From the perspective of experimental practice: High-throughput computational screening in photocatalysis

Photocatalysis,a critical strategy for harvesting sunlight to address energy demand and environmental concerns,is underpinned by the discovery of high-performance photocatalysts,thereby how to design photocatalysts is now generating widespread interest in boosting the conversion effi-ciency of solar energy.In the past decade,computational technologies and theoretical simulations have led to a major leap in the development of high-throughput computational screening strategies for novel high-efficiency photocatalysts.In this viewpoint,we started with introducing the challenges of photocatalysis from the view of experimental practice,especially the inefficiency of the traditional“trial and error”method.Sub-sequently,a cross-sectional comparison between experimental and high-throughput computational screening for photocatalysis is presented and discussed in detail.On the basis of the current experimental progress in photocatalysis,we also exemplified the various challenges associated with high-throughput computational screening strategies.Finally,we offered a preferred high-throughput computational screening procedure for pho-tocatalysts from an experimental practice perspective(model construction and screening,standardized experiments,assessment and revision),with the aim of a better correlation of high-throughput simulations and experimental practices,motivating to search for better descriptors.

High-throughput computational screening and in vitro evaluation identifies 5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl)phenyl]-1H-isoindole-1,3(2H)-dione(C3),as a novel EGFR—HER2 dual inhibitor in gastric tumors

Gastric cancers are caused primarily due to the activation and amplification of the EGFR or HER2 kinases resulting in cell proliferation,adhesion,angiogenesis,and metastasis.Conventional therapies are ineffective due to the intra-tumoral heterogeneity and concomitant genetic mutations.Hence,dual inhibition strategies are recommended to increase potency and reduce cytotoxicity.In this study,we have conducted computational high-throughput screening of the ChemBridge library followed by in vitro assays and identified novel selective inhibitors that have a dual impediment of EGFR/HER2 kinase activities.Diversity-based High-throughput Virtual Screening(D-HTVS)was used to screen the whole ChemBridge small molecular library against EGFR and HER2.The atomistic molecular dynamic simulation was conducted to understand the dynamics and stability of the protein-ligand complexes.EGFR/HER2 kinase enzymes,KATOIII,and Snu-5 cells were used for in vitro validations.The atomistic Molecular Dynamics simulations followed by solvent-based Gibbs binding free energy calculation of top molecules,identified compound C3(5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl)phenyl]-1H-isoindole-1,3(2H)-dione)to have a good affinity for both EGFR and HER2.The predicted compound,C3,was promising with better binding energy,good binding pose,and optimum interactions with the EGFR and HER2 residues.C3 inhibited EGFR and HER2 kinases with IC50 values of 37.24 and 45.83 nM,respectively.The GI50 values of C3 to inhibit KATOIII and Snu-5 cells were 84.76 and 48.26 nM,respectively.Based on these findings,we conclude that the identified compound C3 showed a conceivable dual inhibitory activity on EGFR/HER2 kinase,and therefore can be considered as a plausible lead-like molecule for treating gastric cancers with minimal side effects,though testing in higher models with pharmacokinetic approach is required.

High-throughput computational screening and design of nanoporous materials for methane storage and carbon dioxide capture

The globally increasing concentrations of greenhouse gases in atmosphere after combustion of coal-or petroleum-based fuels give rise to tremendous interest in searching for porous materials to efficiently capture carbon dioxide(CO_2) and store methane(CH4), where the latter is a kind of clean energy source with abundant reserves and lower CO_2 emission. Hundreds of thousands of porous materials can be enrolled on the candidate list, but how to quickly identify the really promising ones, or even evolve materials(namely, rational design high-performing candidates) based on the large database of present porous materials? In this context, high-throughput computational techniques, which have emerged in the past few years as powerful tools, make the targets of fast evaluation of adsorbents and evolving materials for CO_2 capture and CH_4 storage feasible. This review provides an overview of the recent computational efforts on such related topics and discusses the further development in this field.

MatCloud, a high-throughput computational materials infrastructure： Present, future visions, and challenges

MatCloud provides a high-throughput computational materials infrastructure for the integrated management of materials simulation, data, and computing resources. In comparison to AFLOW, Material Project, and NoMad, MatCloud delivers two-fold functionalities： a computational materials platform where users can do on-line job setup, job submission and monitoring only via Web browser, and a materials properties simulation database. It is developed under Chinese Materials Genome Initiative and is a China own proprietary high-throughput computational materials infrastructure. MatCloud has been on line for about one year, receiving considerable registered users, feedbacks, and encouragements. Many users provided valuable input and requirements to MatCloud. In this paper, we describe the present MatCloud, future visions, and major challenges. Based on what we have achieved, we will endeavour to further develop MatCloud in an open and collaborative manner and make MatCloud a world known China-developed novel software in the pressing area of high-throughput materials calculations and materials properties simulation database within Material Genome Initiative.

Transfer learning aided high-throughput computational design of oxygen evolution reaction catalysts in acid conditions

Sluggish oxygen evolution reaction(OER)in acid conditions is one of the bottlenecks that prevent the wide adoption of proton exchange membrane water electrolyzer for green hydrogen production.Despite recent advancements in developing high-performance catalysts for acid OER,the current electrocatalysts still rely on iridium-and ruthenium-based materials,urging continuous efforts to discover better performance catalysts as well as reduce the usage of noble metals.Pyrochlore structured oxide is a family of potential high-performance acid OER catalysts with a flexible compositional space to tune the electrochemical capabilities.However,exploring the large composition space of pyrochlore compounds demands an imperative approach to enable efficient screening.Here we present a highthroughput screening pipeline that integrates density functional theory calculations and a transfer learning approach to predict the critical properties of pyrochlore compounds.The high-throughput screening recommends three sets of candidates for potential acid OER applications,totaling 61 candidates from 6912 pyrochlore compounds.In addition to 3d-transition metals,p-block metals are identified as promising dopants to improve the catalytic activity of pyrochlore oxides.This work demonstrates not only an efficient approach for finding suitable pyrochlores towards acid OER but also suggests the great compositional flexibility of pyrochlore compounds to be considered as a new materials platform for a variety of applications.

High-throughput computational screening of oxide double perovskites for optoelectronic and photocatalysis applications

Oxide double perovskites A2 B’B"O6 are a class of emerging materials in the fields of optoelectronics and catalysis.Due to the chemical flexibilities of perovskite structures,there are multiple elemental combinations of cations A,B’,and B",which leading to tremendous candidates.In this study,we comprehensively screened stable oxide double perovskite A2 B’B"O6 from a pool of 2,018 perovskite candidates using a high-throughput computational approach.By considering a tolerance factor(t)-octahedral factor(μ) phase diagram,138 candidates with Fm 3 m, P21/c,and R3 c phases were selected and systematically studied via first-principles calculations based on density functional theory.The screening procedure finally predicted the existence of 21 stable perovskites,and 14 among them have never been reported.Verification with existing experimental results demonstrates that the prediction accuracy for perovskite formability is approximately 90%.The predicted oxide double perovskites exhibit quasi-direct bandgaps ranging from 0 to 4.4 eV with a significantly small direct-indirect bandgap difference,balanced electron and hole effective masses,and strong optical absorptions.The newly predicted oxide double perovskites may enlarge the pool of material candidates for applications in optoelectronics and photocatalysis.This study provides a route for computational screening of novel perovskites for functional applications.

High-throughput computational screening of Cu-MOFs with open metal sites for efficient C_2H_2/C_2H_4 separation

Cost effective separation of acetylene(C_2H_2)and ethylene(C_2H_4)is of key importance to obtain essential chemical raw materials for polymer industry.Due to the low compression limit of C_2H_2,there is an urgent demand to develop suitable materials for efficiently separating the two gases under ambient conditions.In this paper,we provided a high-throughput screening strategy to study porous metal-organic frameworks(MOFs)containing open metal sites(OMS)for C_2H_2/C_2H_4 separation,followed by a rational design of novel MOFs in-silico.A set of accurate force fields was established from ab initio calculations to describe the critical role of OMS towards guest molecules.From a large-scale computational screening of 916 experimental Cu-paddlewheel-based MOFs,three materials were identified with excellent separation performance.The structure-performance relationships revealed that the optimal materials should have the largest cavity diameter around 5-10?and pore volume in-between 0.3-1.0 cm^3 g^(-1).Based on the systematic screening study result,three novel MOFs were further designed with the incorporation of fluorine functional group.The results showed that Cu-OMS and the-F group on the aromatic rings close to Cu sites could generate a synergistic effect on the preferential adsorption of C_2H_2 over C_2H_4,leading to a remarkable improvement of C_2H_2 separation performance of the materials.The findings could provide insight for future experimental design and synthesis of high-performance nanostructured materials for C_2H_2/C_2H_4 separation.

Data-Driven Healthcare:The Role of Computational Methods in Medical Innovation

The purpose of this review is to explore the intersection of computational engineering and biomedical science,highlighting the transformative potential this convergence holds for innovation in healthcare and medical research.The review covers key topics such as computational modelling,bioinformatics,machine learning in medical diagnostics,and the integration of wearable technology for real-time health monitoring.Major findings indicate that computational models have significantly enhanced the understanding of complex biological systems,while machine learning algorithms have improved the accuracy of disease prediction and diagnosis.The synergy between bioinformatics and computational techniques has led to breakthroughs in personalized medicine,enabling more precise treatment strategies.Additionally,the integration of wearable devices with advanced computational methods has opened new avenues for continuous health monitoring and early disease detection.The review emphasizes the need for interdisciplinary collaboration to further advance this field.Future research should focus on developing more robust and scalable computational models,enhancing data integration techniques,and addressing ethical considerations related to data privacy and security.By fostering innovation at the intersection of these disciplines,the potential to revolutionize healthcare delivery and outcomes becomes increasingly attainable.

Advances in data-assisted high-throughput computations for material design

Extensive trial and error in the variable space is the main cause of low efficiency and high cost in material development.The experimental tasks can be reduced significantly in the case that the variable space is narrowed down by reliable computer simulations.Because of their numerous variables in material design,however,the variable space is still too large to be accessed thoroughly even with a computational approach.High-throughput computations(HTC)make it possible to complete a material screening in a large space by replacing the conventionally manual and sequential operations with automatic,robust,and concurrent streamlines.The efficiency of HTC,which is one of the pillars of materials genome engineering,has been verified in many studies,but its applications are still limited by demanding computational costs.Introduction of data mining and artificial intelligence into HTC has become an effective approach to solve the problem.In the past years,many studies have focused on the development and application of HTC and data combined approaches,which is considered as a new paradigm in computational materials science.This review focuses on the main advances in the field of data-assisted HTC for material research and development and provides our outlook on its future development.

Computational Experiments for Complex Social Systems:Experiment Design and Generative Explanation

Powered by advanced information technology,more and more complex systems are exhibiting characteristics of the cyber-physical-social systems(CPSS).In this context,computational experiments method has emerged as a novel approach for the design,analysis,management,control,and integration of CPSS,which can realize the causal analysis of complex systems by means of“algorithmization”of“counterfactuals”.However,because CPSS involve human and social factors(e.g.,autonomy,initiative,and sociality),it is difficult for traditional design of experiment(DOE)methods to achieve the generative explanation of system emergence.To address this challenge,this paper proposes an integrated approach to the design of computational experiments,incorporating three key modules:1)Descriptive module:Determining the influencing factors and response variables of the system by means of the modeling of an artificial society;2)Interpretative module:Selecting factorial experimental design solution to identify the relationship between influencing factors and macro phenomena;3)Predictive module:Building a meta-model that is equivalent to artificial society to explore its operating laws.Finally,a case study of crowd-sourcing platforms is presented to illustrate the application process and effectiveness of the proposed approach,which can reveal the social impact of algorithmic behavior on“rider race”.

Hypergraph Computation

Practical real-world scenarios such as the Internet,social networks,and biological networks present the challenges of data scarcity and complex correlations,which limit the applications of artificial intelligence.The graph structure is a typical tool used to formulate such correlations,it is incapable of modeling highorder correlations among different objects in systems;thus,the graph structure cannot fully convey the intricate correlations among objects.Confronted with the aforementioned two challenges,hypergraph computation models high-order correlations among data,knowledge,and rules through hyperedges and leverages these high-order correlations to enhance the data.Additionally,hypergraph computation achieves collaborative computation using data and high-order correlations,thereby offering greater modeling flexibility.In particular,we introduce three types of hypergraph computation methods:①hypergraph structure modeling,②hypergraph semantic computing,and③efficient hypergraph computing.We then specify how to adopt hypergraph computation in practice by focusing on specific tasks such as three-dimensional(3D)object recognition,revealing that hypergraph computation can reduce the data requirement by 80%while achieving comparable performance or improve the performance by 52%given the same data,compared with a traditional data-based method.A comprehensive overview of the applications of hypergraph computation in diverse domains,such as intelligent medicine and computer vision,is also provided.Finally,we introduce an open-source deep learning library,DeepHypergraph(DHG),which can serve as a tool for the practical usage of hypergraph computation.

Joint computation offloading and parallel scheduling to maximize delay-guarantee in cooperative MEC systems

The growing development of the Internet of Things(IoT)is accelerating the emergence and growth of new IoT services and applications,which will result in massive amounts of data being generated,transmitted and pro-cessed in wireless communication networks.Mobile Edge Computing(MEC)is a desired paradigm to timely process the data from IoT for value maximization.In MEC,a number of computing-capable devices are deployed at the network edge near data sources to support edge computing,such that the long network transmission delay in cloud computing paradigm could be avoided.Since an edge device might not always have sufficient resources to process the massive amount of data,computation offloading is significantly important considering the coop-eration among edge devices.However,the dynamic traffic characteristics and heterogeneous computing capa-bilities of edge devices challenge the offloading.In addition,different scheduling schemes might provide different computation delays to the offloaded tasks.Thus,offloading in mobile nodes and scheduling in the MEC server are coupled to determine service delay.This paper seeks to guarantee low delay for computation intensive applica-tions by jointly optimizing the offloading and scheduling in such an MEC system.We propose a Delay-Greedy Computation Offloading(DGCO)algorithm to make offloading decisions for new tasks in distributed computing-enabled mobile devices.A Reinforcement Learning-based Parallel Scheduling(RLPS)algorithm is further designed to schedule offloaded tasks in the multi-core MEC server.With an offloading delay broadcast mechanism,the DGCO and RLPS cooperate to achieve the goal of delay-guarantee-ratio maximization.Finally,the simulation results show that our proposal can bound the end-to-end delay of various tasks.Even under slightly heavy task load,the delay-guarantee-ratio given by DGCO-RLPS can still approximate 95%,while that given by benchmarked algorithms is reduced to intolerable value.The simulation results are demonstrated the effective-ness of DGCO-RLPS for delay guarantee in MEC.

Secure and Efficient Outsourced Computation in Cloud Computing Environments

Secure and efficient outsourced computation in cloud computing environments is crucial for ensuring data confidentiality, integrity, and resource optimization. In this research, we propose novel algorithms and methodologies to address these challenges. Through a series of experiments, we evaluate the performance, security, and efficiency of the proposed algorithms in real-world cloud environments. Our results demonstrate the effectiveness of homomorphic encryption-based secure computation, secure multiparty computation, and trusted execution environment-based approaches in mitigating security threats while ensuring efficient resource utilization. Specifically, our homomorphic encryption-based algorithm exhibits encryption times ranging from 20 to 1000 milliseconds and decryption times ranging from 25 to 1250 milliseconds for payload sizes varying from 100 KB to 5000 KB. Furthermore, our comparative analysis against state-of-the-art solutions reveals the strengths of our proposed algorithms in terms of security guarantees, encryption overhead, and communication latency.

EG-STC: An Efficient Secure Two-Party Computation Scheme Based on Embedded GPU for Artificial Intelligence Systems

This paper presents a comprehensive exploration into the integration of Internet of Things(IoT),big data analysis,cloud computing,and Artificial Intelligence(AI),which has led to an unprecedented era of connectivity.We delve into the emerging trend of machine learning on embedded devices,enabling tasks in resource-limited environ-ments.However,the widespread adoption of machine learning raises significant privacy concerns,necessitating the development of privacy-preserving techniques.One such technique,secure multi-party computation(MPC),allows collaborative computations without exposing private inputs.Despite its potential,complex protocols and communication interactions hinder performance,especially on resource-constrained devices.Efforts to enhance efficiency have been made,but scalability remains a challenge.Given the success of GPUs in deep learning,lever-aging embedded GPUs,such as those offered by NVIDIA,emerges as a promising solution.Therefore,we propose an Embedded GPU-based Secure Two-party Computation(EG-STC)framework for Artificial Intelligence(AI)systems.To the best of our knowledge,this work represents the first endeavor to fully implement machine learning model training based on secure two-party computing on the Embedded GPU platform.Our experimental results demonstrate the effectiveness of EG-STC.On an embedded GPU with a power draw of 5 W,our implementation achieved a secure two-party matrix multiplication throughput of 5881.5 kilo-operations per millisecond(kops/ms),with an energy efficiency ratio of 1176.3 kops/ms/W.Furthermore,leveraging our EG-STC framework,we achieved an overall time acceleration ratio of 5–6 times compared to solutions running on server-grade CPUs.Our solution also exhibited a reduced runtime,requiring only 60%to 70%of the runtime of previously best-known methods on the same platform.In summary,our research contributes to the advancement of secure and efficient machine learning implementations on resource-constrained embedded devices,paving the way for broader adoption of AI technologies in various applications.

Secure Computation Efficiency Resource Allocation for Massive MIMO-Enabled Mobile Edge Computing Networks

In this article,the secure computation efficiency(SCE)problem is studied in a massive multipleinput multiple-output(mMIMO)-assisted mobile edge computing(MEC)network.We first derive the secure transmission rate based on the mMIMO under imperfect channel state information.Based on this,the SCE maximization problem is formulated by jointly optimizing the local computation frequency,the offloading time,the downloading time,the users and the base station transmit power.Due to its difficulty to directly solve the formulated problem,we first transform the fractional objective function into the subtractive form one via the dinkelbach method.Next,the original problem is transformed into a convex one by applying the successive convex approximation technique,and an iteration algorithm is proposed to obtain the solutions.Finally,the stimulations are conducted to show that the performance of the proposed schemes is superior to that of the other schemes.

Data driven computational design of stable oxygen evolution catalysts by DFT and machine learning:Promising electrocatalysts

The revolutionary development of machine learning(ML),data science,and analytics,coupled with its application in material science,stands as a significant milestone of the scientific community over the last decade.Investigating active,stable,and cost-efficient catalysts is crucial for oxygen evolution reaction owing to the significance in a range of electrochemical energy co nversion processes.In this work,we have demonstrated an efficient approach of high-throughput screening to find stable transition metal oxides under acid condition for high-performance oxygen evolution reaction(OER)catalysts through density functional theory(DFT)calculation and a machine learning algorithm.A methodology utilizing both the Materials Project database and DFT calculations was introduced to assess the acid stability under specific reaction conditions.Building upon this,OER catalytic activity of acid-stable materials was examined,highlighting potential OER catalysts that meet the required properties.We identified IrO_(2),Fe(SbO_(3))_(2),Co(SbO_(3))_(2),Ni(SbO_(3))_(2),FeSbO_(4),Fe(SbO_(3))4,MoWO_(6),TiSnO_(4),CoSbO_(4),and Ti(WO_(4))_(2)as promising catalysts,several of which have already been experimentally discovered for their robust OER performance,while others are novel for experimental exploration,thereby broadening the chemical scope for efficient OER electrocatalysts.Descriptors of the bond length of TM-O and the first ionization energy were used to unveil the OER activity origin.From the calculated results,guidance has been derived to effectively execute advanced high-throughput screenings for the discovery of catalysts with favorable properties.Furthermore,the intrinsic correlation between catalytic performance and various atomic and structural factors was elucidated using the ML algorithm.Through these approaches,we not only streamline the choice of the promising electrocatalysts but also offer insights for the design of varied catalyst models and the discovery of superior catalysts.

Computational Simulation of Aptamer-target Binding Mechanisms

Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as biochemical sensors for medicine,food safety and environmental monitoring.However,there is little research on aptamer-target binding mechanisms,which limits their application and development.Computational simulation has gained much attention for revealing aptamer-target binding mechanisms at the atomic level.This work summarizes the main simulation methods used in the mechanistic analysis of aptamer-target complexes,the characteristics of binding between aptamers and different targets(metal ions,small organic molecules,biomacromolecules,cells,bacteria and viruses),the types of aptamer-target interactions and the factors influencing their strength.It provides a reference for further use of simulations in understanding aptamer-target binding mechanisms.

A fast forward computational method for nuclear measurement using volumetric detection constraints

Owing to the complex lithology of unconventional reservoirs,field interpreters usually need to provide a basis for interpretation using logging simulation models.Among the various detection tools that use nuclear sources,the detector response can reflect various types of information of the medium.The Monte Carlo method is one of the primary methods used to obtain nuclear detection responses in complex environments.However,this requires a computational process with extensive random sampling,consumes considerable resources,and does not provide real-time response results.Therefore,a novel fast forward computational method(FFCM)for nuclear measurement that uses volumetric detection constraints to rapidly calculate the detector response in various complex environments is proposed.First,the data library required for the FFCM is built by collecting the detection volume,detector counts,and flux sensitivity functions through a Monte Carlo simulation.Then,based on perturbation theory and the Rytov approximation,a model for the detector response is derived using the flux sensitivity function method and a one-group diffusion model.The environmental perturbation is constrained to optimize the model according to the tool structure and the impact of the formation and borehole within the effective detection volume.Finally,the method is applied to a neutron porosity tool for verification.In various complex simulation environments,the maximum relative error between the calculated porosity results of Monte Carlo and FFCM was 6.80%,with a rootmean-square error of 0.62 p.u.In field well applications,the formation porosity model obtained using FFCM was in good agreement with the model obtained by interpreters,which demonstrates the validity and accuracy of the proposed method.

Computational fluid dynamics modeling of rapid pyrolysis of solid waste magnesium nitrate hydrate under different injection methods

This study developed a numerical model to efficiently treat solid waste magnesium nitrate hydrate through multi-step chemical reactions.The model simulates two-phase flow,heat,and mass transfer processes in a pyrolysis furnace to improve the decomposition rate of magnesium nitrate.The performance of multi-nozzle and single-nozzle injection methods was evaluated,and the effects of primary and secondary nozzle flow ratios,velocity ratios,and secondary nozzle inclination angles on the decomposition rate were investigated.Results indicate that multi-nozzle injection has a higher conversion efficiency and decomposition rate than single-nozzle injection,with a 10.3%higher conversion rate under the design parameters.The decomposition rate is primarily dependent on the average residence time of particles,which can be increased by decreasing flow rate and velocity ratios and increasing the inclination angle of secondary nozzles.The optimal parameters are injection flow ratio of 40%,injection velocity ratio of 0.6,and secondary nozzle inclination of 30°,corresponding to a maximum decomposition rate of 99.33%.

Flow Field Characteristics of Multi-Trophic Artificial Reef Based on Computation Fluid Dynamics

On the basis of computational fluid dynamics,the flow field characteristics of multi-trophic artificial reefs,including the flow field distribution features of a single reef under three different velocities and the effect of spacing between reefs on flow scale and the flow state,were analyzed.Results indicate upwelling,slow flow,and eddy around a single reef.Maximum velocity,height,and volume of upwelling in front of a single reef were positively correlated with inflow velocity.The length and volume of slow flow increased with the increase in inflow velocity.Eddies were present both inside and backward,and vorticity was positively correlated with inflow velocity.Space between reefs had a minor influence on the maximum velocity and height of upwelling.With the increase in space from 0.5 L to 1.5 L(L is the reef lehgth),the length of slow flow in the front and back of the combined reefs increased slightly.When the space was 2.0 L,the length of the slow flow decreased.In four different spaces,eddies were present inside and at the back of each reef.The maximum vorticity was negatively correlated with space from 0.5 L to 1.5 L,but under 2.0 L space,the maximum vorticity was close to the vorticity of a single reef under the same inflow velocity.