Soft Matter最新文献_第8页

Probing nanopores: molecular dynamics insights into the mechanisms of DNA and protein translocation through solid-state and biological nanopores

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-11 DOI: 10.1039/D4SM01534G

Yuanshuo Zhang and Mingming Ding

{"title":"Probing nanopores: molecular dynamics insights into the mechanisms of DNA and protein translocation through solid-state and biological nanopores","authors":"Yuanshuo Zhang and Mingming Ding","doi":"10.1039/D4SM01534G","DOIUrl":"10.1039/D4SM01534G","url":null,"abstract":"Nanopore sequencing technology has revolutionized single-molecule analysis through its unique capability to detect and characterize individual biomolecules with unprecedented precision. This perspective provides a comprehensive analysis of molecular dynamics (MD) simulations in nanopore research, with particular emphasis on comparing molecular transport mechanisms between biological and solid-state platforms. We first examine how MD simulations at atomic resolution reveal distinct characteristics: biological nanopores exhibit sophisticated molecular recognition through specific amino acid interactions, while solid-state nanopores demonstrate advantages in structural stability and geometric control. Through detailed analysis of simulation methodologies and their applications, we show how computational approaches have advanced our understanding of critical phenomena such as ion selectivity, conformational dynamics, and surface effects in both nanopore types. Despite computational challenges including limited simulation timescales and force field accuracy constraints, recent advances in high-performance computing and artificial intelligence integration have significantly improved simulation capabilities. By synthesizing perspectives from physics, chemistry, biology, and computational science, this perspective provides both theoretical insights and practical guidelines for developing next-generation nanopore platforms. The integration of computational and experimental approaches discussed here offers promising directions for advancing nanopore technology in applications ranging from DNA/RNA sequencing and protein post-translational modification analysis to disease diagnosis and drug screening.","PeriodicalId":103,"journal":{"name":"Soft Matter","volume":" 13","pages":" 2385-2399"},"PeriodicalIF":2.9,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The underappreciated role of nonspecific interactions in the crystallization of DNA-coated colloids†

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-11 DOI: 10.1039/D5SM00001G

Hunter Seyforth, Sambarta Chatterjee, Thomas E. Videbæk, Manodeep Mondal, William M. Jacobs and W. Benjamin Rogers

{"title":"The underappreciated role of nonspecific interactions in the crystallization of DNA-coated colloids†","authors":"Hunter Seyforth, Sambarta Chatterjee, Thomas E. Videbæk, Manodeep Mondal, William M. Jacobs and W. Benjamin Rogers","doi":"10.1039/D5SM00001G","DOIUrl":"10.1039/D5SM00001G","url":null,"abstract":"Over the last decade, the field of programmable self-assembly has seen an explosion in the diversity of crystal lattices that can be synthesized from DNA-coated colloidal nanometer- and micrometer-scale particles. The prevailing wisdom has been that a particular crystal structure can be targeted by designing the DNA-mediated interactions, to enforce binding between specific particle pairs, and the particle diameters, to control the packing of the various species. In this article, we show that other ubiquitous nonspecific interactions can play equally important roles in determining the relative stability of different crystal polymorphs and therefore what crystal structure is most likely to form in an experiment. For a binary mixture of same-sized DNA-coated colloidal micrometer-scale particles, we show how changing the magnitudes of nonspecific steric and van der Waals interactions gives rise to a family of binary body-centered tetragonal crystals, including both cesium–chloride and copper–gold crystals. Simulations using pair potentials that account for these interactions reproduce our experimental observations quantitatively, and a theoretical model reveals how a subtle balance between specific and nonspecific forces determines the equilibrium crystal structure. These results highlight the importance of accounting for nonspecific interactions in the crystal-engineering design process.","PeriodicalId":103,"journal":{"name":"Soft Matter","volume":" 14","pages":" 2654-2663"},"PeriodicalIF":2.9,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/sm/d5sm00001g?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Smectic-like bundle formation of planktonic bacteria upon nutrient starvation†

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-11 DOI: 10.1039/D4SM01117A

Takuro Shimaya, Fumiaki Yokoyama and Kazumasa A. Takeuchi

引用次数: 0

Immobilization and interfacial activation of lipase at liquid and solid interfaces.

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-10 DOI: 10.1039/d4sm01218f

P Giefer, U Fritsching, L Colombi Ciacchi, S Köppen-Hannemann

{"title":"Immobilization and interfacial activation of lipase at liquid and solid interfaces.","authors":"P Giefer, U Fritsching, L Colombi Ciacchi, S Köppen-Hannemann","doi":"10.1039/d4sm01218f","DOIUrl":"https://doi.org/10.1039/d4sm01218f","url":null,"abstract":"This study investigates the adsorption behaviour of Candida rugosa lipase at silica/water and oil/water interfaces by means of molecular dynamics simulations. The findings reveal distinct adsorption orientations and structural differences that can be related to different enzymatic activities and selectivities. At the silica/water interface, lipase adsorbs with the LID region facing the solvent, in a configuration that is not fully open, but still grants access to its catalytic triad, as shown by tunnel calculations. These also reveal the presence of two ester-exit tunnels, suggesting a high catalytic turnover capability of the adsorbed enzyme. Docking simulations predict binding of triacylglyceride substrates with marked selectivity regarding the length of the hydrophobic chains and the substrate chirality. At the oil/water interface, lipase adsorbs via the LID region with widely open ingress tunnels, facilitating direct substrate extraction from the interface. The two opposite adsorption orientations allow favorable interactions of silica-immobilized lipase with oil droplets that cause no appreciable change in the conformation, activity, or selectivity. These results provide a molecular-scale rationalization of the lipid hydrolysis mechanisms that support the deployment of lipase immobilized in ceramic membranes for lipolytic applications.","PeriodicalId":103,"journal":{"name":"Soft Matter","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Topological sorting of magnetic colloidal bipeds†

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-10 DOI: 10.1039/D4SM01480D

Aneena Rinu Perayil, Piotr Kuświk, Maciej Urbaniak, Feliks Stobiecki, Sapida Akhundzada, Arno Ehresmann, Daniel de las Heras and Thomas M. Fischer

引用次数: 0

Recent advances in nanoprecipitation: from mechanistic insights to applications in nanomaterial synthesis

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-10 DOI: 10.1039/D5SM00006H

Muzammil Kuddushi, Chiranjeevi Kanike, Ben Bin Xu and Xuehua Zhang

{"title":"Recent advances in nanoprecipitation: from mechanistic insights to applications in nanomaterial synthesis","authors":"Muzammil Kuddushi, Chiranjeevi Kanike, Ben Bin Xu and Xuehua Zhang","doi":"10.1039/D5SM00006H","DOIUrl":"10.1039/D5SM00006H","url":null,"abstract":"Nanoprecipitation is a versatile, low-energy technique for synthesizing nanomaterials through controlled precipitation, enabling precise tuning of material properties. This review offers a comprehensive and up-to-date perspective on nanoprecipitation, focusing on its role in nanoparticle synthesis and its adaptability in designing diverse nanostructures. The review begins with the foundational principles of nanoprecipitation, emphasizing the impact of key parameters such as flow rate, mixing approach, injection rate, and Reynolds number on nanomaterial characteristics. It also discusses the influence of physicochemical factors, including solvent choice, polymer type, and drug properties. Various nanoprecipitation configurations—batch, flash, and microfluidic are examined for their specific advantages in controlling particle size, morphology, and internal structure. The review further explores the potential of nanoprecipitation to create complex nanostructures, such as core–shell particles, Janus nanoparticles, and porous and semiconducting polymer nanoparticles. Applications in biomedicine and other fields highlight nanoprecipitation's promise as a sustainable and tunable method for fabricating advanced nanomaterials. Finally, the review identifies future directions, including scaling microfluidic techniques, expanding compatibility with hydrophilic compounds, and integrating machine learning to further enhance the development of nanoprecipitation.","PeriodicalId":103,"journal":{"name":"Soft Matter","volume":" 15","pages":" 2759-2781"},"PeriodicalIF":2.9,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/sm/d5sm00006h?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Combining integral equation closures with force density functional theory for the study of inhomogeneous fluids

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-07 DOI: 10.1039/D4SM01262C

S. M. Tschopp, H. Vahid, A. Sharma and J. M. Brader

引用次数: 0

Investigation on the fast phase transition mechanism of flow-induced oriented iPB-1†

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-06 DOI: 10.1039/D5SM00019J

Lincheng Ji, Heng Zhang, Youxin Ji, Fengmei Su and Chuntai Liu

{"title":"Investigation on the fast phase transition mechanism of flow-induced oriented iPB-1†","authors":"Lincheng Ji, Heng Zhang, Youxin Ji, Fengmei Su and Chuntai Liu","doi":"10.1039/D5SM00019J","DOIUrl":"10.1039/D5SM00019J","url":null,"abstract":"The phase transition mechanism of isotactic polybutene-1 (iPB-1) has always been a central research topic in the fields of polymer physics and industrial application. Phase transition kinetics of the flow-induced oriented form II is significantly faster than the isotropic form II that crystallizes under quiescent condition. In this study, combining the in situ X ray diffraction technique and a homemade extensional rheometer, the influence of amorphous region on the transformation kinetics was been investigated. Results indicated that annealing above the melting temperature (Tm) decreased the phase transition rate, while annealing below the Tm exhibited no obvious impact on the phase transition rate when the annealing time was only 5 min. However, prolonging the annealing time significantly reduced the phase transition kinetics. Remarkably, the crystallinity remained constant during the annealing process, while it exhibited an increase during the subsequent cooling process. The SAXS measurements showed that long spacing decreased after annealing. It is speculated that extended chains in the amorphous region are relaxed and shortened during the annealing process. This work recommends the rapid cooling of iPB-1 products in industrial manufacturing to prevent the relaxation of amorphous chains and promote the phase transition process.","PeriodicalId":103,"journal":{"name":"Soft Matter","volume":" 14","pages":" 2686-2693"},"PeriodicalIF":2.9,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of biobased poly(urethanes-co-oxazolidones) organogels†

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-06 DOI: 10.1039/D5SM00020C

Salvatore Impemba, Damiano Bandelli, Rosangela Mastrangelo, Giovanna Poggi, David Chelazzi and Piero Baglioni

{"title":"Development of biobased poly(urethanes-co-oxazolidones) organogels†","authors":"Salvatore Impemba, Damiano Bandelli, Rosangela Mastrangelo, Giovanna Poggi, David Chelazzi and Piero Baglioni","doi":"10.1039/D5SM00020C","DOIUrl":"10.1039/D5SM00020C","url":null,"abstract":"Polyurethanes are largely employed in various fields such as building, insulation and adhesive industries, but there is the constant need to develop sustainable formulations using “green” components and feasible processes. Here, a new series of sustainable castor oil and epoxidized castor oil-based (CO/EpCO) polyurethane networks was synthetized and characterized. The added epoxy functions react with isocyanates forming oxazolidinone linkages in the gels’ network, reducing the gelation time from over 3 hours up to 0.5 hours, increasing thermal resistance from 385 °C to 400 °C, tuning the gels’ chemical affinity to organic solvents, and modulating some of their structural features at the nanoscale (e.g., polymer mesh size and characteristic persistence lengths), which altogether affect the mechanical behavior and the functionality of the gels. The key features of the new gels are fast gelation, good mechanical properties in the solvent-less and swollen states, and interactions with organic solvents, together with the high sustainability of the whole syntethic process. These features make the novel poly(urethanes-co-oxazolidones) castor oil organogels promising sustainable materials for potential use in several scientific and technological fields, ranging from cleaning/detergency to the adhesives and sealant industry.","PeriodicalId":103,"journal":{"name":"Soft Matter","volume":" 14","pages":" 2623-2632"},"PeriodicalIF":2.9,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/sm/d5sm00020c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Banded phases in topological flocks

IF 2.9 3区化学

Soft Matter Pub Date : 2025-03-06 DOI: 10.1039/D4SM01066C

Charles R. Packard and Daniel M. Sussman

{"title":"Banded phases in topological flocks","authors":"Charles R. Packard and Daniel M. Sussman","doi":"10.1039/D4SM01066C","DOIUrl":"10.1039/D4SM01066C","url":null,"abstract":"Flocking phase transitions arise in many aligning active soft matter systems, and an interesting question concerns the role of “topological” vs. “metric” interactions on these transitions. While recent theoretical work suggests that the order–disorder transition in these polar aligning models is universally first order, numerical studies have suggested that topological models may instead have a continuous transition. Some recent simulations have found that some variations of topologically interacting flocking agents have a discontinuous transition, but unambiguous observations of phase coexistence using common Voronoi-based alignment remains elusive. In this work, we use a custom GPU-accelerated simulation package to perform million-particle-scale simulations of a Voronoi–Vicsek model in which alignment interactions stem from an XY-like Hamiltonian. By accessing such large systems on appropriately long time scales and in the time-continuous limit, we are able to show a regime of stable phase coexistence between the ordered and disordered phases, confirming the discontinuous nature of this transition in the thermodynamic limit.","PeriodicalId":103,"journal":{"name":"Soft Matter","volume":" 14","pages":" 2646-2653"},"PeriodicalIF":2.9,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/sm/d4sm01066c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0