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  1. Article: Properties of Packed Bed Structures Formed during Filtration: A Two and Three-Dimensional Model.

    Eales, William / Price, Chris J / Hicks, William / Mulheran, Paul A

    Organic process research & development

    2023  Volume 27, Issue 9, Page(s) 1631–1640

    Abstract: Agglomeration is an issue that causes many problems during secondary processing for pharmaceutical companies, causing material to need further processing and costing additional time and resources to ensure a satisfactory outcome. A potential source of ... ...

    Abstract Agglomeration is an issue that causes many problems during secondary processing for pharmaceutical companies, causing material to need further processing and costing additional time and resources to ensure a satisfactory outcome. A potential source of agglomeration arises from the particle contacts established during filtration that lead to robust agglomerates forming during drying, so that a necessary first step toward understanding agglomeration is to study the packing properties of filtration beds. Here, we present two and three-dimensional models simulating the formation of packed bed structures during filtration. The models use circular and spherical particles of different sizes, mimicking the bimodal particle size distributions sometimes encountered in industrial practice. The statistics of packing and void formation, along with the distribution of interparticle contacts and percolation structures, are presented and discussed in the context of filtration, drying, and agglomeration. The model paves the way for predictive capabilities that can lead to the rational design of processes to minimize the impact of agglomeration.
    Language English
    Publishing date 2023-08-29
    Publishing country United States
    Document type Journal Article
    ISSN 1083-6160
    ISSN 1083-6160
    DOI 10.1021/acs.oprd.3c00147
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Chitin and Chitosan Binding to the α-Chitin Crystal: A Molecular Dynamics Study.

    Hudek, Magdalena / Kubiak-Ossowska, Karina / Johnston, Karen / Ferro, Valerie A / Mulheran, Paul A

    ACS omega

    2023  Volume 8, Issue 3, Page(s) 3470–3477

    Abstract: Understanding the binding of chitosan oligomers to the surface of a chitin nanocrystal is important for improving the enzymatic deacetylation of chitin and for the design of chitin/chitosan composite films. Here, we study the binding of several chito- ... ...

    Abstract Understanding the binding of chitosan oligomers to the surface of a chitin nanocrystal is important for improving the enzymatic deacetylation of chitin and for the design of chitin/chitosan composite films. Here, we study the binding of several chito-oligomers to the (100) surface of an α-chitin crystal using molecular dynamics (MD), steered MD, and umbrella sampling. The convergence of the free energy was carefully considered and yielded a binding energies of -12.5 and -2 kcal mol
    Language English
    Publishing date 2023-01-10
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.2c07495
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  3. Article: Tuning Interfacial Concentration Enhancement through Dispersion Interactions to Facilitate Heterogeneous Nucleation.

    McKechnie, David / Mulheran, Paul A / Sefcik, Jan / Johnston, Karen

    The journal of physical chemistry. C, Nanomaterials and interfaces

    2022  Volume 126, Issue 38, Page(s) 16387–16400

    Abstract: Classical molecular dynamics simulations were used to investigate how dispersion (van der Waals) interactions between non-polar, hydrophobic surfaces and aqueous glycine solutions affect the solution composition, molecular orientation, and dynamics at ... ...

    Abstract Classical molecular dynamics simulations were used to investigate how dispersion (van der Waals) interactions between non-polar, hydrophobic surfaces and aqueous glycine solutions affect the solution composition, molecular orientation, and dynamics at the interface. Simulations revealed that dispersion interactions lead to a major increase in the concentration of glycine at the interface in comparison with the bulk solution, resulting from a competition between solute and solvent molecules to be or not to be near the interface. This can then lead to kinetic and/or structural effects facilitating heterogeneous nucleation of glycine at non-polar surfaces, in agreement with recent observations for tridecane, graphene, and polytetrafluoroethylene. A novel parameterization process was developed to map a model surface with tunable dispersion interactions to heptane, tridecane, and graphite materials. The model surface was capable of reproducing the solution structure observed in fully atomistic simulations with excellent agreement and also provided good agreement for dynamic properties, at a significantly reduced computational cost. This approach can be used as an effective tool for screening materials for heterogeneous nucleation enhancement or suppression, based on non-specific dispersion interactions based on bulk material molecular properties, rather than interfacial functional groups, templating or confinement effects.
    Language English
    Publishing date 2022-09-16
    Publishing country United States
    Document type Journal Article
    ISSN 1932-7447
    ISSN 1932-7447
    DOI 10.1021/acs.jpcc.2c04410
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: On Linear Growth in COVID-19 Cases

    Grinfeld, Michael / Mulheran, Paul A

    medRxiv

    Abstract: We present an elementary model of COVID-19 propagation that makes explicit the connection between testing strategies and rates of transmission and the linear growth in new cases observed in many parts of the world. An essential feature of the model is ... ...

    Abstract We present an elementary model of COVID-19 propagation that makes explicit the connection between testing strategies and rates of transmission and the linear growth in new cases observed in many parts of the world. An essential feature of the model is that it captures the population-level response to the infection statistics information provided by governments and other organisations. The conclusions from this model have important implications regarding benefits of wide-spread testing for the presence of the virus, something that deserves greater attention.
    Keywords covid19
    Language English
    Publishing date 2020-06-22
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.06.19.20135640
    Database COVID19

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  5. Article ; Online: The Role of Antibodies in the Treatment of SARS-CoV-2 Virus Infection, and Evaluating Their Contribution to Antibody-Dependent Enhancement of Infection.

    Farouq, Mohammed A H / Acevedo, Reinaldo / Ferro, Valerie A / Mulheran, Paul A / Al Qaraghuli, Mohammed M

    International journal of molecular sciences

    2022  Volume 23, Issue 11

    Abstract: Antibodies play a crucial role in the immune response, in fighting off pathogens as well as helping create strong immunological memory. Antibody-dependent enhancement (ADE) occurs when non-neutralising antibodies recognise and bind to a pathogen, but are ...

    Abstract Antibodies play a crucial role in the immune response, in fighting off pathogens as well as helping create strong immunological memory. Antibody-dependent enhancement (ADE) occurs when non-neutralising antibodies recognise and bind to a pathogen, but are unable to prevent infection, and is widely known and is reported as occurring in infection caused by several viruses. This narrative review explores the ADE phenomenon, its occurrence in viral infections and evaluates its role in infection by SARS-CoV-2 virus, which causes coronavirus disease 2019 (COVID-19). As of yet, there is no clear evidence of ADE in SARS-CoV-2, though this area is still subject to further study.
    MeSH term(s) Antibodies, Neutralizing ; Antibodies, Viral/therapeutic use ; Antibody-Dependent Enhancement ; COVID-19 ; Humans ; SARS-CoV-2
    Chemical Substances Antibodies, Neutralizing ; Antibodies, Viral
    Language English
    Publishing date 2022-05-28
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23116078
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  6. Article ; Online: Recent Advances in Photothermal Therapies Against Cancer and the Role of Membrane Transporter Modulators on the Efficacy of This Approach.

    Al-Ali, Ahmed A Abdulhussein / Al Ward, Nameer / Obeid, Mohammad A / Uhd Nielsen, Carsten / Mulheran, Paul A / Al Qaraghuli, Mohammed M

    Technology in cancer research & treatment

    2023  Volume 22, Page(s) 15330338231168016

    Abstract: Recently, much research is focused on the use of photothermal therapy (PTT) as an advanced method to treat various types of cancer. The PTT approach primarily utilizes nanoparticles (NPs) made from metals, carbon, or semiconductors that can convert near- ... ...

    Abstract Recently, much research is focused on the use of photothermal therapy (PTT) as an advanced method to treat various types of cancer. The PTT approach primarily utilizes nanoparticles (NPs) made from metals, carbon, or semiconductors that can convert near-infrared laser irradiation, which penetrates tissues, into local heat that induces cancer cell death. An alternative approach is to utilize NPs (such as liposomes) to carry suitable dye molecules to the same end. Numerous studies concerning PTT have shown that local heat released in cancer cells may suppress the expression of membrane transporter proteins such as P-glycoprotein (P-gp) and multidrug resistance-associated protein 1 (MRP1), thus enhancing cytotoxicity and reverse multidrug resistance. In addition, because NPs may be loaded with different substances, researchers have designed multifunctional NPs for PTT by including several agents such as membrane transporter modulators, anticancer drugs, and photothermal agents. This review will focus on the recent advances in PTT utilizing various types of NPs, and their components and characteristics. In addition, the role of membrane transporters in PTT will be highlighted and different methods of transporter modulation will be summarized from several PTT studies in which multifunctional NPs were used to treat cancers
    MeSH term(s) Humans ; Photothermal Therapy ; Cell Line, Tumor ; Phototherapy/methods ; Nanoparticles ; Infrared Rays ; Membrane Transport Proteins ; Neoplasms/therapy
    Chemical Substances Membrane Transport Proteins
    Language English
    Publishing date 2023-04-27
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2146365-7
    ISSN 1533-0338 ; 1533-0346
    ISSN (online) 1533-0338
    ISSN 1533-0346
    DOI 10.1177/15330338231168016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Structural Analysis of Anti-Hapten Antibodies to Identify Long-Range Structural Movements Induced by Hapten Binding.

    Al Qaraghuli, Mohammed M / Kubiak-Ossowska, Karina / Ferro, Valerie A / Mulheran, Paul A

    Frontiers in molecular biosciences

    2021  Volume 8, Page(s) 633526

    Abstract: Antibodies are well known for their high specificity that has enabled them to be of significant use in both therapeutic and diagnostic applications. Antibodies can recognize different antigens, including proteins, carbohydrates, peptides, nucleic acids, ... ...

    Abstract Antibodies are well known for their high specificity that has enabled them to be of significant use in both therapeutic and diagnostic applications. Antibodies can recognize different antigens, including proteins, carbohydrates, peptides, nucleic acids, lipids, and small molecular weight haptens that are abundantly available as hormones, pharmaceuticals, and pesticides. Here we focus on a structural analysis of hapten-antibody couples and identify potential structural movements originating from the hapten binding by comparison with unbound antibody, utilizing 40 crystal structures from the Protein Data Bank. Our analysis reveals three binding surface trends; S1 where a pocket forms to accommodate the hapten, S2 where a pocket is removed when the hapten binds, and S3 where no pockets changes are found. S1 and S2 are expected for induced-fit binding, whereas S3 indicates that a pre-existing population of optimal binding antibody conformation exists. The structural analysis reveals four classifications of structural reorganization, some of which correlate to S2 but not to the other binding surface changes. These observations demonstrate the complexity of the antibody-antigen interaction, where structural changes can be restricted to the binding sites, or extend through the constant domains to propagate structural changes. This highlights the importance of structural analysis to ensure successful and compatible transformation of small antibody fragments at the early discovery stage into full antibodies during the subsequent development stages, where long-range structural changes are required for an Fc effector response.
    Language English
    Publishing date 2021-03-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.633526
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  8. Article: Biomolecular interactions with nanoparticles: applications for coronavirus disease 2019

    Farouq, Mohammed A.H / Al Qaraghuli, Mohammed M / Kubiak-Ossowska, Karina / Ferro, Valerie A / Mulheran, Paul A

    Current opinion in colloid & interface science. 2021 Aug., v. 54

    2021  

    Abstract: Nanoparticles are small particles sized 1–100 nm, which have a large surface-to-volume ratio, allowing efficient adsorption of drugs, proteins, and other chemical compounds. Consequently, functionalized nanoparticles have potential diagnostic and ... ...

    Abstract Nanoparticles are small particles sized 1–100 nm, which have a large surface-to-volume ratio, allowing efficient adsorption of drugs, proteins, and other chemical compounds. Consequently, functionalized nanoparticles have potential diagnostic and therapeutic applications. A variety of nanoparticles have been studied, including those constructed from inorganic materials, biopolymers, and lipids. In this review, we focus on recent work targeting the severe acute respiratory syndrome coronavirus 2 virus that causes coronavirus disease (COVID-19). Understanding the interactions between coronavirus-specific proteins (such as the spike protein and its host cell receptor angiotensin-converting enzyme 2) with different nanoparticles paves the way to the development of new therapeutics and diagnostics that are urgently needed for the fight against COVID-19, and indeed for related future viral threats that may emerge.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; adsorption ; biopolymers ; diagnostic techniques ; peptidyl-dipeptidase A ; therapeutics ; viruses
    Language English
    Dates of publication 2021-08
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2019683-0
    ISSN 1359-0294
    ISSN 1359-0294
    DOI 10.1016/j.cocis.2021.101461
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study.

    Farouq, Mohammed A H / Kubiak-Ossowska, Karina / Al Qaraghuli, Mohammed M / Ferro, Valerie A / Mulheran, Paul A

    International journal of molecular sciences

    2022  Volume 23, Issue 9

    Abstract: Staphylococcus protein A (SpA) is found in the cell wall ... ...

    Abstract Staphylococcus protein A (SpA) is found in the cell wall of
    MeSH term(s) Adsorption ; Antibodies ; Molecular Dynamics Simulation ; Silicon Dioxide/chemistry ; Staphylococcal Protein A ; Staphylococcus ; Surface Properties
    Chemical Substances Antibodies ; Staphylococcal Protein A ; Silicon Dioxide (7631-86-9)
    Language English
    Publishing date 2022-04-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23094832
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Critical role of tyrosine-20 in formation of gold nanoclusters within lysozyme: a molecular dynamics study.

    Russell, Ben A / Kubiak-Ossowska, Karina / Chen, Yu / Mulheran, Paul A

    Physical chemistry chemical physics : PCCP

    2019  Volume 21, Issue 9, Page(s) 4907–4911

    Abstract: Lysozyme is one of the most commonly used proteins for encapsulating gold nanoclusters, yielding Ly-AuNC complexes. While possible applications of Ly-AuNCs in environmental, biological and trace metal sensing in solution have been demonstrated, there is ... ...

    Abstract Lysozyme is one of the most commonly used proteins for encapsulating gold nanoclusters, yielding Ly-AuNC complexes. While possible applications of Ly-AuNCs in environmental, biological and trace metal sensing in solution have been demonstrated, there is currently a poor understanding of the physical characteristics of the Ly-AuNC complex. In this study we have employed fully atomistic molecular dynamics simulations to gain an understanding of the formation of Au clusters within the protein. It was found that in order to form AuNCs in the simulations, an approach of targeted insertion of Au atoms at a critical surface residue was needed. Tyrosine is known to be crucial for the reduction of Au salts experimentally, and our simulations showed that Tyr20 is the key residue for the formation of an AuNC beneath the protein surface in the α-helical domain. It is hoped these observations will aid future improvements and modification of Ly-AuNCs via alterations of the alpha-helix domain or Tyr20.
    MeSH term(s) Gold/chemistry ; Metal Nanoparticles/chemistry ; Molecular Dynamics Simulation ; Muramidase/chemistry ; Muramidase/metabolism ; Protein Conformation, alpha-Helical ; Protein Domains ; Tyrosine/chemistry ; Tyrosine/metabolism
    Chemical Substances Tyrosine (42HK56048U) ; Gold (7440-57-5) ; Muramidase (EC 3.2.1.17)
    Language English
    Publishing date 2019-02-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c8cp06374e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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