer's disease.展开更多
The extraordinary strength of metal/graphene composites is significantly determined by the characteristic size,distribution and morphology of graphene.However,the effect of the graphene size/distribution on the mechan...The extraordinary strength of metal/graphene composites is significantly determined by the characteristic size,distribution and morphology of graphene.However,the effect of the graphene size/distribution on the mechanical properties and related strengthening mechanisms has not been fully elucidated.Herein,under the same volume fraction and distribution conditions of graphene,molecular dynamics simulations were used to investigate the effect of graphene sheet size on the hardness and deformation behavior of Cu/graphene composites under complex stress field.Two models of pure single crystalline Cu and graphene fully covered Cu matrix composite were constructed for comparison.The results show that the strengthening effect changes with varying the graphene sheet size.Besides the graphene dislocation blocking effect and the load-bearing effect,the deformation mechanisms change from stacking fault tetrahedron,dislocation bypassing and dislocation cutting to dislocation nucleation in turn with decreasing the graphene sheet size.The hardness of Cu/graphene composite,with the graphene sheet not completely covering the metal matrix,can even be higher than that of the fully covered composite.The extra strengthening mechanisms of dislocation bypassing mechanism and the stacking fault tetrahedra pinning dislocation mechanism contribute to the increase in hardness.展开更多
Since the discovery of carbon dots(CDs)in 2004,the unique photoluminescence phenomenon of CDs has attracted widespread attention.However,the molecular weight of CDs has not been adequately quantified at present,due to...Since the discovery of carbon dots(CDs)in 2004,the unique photoluminescence phenomenon of CDs has attracted widespread attention.However,the molecular weight of CDs has not been adequately quantified at present,due to CDs are atomically imprecise and their molecular weight distribution is broad.In this paper,a series of Pluronic-modified CDs were prepared and the structure of the CDs was briefly analyzed.Subsequently,a molecular weight measurement method based on colligative properties was developed,and the correction coefficient in the algorithm was briefly analyzed.The calculated molecular weight was applied to the determination of surface adsorption capacity.This work provided a method for averaging the molecular weight of atomically imprecise particulate materials,which is expected to provide new opportunities in related fields.展开更多
High-quality antiferromagnetic(AFM)θ-phase manganese nitride(MnN)films were successfully grown on MgO(001)substrates by plasma-assisted molecular beam epitaxy.Structural analysis confirms the high-quality MnN film ha...High-quality antiferromagnetic(AFM)θ-phase manganese nitride(MnN)films were successfully grown on MgO(001)substrates by plasma-assisted molecular beam epitaxy.Structural analysis confirms the high-quality MnN film has a tetragonal distortion with a c/a ratio of~0.98.The film exhibits exceptional stability in both aqueous and ambient conditions,which is a crucial factor for practical applications.Electrical transport reveals its metallic behavior with an upturn at low temperatures,which could be attributed to the Kondo effect originated from nitrogen vacancy-induced magnetic impurities.Room temperature exchange bias has been demonstrated in a MnN/CoFeB heterostructure,verifying the AFM ordering of MnN.Considering its high Néel temperature~650 K,superior stability,and low-cost,this work highlights the epitaxial MnN films as a promising candidate for AFM spintronic applications.展开更多
This paper discusses the influence of Sb/In ratio on the transport properties and crystal quality of the 200 nm InAs_(x)Sb_(1-x)thin film.The Sb content of InAs_(x)Sb_(1-x)thin film in all samples was verified by HRXR...This paper discusses the influence of Sb/In ratio on the transport properties and crystal quality of the 200 nm InAs_(x)Sb_(1-x)thin film.The Sb content of InAs_(x)Sb_(1-x)thin film in all samples was verified by HRXRD of the symmetrical 004 reflections and asymmetrical 115 reflections.The calculation results show that the Sb component was 0.6 in the InAs_(x)Sb_(1-x)thin film grown under the conditions of Sb/In ratio of 6 and As/In ratio of 3,which has the highest electron mobility(28560 cm^(2)/V·s)at 300 K.At the same time,the influence ofⅤ/Ⅲratio on the transport properties and crystal quality of Al_(0.2)In_(0.8)Sb/InAs_(x)Sb_(1-x)quantum well heterostructures also has been investigated.As a result,the Al_(0.2)In_(0.8)Sb/InAs_(0.4)Sb_(0.6)quantum well heterostructure with a channel thickness of 30 nm grown under the conditions of Sb/In ratio of 6 and As/In ratio of 3 has a maximum electron mobility of 28300 cm^(2)/V·s and a minimum RMS roughness of 0.68 nm.Through optimizing the growth conditions,our samples have higher electron mobility and smoother surface morphology.展开更多
Background:In this present study,we have screened major phytoconstituents of Nilavembu Kudineer against critical COVID-19 target proteins that cause severe pneumonia globally.In addition,a human receptor protein that ...Background:In this present study,we have screened major phytoconstituents of Nilavembu Kudineer against critical COVID-19 target proteins that cause severe pneumonia globally.In addition,a human receptor protein that facilitates viral entry into the host cell was also targeted.Methods:Phytoconstituents derived from Nilavembu Kudineer formulation were docked against 12 major proteins,which help viral entry,viral proliferation,and a human receptor facilitate the viral entry into the host cells.The major metabolites of Nilavembu Kudineer were retrieved based on literature from the PubChem database.The docked complex was subjected to MD simulation studies to verify its binding mode and the stability of the interactions.The binding energy analysis was performed to estimate the binding affinity between the compounds and their respective receptors using MM/GBSA.Results:Docking studies have shown that three major plants in the polyherbal formulation,Andrographis paniculata,Mollugo cerviana,and Zingiber officinale,have 14 potential compounds that have better binding affinity against COVID-19 proteins and their host receptor protein.MD studies and binding energy calculations also confirmed that these compounds possess better stability and strong binding energy with these proteins.Conclusion:In silico analyses suggest that phytoconstituents from Nilavembu Kudineer possess promising multi-target antiviral activity against COVID-19.These findings provide a rationale for further experimental studies to validate their therapeutic potential for the treatment of COVID-19.展开更多
Glaucoma,a degenerative optic neuropathy,causes retinal ganglion cell(RGC)apoptosis and irreversible vision loss.Current therapies often fail to stop disease progression despite lowering intraocular pressure,the main ...Glaucoma,a degenerative optic neuropathy,causes retinal ganglion cell(RGC)apoptosis and irreversible vision loss.Current therapies often fail to stop disease progression despite lowering intraocular pressure,the main risk factor.Thus,neuroprotective strategies have gained interest.We performed a bibliometric analysis to determine global publishing trends and relationships among prolific authors,publications,institutions,funding agencies,and journals.We also analyzed author keywords to identify research hotspots in glaucoma neuroprotection.Further,based on keyword analysis,we reviewed most recent literature to understand mechanistic pathways underlying glaucomarelated pathophysiological responses leading to RGC loss.Bibliographic data were sourced from Scopus.Basic bibliographic features were characterized using Scopus’s functions.VOSviewer was used for mapping and visualizing bibliometric networks.The analysis included trends in publications since 2000,the most prolific countries,institutions,authors,and the strength of their linkages.A significant increase in publication output over the past two decades was noted.The United States leads in funding support,research output,and citation links,followed by China and the UK.Among the top 10 most cited authors,three are from Japanese institutions.Keyword analysis shows a focus on molecular targets related to ischemia,excitotoxicity,inflammation,and oxidative stress,with fewer emerging drug candidates and limited clinical trials.Based on the most recent literature,emerging molecular targets underlying these key pathophysiological mechanisms are summarized.In conclusion,while pathophysiology and molecular mechanisms are the current focus,there is not much progress in developing new drug candidates and conducting clinical trials.展开更多
基金supported by Macao Science and Technology Development Fund,Macao SAR,China(Grant No.:0043/2023/AFJ)the National Natural Science Foundation of China(Grant No.:22173038)Macao Polytechnic University,Macao SAR,China(Grant No.:RP/FCA-01/2022).
文摘Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction.However,traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules.Similarly,graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information.To address these limitations,we propose a novel fingerprint-enhanced hierarchical graph neural network(FH-GNN)for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints.The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks(D-MPNN)on a hierarchical molecular graph that integrates atomic-level,motif-level,and graph-level information along with their relationships.Addi-tionally,we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features,creating a comprehensive molecular embedding that integrated hierarchical mo-lecular structures with domain knowledge.Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction,validating its capability to comprehensively capture molecular informa-tion.By integrating molecular structure and chemical knowledge,FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates.
基金Supported by the National Human Genetic Resources Sharing Service Platform,No.PT-2024-0303Qingdao Medical and Health Research Guidance Project,No.2023-WJZD202.
文摘Colorectal cancer(CRC)ranks among the top causes of cancer-related fatalities globally.Recent progress in genomics,proteomics,and bioinformatics has greatly improved our comprehension of the molecular underpinnings of CRC,paving the way for targeted therapies and immunotherapies.Nonetheless,obstacles such as tumor heterogeneity and drug resistance persist,hindering advancements in treatment efficacy.In this context,the integration of artificial intelligence(AI)and organoid technology presents promising new avenues.AI can analyze genetic and clinical data to forecast disease risk,prognosis,and treatment responses,thereby expediting drug development and tailoring treatment plans.Organoids replicate the genetic traits and biological behaviors of tumors,acting as platforms for drug testing and the formulation of personalized treatment approaches.Despite notable strides in CRC research and treatment-from genetic insights to therapeutic innovations-numerous challenges endure,including the intricate tumor microen-vironment,tumor heterogeneity,adverse effects of immunotherapies,issues related to AI data quality and privacy,and the need for standardization in organoid culture.Future initiatives should concentrate on clarifying the pathogenesis of CRC,refining AI algorithms and organoid models,and creating more effective therapeutic strategies to alleviate the global impact of CRC.
文摘Pancreatic cancer, particularly pancreatic ductal adenocarcinoma(PDAC), is one of the most lethal malignancies,which is characterized by a complex tumor microenvironment(TME) that fosters immune evasion and treatment resistance. Recent genomic advancements have unveiled diverse molecular subtypes of PDAC, providing insights into targeted therapies and precision medicine. This review synthesizes the current understanding of PDAC's molecular characterization and immunosuppressive TME, as well as emerging therapeutic strategies, including innovative approaches targeting key molecular pathways such as kirsten rat sarcoma viral oncogene homolog(KRAS), epidermal growth factor receptor(EGFR), and immune checkpoints. Despite advances, challenges remain in overcoming treatment resistance and inherent heterogeneity of pancreatic cancer subtypes. We highlight the need for multidisciplinary collaboration to enhance early diagnosis and develop individualized therapeutic protocols, paving the way for improving the outcomes of this aggressive cancer. This integrated perspective underscores the urgency of transforming the innovative research into pancreatic cancer management.
基金funded by the United Arab Emirates UniversityResearch Officegrant number 12F041 to KM。
文摘Advancements in molecular approaches have been utilized to breed crops with a wide range of economically valuable traits to develop superior cultivars.This review provides a concise overview of modern breakthroughs in molecular plant production.Genotyping and high-throughput phenotyping methods for predictive plant breeding are briefly discussed.In this study,we explore contemporary molecular breeding techniques for producing desirable crop varieties.These techniques include cisgenesis,clustered regularly interspaced short palindromic repeat(CRISPR/Cas9)gene editing,haploid induction,and de novo domestication.We examine the speed breeding approach-a strategy for cultivating plants under controlled conditions.We further highlight the significance of modern breeding technologies in efficiently utilizing agricultural resources for crop production in urban areas.The deciphering of crop genomes has led to the development of extensive DNA markers,quantitative trait loci(QTLs),and pangenomes associated with various desirable crop traits.This shift to the genotypic selection of crops considerably expedites the plant breeding process.Based on the plant population used,the connection between genotypic and phenotypic data provides several genetic elements,including genes,markers,and alleles that can be used in genomic breeding and gene editing.The integration of speed breeding with genomic-assisted breeding and cutting-edge genome editing tools has made it feasible to rapidly manipulate and generate multiple crop cycles and accelerate the plant breeding process.Breakthroughs in molecular techniques have led to substantial improvements in modern breeding methods.
基金supported by the Yonsei University graduate school Department of Integrative Biotechnology.
文摘Recently,diffusion models have emerged as a promising paradigm for molecular design and optimization.However,most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geom-etries,with limited research on molecular sequence diffusion models.The International Union of Pure and Applied Chemistry(IUPAC)names are more akin to chemical natural language than the simplified molecular input line entry system(SMILES)for organic compounds.In this work,we apply an IUPAC-guided conditional diffusion model to facilitate molecular editing from chemical natural language to chemical language(SMILES)and explore whether the pre-trained generative performance of diffusion models can be transferred to chemical natural language.We propose DiffIUPAC,a controllable molecular editing diffusion model that converts IUPAC names to SMILES strings.Evaluation results demonstrate that our model out-performs existing methods and successfully captures the semantic rules of both chemical languages.Chemical space and scaffold analysis show that the model can generate similar compounds with diverse scaffolds within the specified constraints.Additionally,to illustrate the model’s applicability in drug design,we conducted case studies in functional group editing,analogue design and linker design.
基金supported by the open research fund of Songshan Lake Materials Laboratory(2023SLABFN18)the Anhui Provincial Natural Science Foundation(2308085QB46)+2 种基金the Scientific Research Foundation of Education Department of Anhui Province of China(2022AH010025,2023AH051109)the Key Research and Development Program of Anhui Province of China(2022l07020011)The open research fund of the Anhui Key Lab of Metal Material and Processing(RZ2200002901)。
文摘Aqueous zinc-ion batteries(AZIBs)have regained interest due to their inherent safety and costeffectiveness.However,the zinc anode is notorious for side reactions and dendrite growth,which plague the practical application of AZIBs.Adjusting the interfacial pH to reduce the by-products has been proven to be effective in protecting the zinc anode.Nevertheless,the dynamic regulation of the inherently unstable zinc interface during prolonged cycling remains a significant challenge.Herein,zwitterionic N-tris(hydroxymethyl)methylglycine(TMG)integrated with negative-COO^(-)and positive NH_(2)^(+)groups is proposed to stabilize the Zn anode and extend the lifespan as a self-regulating interfacial additive.The anionic portion serves as a trapping site to balance the interfacial pH and thus mitigate the unintended side reactions.Simultaneously,the NH_(2)^(+)cations are anchored on the zinc surface,forming a water-shielding,zincophilic molecular layer that guides three-dimensional diffusion and promotes uniform electro-deposition.Thus,an average plating efficiency of 99.74%over 3300 cycles at a current density of2 mA cm^(-2)is achieved.Notably,the TMG additive actualizes ultralong life in Zn‖Zn symmetrical cells(5500 h,exceeding 229 days,1 mA cm^(-2)/1 mA h cm^(-2)),and enables the Zn‖I_(2)cells to reach capacity retention rate of 89.4%after 1000 cycles at 1 A g^(-1).
基金funded by the National Key Research and Development Program of China(No.2022YFC2804101)the Guangdong Provincial Key R&D Program(No.2023B1111050011)+2 种基金the Guangdong Basic and Applied Basic Research Foundation(No.2023A1515010432)the Guangzhou Basic and Applied Basic Research Foundation(No.202201010305)the High-Level Talents Special Program of Zhejiang(No.2022R52036)。
文摘Guided by molecular networking,nine novel curvularin derivatives(1-9)and 16 known analogs(10-25)were isolated from the hydrothermal vent sediment fungus Penicillium sp.HL-50.Notably,compounds 5-7 represented a hybrid of curvularin and purine.The structures and absolute configurations of compounds 1-9 were elucidated via nuclear magnetic resonance(NMR)spectroscopy,X-ray diffraction,electronic circular dichroism(ECD)calculations,^(13)C NMR calculation,modified Mosher's method,and chemical derivatization.Investigation of anti-inflammatory activities revealed that compounds 7-9,11,12,14,15,and 18 exhibited significant suppressive effects against lipopolysaccharide(LPS)-induced nitric oxide(NO)production in murine macrophage RAW264.7 cells,with IC_(50)values ranging from 0.44 to 4.40μmol·L^(-1).Furthermore,these bioactive compounds were found to suppress the expression of inflammation-related proteins,including inducible NO synthase(i NOS),cyclooxygenase-2(COX-2),NLR family pyrin domain-containing protein 3(NLRP3),and nuclear factor kappa-B(NF-κB).Additional studies demonstrated that the novel compound 7 possessed potent antiinflammatory activity by inhibiting the transcription of inflammation-related genes,downregulating the expression of inflammation-related proteins,and inhibiting the release of inflammatory cytokines,indicating its potential application in the treatment of inflammatory diseases.
基金supported by the National Natural Science Foundation of China(52304021,52104022,52204031)the Natural Science Foundation of Sichuan Province(2022NSFSC0205,2024NSFSC0201,2023NSFSC0947)the National Science and Technology Major Projects of China(2017ZX05049006-010).
文摘The global energy demand is increasing rapidly,and it is imperative to develop shale hydrocarbon re-sources vigorously.The prerequisite for enhancing the exploitation efficiency of shale reservoirs is the systematic elucidation of the occurrence characteristics,flow behavior,and enhanced oil recovery(EOR)mechanisms of shale oil within commonly developed nanopores.Molecular dynamics(MD)technique can simulate the occurrence,flow,and extraction processes of shale oil at the nanoscale,and then quantitatively characterize various fluid properties,flow characteristics,and action mechanisms under different reservoir conditions by calculating and analyzing a series of MD parameters.However,the existing review on the application of MD simulation in shale oil reservoirs is not systematic enough and lacks a summary of technical challenges and solutions.Therefore,recent MD studies on shale oil res-ervoirs were summarized and analyzed.Firstly,the applicability of force fields and ensembles of MD in shale reservoirs with different reservoir conditions and fluid properties was discussed.Subsequently,the calculation methods and application examples of MD parameters characterizing various properties of fluids at the microscale were summarized.Then,the application of MD simulation in the study of shale oil occurrence characteristics,flow behavior,and EOR mechanisms was reviewed,along with the elucidation of corresponding micro-mechanisms.Moreover,influencing factors of pore structure,wall properties,reservoir conditions,fluid components,injection/production parameters,formation water,and inorganic salt ions were analyzed,and some new conclusions were obtained.Finally,the main challenges associated with the application of MD simulations to shale oil reservoirs were discussed,and reasonable prospects for future MD research directions were proposed.The purpose of this review is to provide theoretical basis and methodological support for applying MD simulation to study shale oil reservoirs.
基金Funded by the National Natural Science Foundation of China(No.52370128)the Fundamental Research Funds for the Central Universities(No.2572022AW54)。
文摘This study identified castor oil and phosphate ester as effective retarders through setting time,tensile,and flexural tests,and determined their optimal dosages.The mechanism by which phosphate ester affects the setting time of polyurethane was further investigated using molecular dynamics simulations.Fourier transform infrared spectroscopy was also employed to systematically study the physical and chemical interactions between phosphate esters and polyurethane materials.The results demonstrate that a 1%concentration of phosphate ester provides the most effective retarding effect with minimal impact on the strength of polyurethane.When phosphate ester is added to the B component of the two-component polyurethane system,its interaction energy with component A decreases,as do the diffusion coefficient and aggregation degree of component B on the surface of component A.This reduction in interaction slows the setting time.Additionally,the addition of phosphate ester to polyurethane leads to the disappearance or weakening of functional groups,indicating competitive interactions within the phosphate ester components that inhibit the reaction rate.
基金financial support from the National Key R&D Program of China(2021YFB3801200)the National Natural Science Foundation of China(22278051,22178044,22308043)CNPC Innovation Found(2022DQ02-0608)。
文摘Carbon capture is an important strategy and is implemented to achieve the goals of CO_(2)reduction and carbon neutrality.As a high energy-efficient technology,membrane-based separation plays a crucial role in CO_(2)capture.It is urgently needed for membrane-based CO_(2)capture to develop the high-performance membrane materials with high permeability,selectivity,and stability.Herein,ultrapermeable carbon molecular sieve(CMS)membranes are fabricated by py roly zing a finely-engineered benzoxazole-containing copolyimide precursor for efficient CO_(2)capture.The microstructure of CMS membrane has been optimized by initially engineering the precursor-chemistry and subsequently tuning the pyrolysis process.Deep insights into the structure-property relationship of CMSs are provided in detail by a combination of experimental characterization and molecular simulations.We demonstrate that the intrinsically high free volume environment of the precursor,coupled with the steric hindrance of thermostable contorted fragments,promotes the formation of loosely packed and ultramicroporous carbon structures within the resultant CMS membrane,thereby enabling efficient CO_(2)discrimination via size sieving and affinity.The membrane achieves an ultrahigh CO_(2)permeability,good selectivity,and excellent stability.After one month of long-term operation,the CO_(2)permeability in the mixed gas is maintained at 11,800 Barrer,with a CO_(2)/N_(2)selectivity exceeding 60.This study provides insights into the relationship between precursor-chemistry and CMS performance,and our ultrapermeable CMS membrane,which is scalable using thin film manufacturing,holds great potential for industrial CO_(2)capture.
基金Funded by the Research Funds of China University of Mining and Technology(No.102523215)。
文摘The pre-wetting of aggregate surface is a means to improve the interface performance of SBS modified asphalt and aggregate.The effect of pre-wetting technology on the interaction between SBS modified asphalt and aggregate was analyzed by molecular dynamics simulation.The diffusion coefficient and concentration distribution of SBS modified asphalt on aggregate surface are included.The simulation results show that the diffusion coefficient of the aggregate surface of SBS modified asphalt is increased by 47.6%and 70.5%respectively after 110#asphalt and 130#asphalt are pre-wetted.The concentration distribution of SBS modified asphalt on the aggregate surface after pre-wetting is more uniform.According to the results of interface energy calculation,the interface energy of SBS modified bitumen and aggregate can be increased by about 5%after pre-wetting.According to the results of molecular dynamics simulation,the pre-wetting technology can effectively improve the interface workability of SBS modified bitumen and aggregate,so as to improve the interface performance.
基金funding from National Science Foundation of China(52202337 and 22178015)the Young Taishan Scholars Program of Shandong Province(tsqn202211082)+1 种基金Natural Science Foundation of Shandong Province(ZR2023MB051)Independent Innovation Research Project of China University of Petroleum(East China)(22CX06023A).
文摘Layer-structured Ruddlesden–Popper(RP)perovskites(RPPs)with decent stability have captured the imagination of the photovoltaic research community and bring hope for boosting the development of perovskite solar cell(PSC)technology.However,two-dimensional(2D)or quasi-2D RP PSCs are encountered with some challenges of the large exciton binding energy,blocked charge transport and poor film quality,which restrict their photovoltaic performance.Fortunately,these issues can be readily resolved by rationally designing spacer cations of RPPs.This review mainly focuses on how to design the molecular structures of organic spacers and aims to endow RPPs with outstanding photovoltaic applications.We firstly elucidated the important roles of organic spacers in impacting crystallization kinetics,charge transporting ability and stability of RPPs.Then we brought three aspects to attention for designing organic spacers.Finally,we presented the specific molecular structure design strategies for organic spacers of RPPs aiming to improve photovoltaic performance of RP PSCs.These proposed strategies in this review will provide new avenues to develop novel organic spacers for RPPs and advance the development of RPP photovoltaic technology for future applications.
文摘The complex morphological,anatomical,physiological,and chemical mechanisms within the aging brain have been the hot topic of research for centuries.The aging process alters the brain structure that affects functions and cognitions,but the worsening of such processes contributes to the pathogenesis of neurodegenerative disorders,such as Alzheimer's disease.Beyond these observable,mild morphological shifts,significant functional modifications in neurotransmission and neuronal activity critically influence the aging brain.Understanding these changes is important for maintaining cognitive health,especially given the increasing prevalence of age-related conditions that affect cognition.This review aims to explore the age-induced changes in brain plasticity and molecular processes,differentiating normal aging from the pathogenesis of Alzheimer's disease,thereby providing insights into predicting the risk of dementia,particularly Alzheimer's disease.
基金Foundation of Northwest Institute for Nonferrous Metal Research(ZZXJ2203)Capital Projects of Financial Department of Shaanxi Province(YK22C-12)+3 种基金Innovation Capability Support Plan in Shaanxi Province(2023KJXX-083)Key Research and Development Projects of Shaanxi Province(2024GXYBXM-351,2024GX-YBXM-356)National Natural Science Foundation of China(62204207,12204383)Xi'an Postdoctoral Innovation Base Funding Program。
文摘The extraordinary strength of metal/graphene composites is significantly determined by the characteristic size,distribution and morphology of graphene.However,the effect of the graphene size/distribution on the mechanical properties and related strengthening mechanisms has not been fully elucidated.Herein,under the same volume fraction and distribution conditions of graphene,molecular dynamics simulations were used to investigate the effect of graphene sheet size on the hardness and deformation behavior of Cu/graphene composites under complex stress field.Two models of pure single crystalline Cu and graphene fully covered Cu matrix composite were constructed for comparison.The results show that the strengthening effect changes with varying the graphene sheet size.Besides the graphene dislocation blocking effect and the load-bearing effect,the deformation mechanisms change from stacking fault tetrahedron,dislocation bypassing and dislocation cutting to dislocation nucleation in turn with decreasing the graphene sheet size.The hardness of Cu/graphene composite,with the graphene sheet not completely covering the metal matrix,can even be higher than that of the fully covered composite.The extra strengthening mechanisms of dislocation bypassing mechanism and the stacking fault tetrahedra pinning dislocation mechanism contribute to the increase in hardness.
文摘Since the discovery of carbon dots(CDs)in 2004,the unique photoluminescence phenomenon of CDs has attracted widespread attention.However,the molecular weight of CDs has not been adequately quantified at present,due to CDs are atomically imprecise and their molecular weight distribution is broad.In this paper,a series of Pluronic-modified CDs were prepared and the structure of the CDs was briefly analyzed.Subsequently,a molecular weight measurement method based on colligative properties was developed,and the correction coefficient in the algorithm was briefly analyzed.The calculated molecular weight was applied to the determination of surface adsorption capacity.This work provided a method for averaging the molecular weight of atomically imprecise particulate materials,which is expected to provide new opportunities in related fields.
文摘High-quality antiferromagnetic(AFM)θ-phase manganese nitride(MnN)films were successfully grown on MgO(001)substrates by plasma-assisted molecular beam epitaxy.Structural analysis confirms the high-quality MnN film has a tetragonal distortion with a c/a ratio of~0.98.The film exhibits exceptional stability in both aqueous and ambient conditions,which is a crucial factor for practical applications.Electrical transport reveals its metallic behavior with an upturn at low temperatures,which could be attributed to the Kondo effect originated from nitrogen vacancy-induced magnetic impurities.Room temperature exchange bias has been demonstrated in a MnN/CoFeB heterostructure,verifying the AFM ordering of MnN.Considering its high Néel temperature~650 K,superior stability,and low-cost,this work highlights the epitaxial MnN films as a promising candidate for AFM spintronic applications.
基金Supported by the Natural Science Basic Research Program of Shaanxi Province(2023-JC-QN-0758)Shaanxi University of Science and Technology Research Launch Project(2020BJ-26)Doctoral Research Initializing Fund of Hebei University of Science and Technology,China(1181476).
文摘This paper discusses the influence of Sb/In ratio on the transport properties and crystal quality of the 200 nm InAs_(x)Sb_(1-x)thin film.The Sb content of InAs_(x)Sb_(1-x)thin film in all samples was verified by HRXRD of the symmetrical 004 reflections and asymmetrical 115 reflections.The calculation results show that the Sb component was 0.6 in the InAs_(x)Sb_(1-x)thin film grown under the conditions of Sb/In ratio of 6 and As/In ratio of 3,which has the highest electron mobility(28560 cm^(2)/V·s)at 300 K.At the same time,the influence ofⅤ/Ⅲratio on the transport properties and crystal quality of Al_(0.2)In_(0.8)Sb/InAs_(x)Sb_(1-x)quantum well heterostructures also has been investigated.As a result,the Al_(0.2)In_(0.8)Sb/InAs_(0.4)Sb_(0.6)quantum well heterostructure with a channel thickness of 30 nm grown under the conditions of Sb/In ratio of 6 and As/In ratio of 3 has a maximum electron mobility of 28300 cm^(2)/V·s and a minimum RMS roughness of 0.68 nm.Through optimizing the growth conditions,our samples have higher electron mobility and smoother surface morphology.
文摘Background:In this present study,we have screened major phytoconstituents of Nilavembu Kudineer against critical COVID-19 target proteins that cause severe pneumonia globally.In addition,a human receptor protein that facilitates viral entry into the host cell was also targeted.Methods:Phytoconstituents derived from Nilavembu Kudineer formulation were docked against 12 major proteins,which help viral entry,viral proliferation,and a human receptor facilitate the viral entry into the host cells.The major metabolites of Nilavembu Kudineer were retrieved based on literature from the PubChem database.The docked complex was subjected to MD simulation studies to verify its binding mode and the stability of the interactions.The binding energy analysis was performed to estimate the binding affinity between the compounds and their respective receptors using MM/GBSA.Results:Docking studies have shown that three major plants in the polyherbal formulation,Andrographis paniculata,Mollugo cerviana,and Zingiber officinale,have 14 potential compounds that have better binding affinity against COVID-19 proteins and their host receptor protein.MD studies and binding energy calculations also confirmed that these compounds possess better stability and strong binding energy with these proteins.Conclusion:In silico analyses suggest that phytoconstituents from Nilavembu Kudineer possess promising multi-target antiviral activity against COVID-19.These findings provide a rationale for further experimental studies to validate their therapeutic potential for the treatment of COVID-19.
基金Supported by the Ministry of Higher Education(Malaysia)(No.FRGS/1/2023/SKK15/IMU/01/1)International Medical University[No.PHMS I-2023(01)].
文摘Glaucoma,a degenerative optic neuropathy,causes retinal ganglion cell(RGC)apoptosis and irreversible vision loss.Current therapies often fail to stop disease progression despite lowering intraocular pressure,the main risk factor.Thus,neuroprotective strategies have gained interest.We performed a bibliometric analysis to determine global publishing trends and relationships among prolific authors,publications,institutions,funding agencies,and journals.We also analyzed author keywords to identify research hotspots in glaucoma neuroprotection.Further,based on keyword analysis,we reviewed most recent literature to understand mechanistic pathways underlying glaucomarelated pathophysiological responses leading to RGC loss.Bibliographic data were sourced from Scopus.Basic bibliographic features were characterized using Scopus’s functions.VOSviewer was used for mapping and visualizing bibliometric networks.The analysis included trends in publications since 2000,the most prolific countries,institutions,authors,and the strength of their linkages.A significant increase in publication output over the past two decades was noted.The United States leads in funding support,research output,and citation links,followed by China and the UK.Among the top 10 most cited authors,three are from Japanese institutions.Keyword analysis shows a focus on molecular targets related to ischemia,excitotoxicity,inflammation,and oxidative stress,with fewer emerging drug candidates and limited clinical trials.Based on the most recent literature,emerging molecular targets underlying these key pathophysiological mechanisms are summarized.In conclusion,while pathophysiology and molecular mechanisms are the current focus,there is not much progress in developing new drug candidates and conducting clinical trials.
