Molecular Systems Design & Engineering最新文献

{"title":"Advancing the self-assembly of binary colloidal crystals of tetrahedra and octahedra with confinement","authors":"Nathan C. Huang, Rachael S. Skye and Julia Dshemuchadse","doi":"10.1039/D5ME00092K","DOIUrl":"https://doi.org/10.1039/D5ME00092K","url":null,"abstract":"<p >Photonic crystals can be self-assembled from binary colloidal dispersions, but the robust assembly of high-quality crystals in quantities sufficient for large-scale applications remains challenging. Here, we study the assembly of polyhedral colloidal nanoparticles at surfaces with spherical and flat-wall geometries to examine the influence of confinement on the process and products of crystallization compared to the bulk. We find that confinement improves crystallization at non-ideal stoichiometries but does not lower the minimal packing fraction at which crystallization occurs. Crystals formed in confinement exhibit higher degrees of crystallinity and lower quantities of secondary-phase defects: the formation of well-ordered layers and shells appears to be promoted by flat walls and spherical container interfaces. These findings demonstrate the potential for enhanced control over the synthesis of novel materials with tailored structures and properties for photonic applications.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 1","pages":" 62-69"},"PeriodicalIF":3.2,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2026/me/d5me00092k?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145982391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and evaluation of novel hydrazide derivatives as NS1 inhibitors for dengue virus: synthesis, experimental, and computational studies","authors":"Swathi Venkatesan, Prathima T. S., Badruzzaman Choudhury, Kaushik Chanda and Balamurali M. M.","doi":"10.1039/D5ME00097A","DOIUrl":"https://doi.org/10.1039/D5ME00097A","url":null,"abstract":"<p >The lack of highly effective therapeutics to treat the life threatening disease caused by dengue virus (Denv) has posed several challenges to the human community. The increasing prevalence of dengue infections has demanded advanced strategies for disease surveillance and to accomplish precise diagnosis across all reported serotypes of Denv. A promising combating approach involved the targeted inhibition of specific viral proteins that are involved in the pathogenesis pathway of the virus. With the recently developed advanced strategies of rational drug design and chemical modifications such approaches have been more successful. Further, the efficacy and specificity of the proposed drugs can further be optimized through structure–activity relationship (SAR) evaluations. With the established role of non-structural protein 1 (NS1) of the dengue virus (dNS1) in pathogenesis, herein a few hydrazide-based derivatives were strategically designed to block its functions including replication, immune evasion, endothelial dysfunction, <em>etc.</em> The inhibition of this protein could effectively curb the viral pathogenicity. Moreover, this study explores the rational design and synthesis of novel hydrazide derivatives to target NS1, thereby offering a potential therapeutic intervention against dengue. The findings could contribute to the advancement of antiviral drug development, addressing the urgent need for effective treatment options against dengue infections.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 208-223"},"PeriodicalIF":3.2,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146147814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction: Identification of MIG7, TGM2, CXCL8, and PDGFC as key genes in colon cancer with a bioinformatics-driven strategy for multi-epitope vaccine design","authors":"Zhenhai Jing, Qing Zhou, Yan Wang, Peng Meng, Yuting Duan and Qing Hong","doi":"10.1039/D5ME90041G","DOIUrl":"https://doi.org/10.1039/D5ME90041G","url":null,"abstract":"<p >Retraction of ‘Identification of MIG7, TGM2, CXCL8, and PDGFC as key genes in colon cancer with a bioinformatics-driven strategy for multi-epitope vaccine design’ by Zhenhai Jing <em>et al.</em>, <em>Mol. Syst. Des. Eng.</em>, 2025, https://doi.org/10.1039/D5ME00104H.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 12","pages":" 1099-1099"},"PeriodicalIF":3.2,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d5me90041g?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145584789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation of the microalgae-enriched nitrogen fertilizer granulation mechanism using the DEM method","authors":"Rasa Šlinkšienė, Vaidas Bivainis and Austėja Mikolaitienė","doi":"10.1039/D5ME00091B","DOIUrl":"https://doi.org/10.1039/D5ME00091B","url":null,"abstract":"<p >The use of granular fertilizers offers significant advantages over traditional powder forms, including improved nutrient distribution, reduced dust, and controlled nutrient release. These benefits enhance plant growth while minimizing negative environmental impacts. The addition of reused materials (recycle) significantly influences the size distribution and strength of granular fertilizers. It was determined that incorporating 60% recycle increases the part of commercial granules (size 2.0–4.0 mm) from 22% to about 68%. However, this increase is accompanied by a decrease in static strength, which drops from 2.8–3.8 MPa to 1.7–2.3 MPa. Modelling granulation processes holds substantial potential for the fertilizer industry, enabling the optimization of high-quality granular fertilizer production while minimizing the need for extensive experimental trials. This approach not only streamlines manufacturing but also ensures consistent nutrient supply, ultimately contributing to improved crop yields and sustainable agricultural practices. In this study, a simulation model based on an actual granulation drum was used to investigate the granulation process of a mixture containing recycled material, crystalline urea, and the microalgae <em>Chlorella vulgaris</em> sp. The granulation simulation data showed that granule formation began within 30 seconds and that the desired quantity of the mixture was produced in just 30 seconds. Throughout the process, the segregation coefficient remained near zero, indicating effective granule formation and distribution.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 1","pages":" 126-138"},"PeriodicalIF":3.2,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2026/me/d5me00091b?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145982389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiscale, techno-economic evaluation of isoreticular series of CALF-20 for biogas upgrading using a pressure/vacuum swing adsorption (PVSA) process","authors":"Changdon Shin, Sunghyun Yoon and Yongchul G. Chung","doi":"10.1039/D5ME00131E","DOIUrl":"https://doi.org/10.1039/D5ME00131E","url":null,"abstract":"<p >Cyclic swing adsorption processes, such as pressure/vacuum swing adsorption (PVSA), is a promising technology for upgrading biogas by separating carbon dioxide (CO<small>₂</small>) from methane (CH<small>₄</small>). The rational design of adsorbent materials with tailored properties is important for deployment of high-performance PVSA technology. Metal–organic frameworks (MOFs), particularly the CALF-20 isoreticular series, have attracted interest due to their high CO<small>₂</small> selectivity, thermal and water stability. In this study, we report a multiscale assessment of CALF-20 and its isoreticular five derivatives by integrating molecular simulations with PVSA process optimization and techno-economic analysis. Structural and adsorption characteristics were calculated and employed to assess how each material performs in terms of energy efficiency and cost. The analysis reveals distinct differences in cost performance among the CALF-20 series, with CALF-20 showing the most favorable economics with &gt;97% purity CH<small>₄</small> production cost at $4.31 per kg of CH<small>₄</small> and energy consumption of 9.35 kWh kg<small>⁻¹</small> of CH<small>₄</small>. This study demonstrates that the integrated material-process optimization framework can effectively guide the search for adsorbent materials for biogas upgrading.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 181-194"},"PeriodicalIF":3.2,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146147813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning-enabled discovery of ionic liquid–solvent electrolytes exhibiting high ionic conductivity","authors":"Masrur Ahmed and Jindal K. Shah","doi":"10.1039/D5ME00146C","DOIUrl":"https://doi.org/10.1039/D5ME00146C","url":null,"abstract":"<p >Ionic liquids (ILs), which are a class of materials with versatile nature and growing popularity, are facing impediments toward widespread usage as electrolytes due to various factors such as low ionic conductivity, high viscosity, high market price <em>etc.</em> One of the ways these limitations can be addressed is by mixing ILs with a molecular solvent. In a combinatorial sense, there exists an immense number of specific IL–solvent combinations. An exhaustive experimental or even simulation-based investigation of the chemical space spanned by such combinations can be extremely time-consuming, expensive, and nearly impossible. An alternative approach is to employ machine learning-based models developed from available databases. Although there exists prior literature that integrates machine learning to investigate mixtures of specific solvents with ILs, these models lack generalization necessitating development of a large number of ML models to handle various solvents. To remedy this shortcoming, as a part of designing green electrolytes with high ionic conductivity that can have potential applications in next-generation batteries and solar cells, this work aims to develop a unified machine learning model to predict ionic conductivity of any IL–solvent mixture system. In this regard, three models, namely, Random Forest, extreme gradient boosting (XGBoost), and artificial neural network (ANN) were formulated using the NIST ILThermo database. The dataset contained 549 unique ionic liquids from 16 cation families and 81 unique solvents, representing a total of 23 712 datapoints. SHAPLEY additive explanation (SHAP) method was used to assess the impact of various features on model prediction and their significance was compared with literature to gain physical insight about the model behavior. Finally, using the developed models, approximately 2.5 million IL–solvent mixtures at five different compositions were screened at room temperature. The high-throughput screening yielded nearly 19 000 IL–solvent mixtures for which ionic conductivity was found to exceed the ionic conductivity of conventional Li-ion battery electrolyte.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 167-180"},"PeriodicalIF":3.2,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2026/me/d5me00146c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146147812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the temperature stability of CRISPR-Cas12b using molecular dynamics simulations","authors":"Yinhao Jia, Katelynn Horvath, Santosh R. Rananaware, Piyush K. Jain and Janani Sampath","doi":"10.1039/D5ME00140D","DOIUrl":"10.1039/D5ME00140D","url":null,"abstract":"<p >The thermal stability of CRISPR-Cas nucleases is a critical factor for their successful application in ‘one-pot’ diagnostic assays that utilize high-temperature isothermal amplification. To understand the atomistic mechanism of stabilization in a previously engineered variant of the thermostable BrCas12b protein, we performed all-atom molecular dynamics (MD) simulations on the wild-type and mutant forms of apo BrCas12b. High-temperature simulations reveal a small structural change along with greater flexibility in the PAM-interacting domain of the mutant BrCas12b, with marginal structural and flexibility changes in the other mutated domains. Comparative essential dynamics analysis between the wild-type and mutant BrCas12b at both ambient and elevated temperatures provides insights into the stabilizing effects of the mutations. Our findings offer comprehensive insights into the important protein motions induced by these mutations. These results provide insights into thermal stability mechanisms in BrCas12b that may inform the future design of CRISPR-based tools.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 195-207"},"PeriodicalIF":3.2,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12624333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145555896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soft material engineered synthetic polymer membranes: bridging design and application","authors":"Ashok K. Pandey","doi":"10.1039/D5ME00121H","DOIUrl":"https://doi.org/10.1039/D5ME00121H","url":null,"abstract":"<p >Soft material-based synthetic polymer membranes are emerging as transformative platforms for energy, environmental, and healthcare technologies, attributed to their flexibility, tunability, and multifunctionality. These membranes are designed through two principal strategies, <em>i.e.</em> pore-filling and surface/interface engineering. Hydrogels could also be used, especially in biomedical applications, with fibre reinforcement to enhance mechanical stability. Pore-filled or “gel-in-shell” membranes incorporate hydrogels or functional soft materials within porous polymer matrices, combining chemical functionality with structural support. These systems enable the fast and selective transport of ions or molecules, finding applications in fuel cells, batteries, solar desalination, and water purification. Stimuli-responsive designs, where thermally, chemically, piezoelectric or optically sensitive polymers are grafted within or onto membrane pores, enable dynamic control over permeability, critical for smart drug delivery and adaptive filtration. Self-healing hydrogels, driven by dynamic bonding or ionic crosslinking, further enhance membrane longevity under operational stress. On the surface engineering side, functionalization <em>via</em> plasma treatment, graft polymerization, layer-by-layer assembly, molecular layer deposition, or mussel-inspired polydopamine coatings enables control over surface charge, hydrophilicity, and antifouling performance. Advanced materials such as MOFs and MXenes could also be incorporated in membrane designs to enhance functional properties. These engineered interfaces, such as surface patterning or nanofiber anchoring of the surface, are crucial for addressing challenges such as fouling, poor selectivity, and biocompatibility issues typically encountered in traditional membranes. Fibre-reinforced hydrogels further expand the application scope into biomedical systems, offering tissue-like mechanical resilience for tissue scaffolds, wound dressings, and wearable biosensors. This review highlights the integrated design of soft material-based membrane systems and their application across clean energy, sustainable water technology, environmental remediation, and biomedical fields. Such multifunctional membranes are central to next-generation technologies aligned with global sustainability goals.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 1","pages":" 7-49"},"PeriodicalIF":3.2,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145982393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A first-principles examination of the ice–cellulose interface: towards bioinspired antifreeze design","authors":"Aakash Kumar and Dilip Gersappe","doi":"10.1039/D5ME00137D","DOIUrl":"https://doi.org/10.1039/D5ME00137D","url":null,"abstract":"<p >Examination of binding of cellulose to ice using <em>ab initio</em> modeling reveals that new C–O bonds are formed on the basal ice surfaces, where some of the O atoms are exposed at the surface due to missing H bonds. Further analysis suggests that the cellulose unit binds in such a way as to form a tetrahedral arrangement at the ice surface, evidenced by a geometric measure of tetrahedrality. This hypothesis is further validated for both primary and secondary prismatic planes. This leads us to conclude that in the case of cellulose molecules, binding at ice is dependent on preserving its tetrahedral bonding arrangement. Our findings suggest that the idea of tetrahedrality is very widely applicable to coordination ranging from water to ice-binding proteins, highlighting a design criterion for novel ice-binding/antifreeze proteins/materials.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 1","pages":" 107-117"},"PeriodicalIF":3.2,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145982324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strategy for the isomerization of dibenzo[b,d]furan-based carbazole derivatives as hole transporting materials for perovskite solar cells: theoretical design and experimental study","authors":"Xin Chen, Jiayi Qi, Xin Jiang, Fei Wu and Xiaorui Liu","doi":"10.1039/D5ME00155B","DOIUrl":"https://doi.org/10.1039/D5ME00155B","url":null,"abstract":"<p >The structural design of hole transport materials (HTMs) is a crucial approach to improving the efficiency and stability of perovskite solar cells (PSCs). In this study, a series of isomeric dibenzo[<em>b</em>,<em>d</em>]furan-based carbazole derivatives (CX11–CX14) were designed to provide a design strategy for the development of HTMs in PSC applications. Side chain isomerism has a significant impact on molecular conjugation, exhibiting distinct isomer-dependent effects in terms of energy levels, planarity, dipole moment, and hole mobility. Furthermore, theoretical calculations and experimental results indicate that the molecule CX11 with superior hole mobility and stronger adsorption on the perovskite surface can act as a potential HTM for PSC applications. According to the results of the optimized PSC devices, the power conversion efficiency (PCE) of the CX11-based PSC exceeded 23%, which is higher than that of devices based on other molecules. The close agreement between computational predictions and experimental validation not only validates the theoretical framework for designing molecular isomers of HTMs but also provides crucial molecular-level insights. The demonstrated methodology is expected to motivate researchers to develop even more efficient HTM isomers for PSCs with higher PCEs.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 1","pages":" 118-125"},"PeriodicalIF":3.2,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145982325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}