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  1. Article ; Online: IgG1-b12-HIV-gp120 Interface in Solution: A Computational Study.

    Martí, Didac / Alemán, Carlos / Ainsley, Jon / Ahumada, Oscar / Torras, Juan

    Journal of chemical information and modeling

    2021  Volume 62, Issue 2, Page(s) 359–371

    Abstract: The use of broadly neutralizing antibodies against human immunodeficiency virus type 1 (HIV-1) has been shown to be a promising therapeutic modality in the prevention of HIV infection. Understanding the b12-gp120 binding mechanism under physiological ... ...

    Abstract The use of broadly neutralizing antibodies against human immunodeficiency virus type 1 (HIV-1) has been shown to be a promising therapeutic modality in the prevention of HIV infection. Understanding the b12-gp120 binding mechanism under physiological conditions may assist the development of more broadly effective antibodies. In this work, the main conformations and interactions between the receptor-binding domain (RBD) of spike glycoprotein gp120 of HIV-1 and the IgG1-b12 mAb are studied. Accelerated molecular dynamics (aMD) and ab initio hybrid molecular dynamics have been combined to determine the most persistent interactions between the most populated conformations of the antibody-antigen complex under physiological conditions. The results show the most persistent receptor-binding mapping in the conformations of the antibody-antigen interface in solution. The binding-free-energy decomposition reveals a small enhancement in the contribution played by the CDR-H3 region to the b12-gp120 interface compared to the crystal structure.
    MeSH term(s) Amino Acid Sequence ; HIV Antibodies/chemistry ; HIV Envelope Protein gp120 ; HIV Infections ; HIV-1 ; Humans ; Immunoglobulin G
    Chemical Substances HIV Antibodies ; HIV Envelope Protein gp120 ; Immunoglobulin G
    Language English
    Publishing date 2021-12-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.1c01143
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Amplitude-Resolved Single Particle Spectrophotometry: A Robust Tool for High-Throughput Size Characterization of Plasmonic Nanoparticles.

    Calvo, Rodrigo / Pini, Valerio / Thon, Andreas / Saad, Asis / Salvador-Matar, Antonio / Manso Silván, Miguel / Ahumada, Óscar

    Nanomaterials (Basel, Switzerland)

    2023  Volume 13, Issue 17

    Abstract: Plasmonic nanoparticles have a wide range of applications in science and industry. Despite the numerous synthesis methods reported in the literature over the last decades, achieving precise control over the size and shape of large nanoparticle ... ...

    Abstract Plasmonic nanoparticles have a wide range of applications in science and industry. Despite the numerous synthesis methods reported in the literature over the last decades, achieving precise control over the size and shape of large nanoparticle populations remains a challenge. Since variations in size and shape significantly affect the plasmonic properties of nanoparticles, accurate metrological techniques to characterize their morphological features are essential. Here, we present a novel spectrophotometric method, called Amplitude-Resolved Single Particle Spectrophotometry, that can measure the individual sizes of thousands of particles with nanometric accuracy in just a few minutes. This new method, based on the measurement of the scattering amplitude of each nanoparticle, overcomes some of the limitations observed in previous works and theoretically allows the characterization of nanoparticles of any size with a simple extra calibration step. As proof of concept, we characterized thousands of spherical nanoparticles of different sizes. This new method shows excellent accuracy, with less than a 3% discrepancy in direct comparison with transmission electron microscopy. Although the effectiveness of this method has been demonstrated with spherical nanoparticles, its real strength lies in its adaptability to more complex geometries by using an alternative analytical method to the one described here.
    Language English
    Publishing date 2023-08-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662255-5
    ISSN 2079-4991
    ISSN 2079-4991
    DOI 10.3390/nano13172401
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Tethering of the IgG1 Antibody to Amorphous Silica for Immunosensor Development: A Molecular Dynamics Study.

    Martí, Didac / Ainsley, Jon / Ahumada, Oscar / Alemán, Carlos / Torras, Juan

    Langmuir : the ACS journal of surfaces and colloids

    2020  Volume 36, Issue 42, Page(s) 12658–12667

    Abstract: A key factor for improving the sensitivity and performance of immunosensors based on mechanical-plasmonic methods is the orientation of the antibody proteins immobilized on the inorganic surface. Although experimental techniques fail to determine surface ...

    Abstract A key factor for improving the sensitivity and performance of immunosensors based on mechanical-plasmonic methods is the orientation of the antibody proteins immobilized on the inorganic surface. Although experimental techniques fail to determine surface phenomena at the molecular level, modern simulations open the possibility for improving our understanding of protein-surface interactions. In this work, replica exchange molecular dynamics (REMD) simulations have been used to model the IgG1 protein tethered onto the amorphous silica surface by considering a united-atom model and a relatively large system (2500 nm
    MeSH term(s) Biosensing Techniques ; Immunoassay ; Immunoglobulin G ; Molecular Dynamics Simulation ; Silicon Dioxide
    Chemical Substances Immunoglobulin G ; Silicon Dioxide (7631-86-9)
    Language English
    Publishing date 2020-10-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2005937-1
    ISSN 1520-5827 ; 0743-7463
    ISSN (online) 1520-5827
    ISSN 0743-7463
    DOI 10.1021/acs.langmuir.0c02203
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Size characterization of plasmonic nanoparticles with dark-field single particle spectrophotometry.

    Calvo, Rodrigo / Thon, Andreas / Saad, Asis / Salvador-Matar, Antonio / Manso-Silván, Miguel / Ahumada, Óscar / Pini, Valerio

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 17231

    Abstract: Plasmonic nanoparticles are widely used in multiple scientific and industrial applications. Although many synthesis methods have been reported in the literature throughout the last decade, controlling the size and shape of large populations still remains ...

    Abstract Plasmonic nanoparticles are widely used in multiple scientific and industrial applications. Although many synthesis methods have been reported in the literature throughout the last decade, controlling the size and shape of large populations still remains as a challenge. As size and shape variations have a strong impact in their plasmonic properties, the need to have metrological techniques to accurately characterize their morphological features is peremptory. We present a new optical method referred as Dark-Field Single Particle Spectrophotometry which is able to measure the individual sizes of thousands of particles with nanometric accuracy in just a couple of minutes. Our method also features an easy sample preparation, a straightforward experimental setup inspired on a customized optical microscope, and a measurement protocol simple enough to be carried out by untrained technicians. As a proof of concept, thousands of spherical nanoparticles of different sizes have been measured, and after a direct comparison with metrological gold standard electron microscopy, a discrepancy of 3% has been attested. Although its feasibility has been demonstrated on spherical nanoparticles, the true strengthness of the method is that it can be generalized also to nanoparticles with arbitrary shapes and geometries, thus representing an advantageous alternative to the gold-standard electron microscopy.
    MeSH term(s) Metal Nanoparticles ; Spectrophotometry ; Microscopy, Electron ; Particle Size
    Language English
    Publishing date 2022-10-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-21649-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Novel Characterization Techniques for Multifunctional Plasmonic-Magnetic Nanoparticles in Biomedical Applications.

    Calvo, Rodrigo / Rodriguez Mariblanca, Isabel / Pini, Valerio / Dias, Monica / Cebrian, Virginia / Thon, Andreas / Saad, Asis / Salvador-Matar, Antonio / Ahumada, Óscar / Manso Silván, Miguel / Saunders, Aaron E / Wang, Wentao / Stassinopoulos, Adonis

    Nanomaterials (Basel, Switzerland)

    2023  Volume 13, Issue 22

    Abstract: In the rapidly emerging field of biomedical applications, multifunctional nanoparticles, especially those containing magnetic and plasmonic components, have gained significant attention due to their combined properties. These hybrid systems, often ... ...

    Abstract In the rapidly emerging field of biomedical applications, multifunctional nanoparticles, especially those containing magnetic and plasmonic components, have gained significant attention due to their combined properties. These hybrid systems, often composed of iron oxide and gold, provide both magnetic and optical functionalities and offer promising avenues for applications in multimodal bioimaging, hyperthermal therapies, and magnetically driven selective delivery. This paper focuses on the implementation of advanced characterization methods, comparing statistical analyses of individual multifunctional particle properties with macroscopic properties as a way of fine-tuning synthetic methodologies for their fabrication methods. Special emphasis is placed on the size-dependent properties, biocompatibility, and challenges that can arise from this versatile nanometric system. In order to ensure the quality and applicability of these particles, various novel methods for characterizing the magnetic gold particles, including the analysis of their morphology, optical response, and magnetic response, are also discussed, with the overall goal of optimizing the fabrication of this complex system and thus enhancing its potential as a preferred diagnostic agent.
    Language English
    Publishing date 2023-11-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662255-5
    ISSN 2079-4991
    ISSN 2079-4991
    DOI 10.3390/nano13222929
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online ; Thesis: Attenuated total reflection spectroscopy: linear and non-linear optical properties of polymeric materials

    Ahumada, Oscar

    1998  

    Author's details by Oscar Ahumada
    Language English
    Size Online-Ressource (1 Band (mehrere Zählungen)), 21 cm
    Publishing place Zürich
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Diss. Naturwiss. ETH Zürich, Nr. 12776. Ref.: Ulrich W. Suter ; Korref.: N. Spencer--Zürich, 1277
    Database Former special subject collection: coastal and deep sea fishing

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  7. Book ; Online ; Thesis: Attenuated total reflection spectroscopy: linear and non-linear optical properties of polymeric materials

    Ahumada, Oscar

    1998  

    Author's details by Oscar Ahumada
    Language English
    Size Online-Ressource (1 Band (mehrere Zählungen)), 21 cm
    Publishing place Zürich
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Diss. Naturwiss. ETH Zürich, Nr. 12776. Ref.: Ulrich W. Suter ; Korref.: N. Spencer--Zürich, 1277
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  8. Book ; Thesis: Attenuated total reflection spectroscopy: Linear and non-linear optical properties of polymeric materials

    Ahumada, Oscar

    1998  

    Author's details by Oscar Ahumada
    Language English
    Size 2 Mikrofiches, graph. Darst
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Swiss Fed. Inst. of Techn., Diss.--Zurich, 1998
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  9. Book ; Online ; Thesis: Attenuated total reflection spectroscopy

    Ahumada, Oscar

    linear and non-linear optical properties of polymeric materials

    1998  

    Author's details by Oscar Ahumada
    Language English
    Size Online-Ressource, XII, 119 p., text and images
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Swiss Fed. Inst. of Techn., Diss.--Zurich, 1998
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  10. Article: Development of a methodology for reversible chemical modification of silicon surfaces with application in nanomechanical biosensors

    Sato, Roseli H / Ahumada, Óscar / Calleja, Montserrat / Cunha, Rodrigo L.O.R / Domínguez, Carmen M / Ferreira, Edgard A / Fiorito, Pablo A / Kosaka, Priscila M / Malvar, Óscar / Omori, Álvaro T / Petri, Denise F.S / Pini, Valerio / Tamayo, Javier

    Biosensors & bioelectronics. 2019 July 15, v. 137

    2019  

    Abstract: Hypervalent tellurium compounds have a particular reactivity towards thiol compounds which are related to their biological properties. In this work, this property was assembled to tellurium-functionalized surfaces. These compounds were used as linkers in ...

    Abstract Hypervalent tellurium compounds have a particular reactivity towards thiol compounds which are related to their biological properties. In this work, this property was assembled to tellurium-functionalized surfaces. These compounds were used as linkers in the immobilization process of thiolated biomolecules (such as DNA) on microcantilever surfaces. The telluride derivatives acted as reversible binding agents due to their redox properties, providing the regeneration of microcantilever surfaces and allowing their reuse for further biomolecules immobilizations, recycling the functional surface. Initially, we started from the synthesis of 4-((3-((4-methoxyphenyl) tellanyl) phenyl) amino)-4-oxobutanoic acid, a new compound, which was immobilized on a silicon surface. In nanomechanical systems, the detection involved a hybridization study of thiolated DNA sequences. Fluorescence microscopy technique was used to confirm the immobilization and removal of the telluride-DNA system and provided revealing results about the potentiality of applying redox properties to chalcogen derivatives at surfaces.
    Keywords binding agents ; biosensors ; DNA ; fluorescence microscopy ; nucleotide sequences ; recycling ; silicon ; tellurium ; thiols
    Language English
    Dates of publication 2019-0715
    Size p. 287-293.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1011023-9
    ISSN 1873-4235 ; 0956-5663
    ISSN (online) 1873-4235
    ISSN 0956-5663
    DOI 10.1016/j.bios.2019.04.028
    Database NAL-Catalogue (AGRICOLA)

    Full text online

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