Article
Biochemistry & Molecular Biology
Annalisa Calo, Aitziber Eleta-Lopez, Thierry Ondarcuhu, Albert Verdaguer, Alexander M. Bittner
Summary: This study used atomic force microscopy to investigate the nanoscale wetting of Tobacco Mosaic virions, revealing a high sensitivity of multifrequency AFM in visualizing condensed water and sub-micrometer droplets at relative humidity levels above 100%.
Article
Chemistry, Multidisciplinary
Levente Juhasz, Roberto D. Ortuso, Kaori Sugihara
Summary: The study utilized quantitative friction force microscopy to measure the response of polydiacetylene to lateral forces, revealing the necessity of applying shear forces to characterize it at the nanoscale. The experiment confirmed the erroneous nature of the hypothesis regarding the higher force sensitivity at the edges and discovered a correlation between mechanochromism and thermochromism.
Article
Chemistry, Multidisciplinary
Egbert Zojer
Summary: Decorating pore walls of covalent organic frameworks (COFs) with assemblies of polar entities can tune the electronic properties of the inner surfaces. This modification changes the electrostatic energy within the pores, affecting charge separation, redox reactions, and catalysis in COF heterojunctions.
Article
Chemistry, Multidisciplinary
Victor G. Gisbert, Carlos A. Amo, Miriam Jaafar, Agustina Asenjo, Ricardo Garcia
Summary: Bimodal AFM operated in a bimodal configuration enables high quantitative accuracy and high-spatial resolution mapping of magnetic interactions, providing a self-evaluation protocol to test the accuracy of measurements and supporting the application of mapping long-range magnetic interactions quantitatively.
Article
Biochemical Research Methods
Kosuke Ogata, Chia-Feng Tsai, Yasushi Ishihama
Summary: An improved workflow was established for highly sensitive multiplexed quantitative phosphoproteomics using a nanoscale solid-phase TMT labeling reactor. The optimized protocol allowed for quantifying selumetinib-regulated phosphorylated sites in HeLa proteins with a nearly 10-fold increase in sensitivity compared to conventional methods. Raw MS data files have been deposited and made publicly available for further analysis.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Iris Kemler, Bhargav Karamched, Claudia Neuhauser, David Dingli
Summary: Using engineered viruses for tumor therapy is an exciting and novel approach, but success depends on establishing infection and ongoing propagation of the virus within the tumor. Understanding these complex dynamics requires mathematical and computational models as well as noninvasive monitoring methods.
Article
Materials Science, Multidisciplinary
D. E. Feldman, Bertrand I. Halperin
Summary: Fabry-Pérot interferometry is a tool to study anyon statistics in the quantum Hall effect. The interference phase is a combination of quantized statistical phase and Aharonov-Bohm phase. However, there are challenges due to the finite width of edge states and the presence of multiple localized anyons.
Article
Biochemical Research Methods
Ning Zhang, Chao Yue, Xiaobo Zhan, Zhi Cheng, Chao Li, Yaohua Du, Feng Tian
Summary: The quantitative analysis of respiratory viruses is important for diagnosis, medicine and prognosis. In this study, a lab-on-a-chip platform combined with an automated control system was used to achieve quantitative analysis of COVID-19 pseudovirus from large-volume nasal swab samples. The method can be extended to other respiratory viruses and sample types.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Hadrien M. L. Robert, Kristyna Holanova, Lukasz Bujak, Milan Vala, Verena Henrichs, Zdenek Lansky, Marek Piliarik
Summary: The study introduces a high-speed photothermal spatial light modulator capable of generating a step-like wavefront change without diffraction artifacts, used for quantitative phase imaging to capture nanometer-scale 3D displacements.
NATURE COMMUNICATIONS
(2021)
Review
Materials Science, Multidisciplinary
Jeena George, Sowjanya Mannepalli, Kiran S. R. N. Mangalampalli
Summary: This comprehensive review discusses the use of in situ conductive nanoindentation to study the electromechanical behavior of materials, providing valuable insights into nanoscale plasticity and electrical phenomena. By monitoring real-time electrical signal changes during indentation cycles, researchers can quantify electromechanical properties and understand phenomena like dielectric breakdown and electrical contacts in thin films. This method is crucial for developing miniaturized smart technologies and advancing our understanding of material plasticity at the nanoscale.
ADVANCED ENGINEERING MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Kyle Crocker, Joshua Johnson, Wolfgang Pfeifer, Carlos Castro, Ralf Bundschuh
Summary: A physical model is developed to predict the probability of DNA origami nano-hinges containing gold nanoparticles being open at different temperatures based on partition function analysis. The model accurately matches experimental data and reveals important microscopic interactions influencing macroscopic behavior. This insight could inform future designs incorporating nanoparticles into dynamic DNA origami structures.
Article
Food Science & Technology
Zhendi Yu, Zhangkai Xu, Jiang Chen, Lili Chen, Ningbo Liao, Ronghua Zhang, Dongqing Cheng
Summary: Foodborne diseases are a critical food safety issue globally, with shellfish carrying various foodborne viruses posing a risk of infection. Factors such as age, season, and type of shellfish are associated with different levels of infection risk.
Article
Chemistry, Multidisciplinary
Ian Hamilton, Magdalena Gebala, Daniel Herschlag, Rick Russell
Summary: We developed a disulfide cross-linking approach, xHEED, to measure the distance-dependent encounter frequency of DNA helices in solution. Our measurements define the relevant distances for electrostatic interactions of nucleic-acid helices and provide insights into the impact of different ionic conditions on these forces.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Materials Science, Multidisciplinary
Ebenezer O. Fanijo, Joseph G. Thomas, Yizheng Zhu, Javier Esquivel Guerrero, Niamh C. Hosking, Wenjun Cai, F. Marc Michel, Alexander S. Brand
Summary: This research study demonstrates the application of spectral modulation interferometry (SMI) for in situ nanoscale characterization of corrosion of an aluminum alloy. SMI provides accurate real-time quantification of surface topography evolution during corrosion with high sensitivity and rapid image acquisition. The results validate the applicability of SMI for in situ nanoscale characterization of a corroding alloy surface.
MATERIALS CHARACTERIZATION
(2022)
Article
Food Science & Technology
Ewelina Bigoraj, Iwona Kozyra, Agnieszka Kaupke, Zbigniew Osinski, James Lowther, Artur Rzezutka
Summary: The aim of this study was to assess the prevalence of human enteric viruses in mussels sold on the Polish market and study the fecal contamination of shellfish. The study found that human enteric viruses were commonly present in shellfish, with norovirus being the most frequently detected. The study also observed a seasonal distribution pattern of viruses in shellfish samples.
Article
Biophysics
Aida Sanz Calderon, Miguel Cantero, Uxia Perez, Paula Ortega-Gonzalez, Carmen San Martin, Pedro. J. de Pablo, Miguel Manso Silvan, Mercedes Hernando-Perez
Summary: Studies on the adsorption of viruses on surfaces with optimized properties have attracted attention due to their influence on the retention, orientation, and stability of viral capsids. Additionally, viruses can be used as cages or vectors in various fields. The physical properties of virus nanocages, such as their mechanical response and surface charge distribution, are crucial for their applications. This study demonstrates the strong surface interactions of two viruses on homogeneous hydrophobic surfaces and compares their mechanical properties with those on mica and graphite surfaces. The functionalized surfaces are validated as platforms for the characterization of virus particles, contributing to the understanding of their physical properties.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Physics, Multidisciplinary
R. Blossey, R. Podgornik
Summary: We present a comprehensive continuum model that can handle both electrostatic and structural interactions in liquid dielectrics. Using a two-order parameter description based on charge density and polarization, we derive a field-theoretic model that generalizes previous theories. Our theory explicitly includes electrostatic and structural interactions in the bulk of the liquid and allows for polarization charges within a Drude model. We provide a detailed description of the boundary conditions, including the charge regulation mechanism and surface polarization, and analyze an exemplary model case. Future applications for predicting and validating experimental results are outlined.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2023)
Article
Biochemistry & Molecular Biology
Daniel Luque, Alvaro Ortega-Esteban, Alejandro Valbuena, Jose Luis Vilas, Alicia Rodriguez-Huete, Mauricio G. Mateu, Jose R. Caston
Summary: The biological function of macromolecular complexes depends on large-scale transitions and small-scale conformational fluctuations. This study validates the use of cryo-EM to investigate the equilibrium dynamics of biomolecular complexes by comparing LR data with quantitative information obtained by an established solution technique. Cryo-EM provides high spatial resolution and allows simultaneous acquisition of atomic structure and local equilibrium dynamics.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Virology
K. Strobl, M. G. Mateu, Pedro J. de Pablo
Summary: In the infection cycle of viruses, the release of their genome in the host cell occurs during uncoating. Through various physicochemical procedures, we induce and monitor the in vitro uncoating of ssDNA from individual MVM particles. Our experiments reveal two pathways of genome release: i) filamentous ssDNA appears around intact virus particles with gradual mechanical fatigue and moderate heating (50 degrees C). ii) condensed ssDNA structures appear when the virus particles are disrupted by mechanical nanoindentations, guanidinium chloride denaturing agent, and high temperature (70 degrees C). It is proposed that filamentous ssDNA is externalized through one channel of the capsid pores when the capsid integrity is conserved. However, the disruption of virus particles reveals a native structure of condensed genome. Mechanical analysis confirms the stabilization role of ssDNA in MVM after DNA strands ejection.
Article
Multidisciplinary Sciences
Natalia Martin-Gonzalez, Alfonso Gomez-Gonzalez, Mercedes Hernando-Perez, Michael Bauer, Urs F. Greber, Carmen San Martin, Pedro J. de Pablo
Summary: Protein V in human adenovirus connects the inner capsid surface to the outer genome layer, providing mechanical reinforcement and facilitating genome release.
Review
Biochemistry & Molecular Biology
Wai-Yim Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
Summary: In this review, the authors use density functional theory calculations to analyze the atomic-scale interactions and consequences of mutations in the spike protein of SARS-CoV-2. They provide a detailed description of the key amino acids and functions of each domain and speculate on how mutations affect these properties. The results show that S-protein mutations in different variants cause increased positive charge, altered interatomic interactions, and disrupted hydrogen bond networks.
Article
Biotechnology & Applied Microbiology
Kevin Isgrig, Alexander X. Cartagena-Rivera, Hong Jun Wang, Mhamed Grati, Katharine A. Fernandez, Thomas B. Friedman, Inna A. Belyantseva, Wade Chien
Summary: Recent studies have shown that inner ear gene therapy can improve auditory function in hereditary hearing loss, and the gene therapy for Ildr1w-/- mice has multiple effects on auditory function.
Article
Chemistry, Multidisciplinary
Alejandro Valbuena, Klara Strobl, Juan Carlos Gil-Redondo, Luis Valiente, Pedro J. de Pablo, Mauricio G. Mateu
Summary: This study investigates the uncoating process of human rhinovirus particles using an atomic force microscope. The results show that the high-force event is a stochastic process that leads to structurally weakened virus particles, with different fractions of the RNA molecule being externalized. The kinetics of this reaction are influenced by antiviral compounds or capsid mutation.
Article
Chemistry, Multidisciplinary
Olga V. Konevtsova, Ivan Yu. Golushko, Rudolf Podgornik, Sergei B. Rochal
Summary: Unlike other viruses, Cypoviruses have a doubly protected genome due to being embedded in a perfect polyhedrin crystal. A symmetry-based approach is proposed to predict the interface structure between the capsids and the crystal. The study reveals a remarkable match between the surfaces of Cypovirus and the polyhedrin matrix, highlighting the important role of VP5 proteins in embedding the virus and discussing the relationship between protein activity and superstructure formation.
NANOSCALE ADVANCES
(2023)
Article
Physics, Multidisciplinary
James Daniel Farrell, Jure Dobnikar, Rudolf Podgornik
Summary: The stability of RNA viruses is influenced by genome topology and the interactions between RNA and capsid proteins. Through modeling, the genome topology is encoded as a graph, with adjacent packaging signals mapped to edges. Through simulations and evaluation of osmotic pressure, it is found that virion stability is dependent on both genome topology and degree of confinement. It is predicted that MS2 bacteriophage would prefer a more linear genome topology.
PHYSICAL REVIEW RESEARCH
(2023)
Article
Chemistry, Physical
Hu Ruixuan, Arghya Majee, Jure Dobnikar, Rudolf Podgornik
Summary: This study investigates the interaction between two charge regulating spherical macroions with dielectric interior and dissociable surface groups in a monovalent electrolyte solution. The research finds symmetry breaking transitions from symmetric to asymmetric charge distribution, resulting in annealed charge patchiness and like-charge attraction even in a univalent electrolyte.
EUROPEAN PHYSICAL JOURNAL E
(2023)
Article
Chemistry, Physical
Maria J. Rodriguez-Espinosa, Javier M. Rodriguez, Jose R. Caston, Pedro J. de Pablo
Summary: In this study, we investigated the cargo retention of individual human picobirnavirus virus-like particles with different N-terminal topologies of the capsid protein. Our results show that these different topologies result in distinct cargo release dynamics during mechanical disassembly experiments due to their different interaction with RNA.
NANOSCALE HORIZONS
(2023)
Article
Chemistry, Physical
Sergei B. Rochal, Olga V. Konevtsova, Ivan Yu. Golushko, Rudolf Podgornik
Summary: Understanding the principles of protein arrangement in viral capsids and similar protein shells can lead to the development of new antiviral strategies and the design of artificial protein cages. By analyzing small spherical shells made from a single type of protein, researchers have discovered correlations between protein mass centers and packing arrangements, as well as proposed models for different shapes and anisotropy of proteins. The study also reveals energy and symmetry reasons controlling capsid structures, including handedness and interprotein bonds.
Article
Chemistry, Multidisciplinary
Laetitia Bardet, Herve Roussel, Stefano Saroglia, Masoud Akbari, David Munoz-Rojas, Carmen Jimenez, Aurore Denneulin, Daniel Bellet
Summary: The thermal instability of silver nanowires leads to increased electrical resistance in AgNW networks. Understanding the relationship between structural and electrical properties of AgNW networks is crucial for their integration as transparent electrodes in flexible optoelectronics. In situ X-ray diffraction measurements were used to study the crystallographic evolution of Ag-specific Bragg peaks during thermal ramping, revealing differences in thermal and structural transitions between bare and SnO2-coated AgNW networks.
Article
Chemistry, Multidisciplinary
Nathalia Cancino-Fuentes, Arnau Manasanch, Joana Covelo, Alex Suarez-Perez, Enrique Fernandez, Stratis Matsoukis, Christoph Guger, Xavi Illa, Anton Guimera-Brunet, Maria V. Sanchez-Vives
Summary: This study provides a comprehensive characterization of graphene-based solution-gated field-effect transistors (gSGFETs) for brain recordings, highlighting their potential clinical applications.
Article
Chemistry, Multidisciplinary
Sikandar Aftab, Hailiang Liu, Dhanasekaran Vikraman, Sajjad Hussain, Jungwon Kang, Abdullah A. Al-Kahtani
Summary: This study examines the effects of hybrid nanoparticles made of NiO@rGO and NiO@CNT on the active layers of polymer solar cells and X-ray photodetectors. The findings show that these hybrid nanoparticles can enhance the charge carrier capacities and exciton dissociation properties of the active layers. Among the tested configurations, the NiO@CNT device demonstrates superior performance in converting sunlight into electricity, and achieves the best sensitivity for X-ray detection.
Article
Chemistry, Multidisciplinary
Hyo Jung Shin, Seung Gyu Choi, Fengrui Qu, Min-Hee Yi, Choong-Hyun Lee, Sang Ryong Kim, Hyeong-Geug Kim, Jaewon Beom, Yoonyoung Yi, Do Kyung Kim, Eun-Hye Joe, Hee-Jung Song, Yonghyun Kim, Dong Woon Kim
Summary: This study investigates the role of SOX9 in reactive astrocytes following ischemic brain damage using a PLGA nanoparticle plasmid delivery system. The results demonstrate that PLGA nanoparticles can reduce ischemia-induced neurological deficits and infarct volume, providing a potential opportunity for stroke treatment.
Article
Chemistry, Multidisciplinary
Anurag Chaudhury, Koushik Debnath, Nikhil R. Jana, Jaydeep K. Basu
Summary: The study investigates the interaction between nanoparticles and cell membranes, and identifies key parameters, including charge, crowding, and membrane fluidity, that determine the adsorbed concentration and unbinding transition of nanoparticles.
Article
Chemistry, Multidisciplinary
Sina Sadeghi, Fazel Bateni, Taekhoon Kim, Dae Yong Son, Jeffrey A. Bennett, Negin Orouji, Venkat S. Punati, Christine Stark, Teagan D. Cerra, Rami Awad, Fernando Delgado-Licona, Jinge Xu, Nikolai Mukhin, Hannah Dickerson, Kristofer G. Reyes, Milad Abolhasani
Summary: In this study, an autonomous approach for the development of lead-free metal halide perovskite nanocrystals is presented, which integrates a modular microfluidic platform with machine learning-assisted synthesis modeling. This approach enables rapid and optimized synthesis of copper-based lead-free nanocrystals.
Article
Chemistry, Multidisciplinary
Zahir Abbas, Nissar Hussain, Surender Kumar, Shaikh M. Mobin
Summary: The rational construction of free-standing and flexible electrodes for electrochemical energy storage devices is an emerging research focus. In this study, a redox-active metal-organic framework (MOF) was prepared on carbon nanofibers using an in situ approach, resulting in a flexible electrode with high redox-active behavior and unique properties such as high flexibility and lightweight. The prepared electrode showed excellent cyclic retention and rate capability in supercapacitor applications. Additionally, it could be used as a freestanding electrode in flexible devices at different bending angles.
Article
Chemistry, Multidisciplinary
Lishan Zhang, Xiaoting Zhang, Hui Ran, Ze Chen, Yicheng Ye, Jiamiao Jiang, Ziwei Hu, Miral Azechi, Fei Peng, Hao Tian, Zhili Xu, Yingfeng Tu
Summary: Photodynamic therapy (PDT) is a promising local treatment modality in cancer therapy, but its therapeutic efficacy is restricted by ineffective delivery of photosensitizers and tumor hypoxia. In this study, a phototactic Chlorella-based near-infrared (NIR) driven green affording-oxygen microrobot system was developed for enhanced PDT. The system exhibited desirable phototaxis and continuous oxygen generation, leading to the inhibition of tumor growth in mice. This study demonstrates the potential of using a light-driven green affording-oxygen microrobot to enhance photodynamic therapy.
Article
Chemistry, Multidisciplinary
Yujin Li, Jing Xu, Xinqi Luo, Futing Wang, Zhong Dong, Ke-Jing Huang, Chengjie Hu, Mengyi Hou, Ren Cai
Summary: In this study, hollow heterostructured materials were constructed using an innovative template-engaged method as cathodes for zinc-ion batteries. The materials exhibited fast Zn2+ transport channels, improved electrical conductivity, and controlled volume expansion during cycling. The designed structure allowed for an admirable reversible capacity and high coulombic efficiency.
Article
Chemistry, Multidisciplinary
Paritosh Mahato, Shashi Shekhar, Rahul Yadav, Saptarshi Mukherjee
Summary: This study comprehensively elucidates the role of the core and electrostatic surface of metal nanoclusters in catalytic reduction reactions. The electrostatic surface dramatically modulates the reactivity of metal nanoclusters.
Article
Chemistry, Multidisciplinary
Pei Liu, Mengdi Liang, Zhengwei Liu, Haiyu Long, Han Cheng, Jiahe Su, Zhongbiao Tan, Xuewen He, Min Sun, Xiangqian Li, Shuai He
Summary: This study demonstrates a simple and environmentally-friendly method for the synthesis of zinc oxide nanozymes (ZnO NZs) using wasted hop extract (WHE). The WHE-ZnO NZs exhibit exceptional peroxidase-like activity and serve as effective catalysts for the oxidation of 3,3,5,5-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide (H2O2). In addition, a straightforward colorimetric technique for detecting both H2O2 and glucose was developed using the WHE-ZnO NZs as peroxidase-like catalysts.
Article
Chemistry, Multidisciplinary
Hyunkyu Oh, Young Jun Lee, Eun Ji Kim, Jinseok Park, Hee-Eun Kim, Hyunsoo Lee, Hyunjoo Lee, Bumjoon J. Kim
Summary: Mesoporous carbon particles have unique structural properties that make them suitable as support materials for catalytic applications. This study investigates the impact of channel nanostructures on the catalytic activity of porous carbon particles (PCPs) by fabricating PCPs with controlled channel exposure on the carbon surface. The results show that PCPs with highly open channel nanostructures exhibit significantly higher catalytic activity compared to those with closed channel nanostructures.
Article
Chemistry, Multidisciplinary
Yunjie Lu, Zhaohui Li, Zewei Li, Shihao Zhou, Ning Zhang, Jianming Zhang, Lu Zong
Summary: A tough, long-lasting adhesive and highly conductive nanocomposite hydrogel (PACPH) was fabricated via the synergy of interfacial entanglement and adhesion group densification. PACPH possesses excellent mechanical properties, interfacial adhesion strength, and conductivity, making it a promising material for long-term monitoring of human activities and electrocardiogram signals.
Article
Chemistry, Multidisciplinary
Zichao Wei, Audrey Vandergriff, Chung-Hao Liu, Maham Liaqat, Mu-Ping Nieh, Yu Lei, Jie He
Summary: We have developed a simple method to prepare polymer-grafted plasmonic metal nanoparticles with pH-responsive surface-enhanced Raman scattering. By using pH-responsive polymers as ligands, the aggregation of nanoparticles can be controlled, leading to enhanced SERS. The pH-responsive polymer-grafted nanoparticles show high reproducibility and sensitivity in solution, providing a novel approach for SERS without the need for sample pre-concentration.
Article
Chemistry, Multidisciplinary
Melis Ozge Alas Colak, Ahmet Gungor, Merve Buldu Akturk, Emre Erdem, Rukan Genc
Summary: This research investigates the effect of functionalizing carbon dots with hydroxyl polymers on their performance as electrode materials in a supercapacitor. The results show that the functionalized carbon dots exhibit excellent electrochemical performance and improved stability.
