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Nedylakova M, Medinger J, Mirabello G, Lattuada M. Iron oxide magnetic aggregates: Aspects of synthesis, computational approaches and applications. Adv Colloid Interface Sci 2024; 323:103056. [PMID: 38056225 DOI: 10.1016/j.cis.2023.103056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Superparamagnetic magnetite nanoparticles have been central to numerous investigations in the past few decades for their use in many applications, such as drug delivery, medical diagnostics, magnetic separation, and material science. However, the properties of single magnetic nanoparticles are sometimes not sufficient to accomplish tasks where a strong magnetic response is required. In light of this, aggregated magnetite nanoparticles have been proposed as an alternative advanced material, which may expand and combine some of the advantages of single magnetic nanoparticles, including superparamagnetism, with an enhanced magnetic moment and increased colloidal stability. This review comprehensively discusses the current literature on aggregates made of magnetic iron oxide nanoparticles. This review is divided into three sections. First, the current synthetic strategies for magnetite nanoparticle aggregates are discussed, together with the influence of different stabilizers on the primary crystals and the final aggregate size and morphology. The second section is dedicated to computational approaches, such as density functional methods (which permit accurate predictions of electronic and magnetic properties and shed light on the behavior of surfactant molecules on iron oxide surfaces) and molecular dynamics simulations (which provide additional insight into the influence of ligands on the surface chemistry of iron oxide nanocrystals). The last section discusses current and possible future applications of iron oxide magnetic aggregates, including wastewater treatment, water purification, medical applications, and magnetic aggregates for materials displaying structural colors.
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Affiliation(s)
- Miroslava Nedylakova
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, Fribourg 1700, Switzerland
| | - Joelle Medinger
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, Fribourg 1700, Switzerland
| | - Giulia Mirabello
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, Fribourg 1700, Switzerland
| | - Marco Lattuada
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, Fribourg 1700, Switzerland.
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2
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Sodomaco S, Gómez S, Giovannini T, Cappelli C. Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces. J Phys Chem A 2023; 127:10282-10294. [PMID: 37993110 DOI: 10.1021/acs.jpca.3c05560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.
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Affiliation(s)
- Sveva Sodomaco
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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3
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Del Giudice G, Serra A, Saarimäki LA, Kotsis K, Rouse I, Colibaba SA, Jagiello K, Mikolajczyk A, Fratello M, Papadiamantis AG, Sanabria N, Annala ME, Morikka J, Kinaret PAS, Voyiatzis E, Melagraki G, Afantitis A, Tämm K, Puzyn T, Gulumian M, Lobaskin V, Lynch I, Federico A, Greco D. An ancestral molecular response to nanomaterial particulates. NATURE NANOTECHNOLOGY 2023; 18:957-966. [PMID: 37157020 PMCID: PMC10427433 DOI: 10.1038/s41565-023-01393-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 03/31/2023] [Indexed: 05/10/2023]
Abstract
The varied transcriptomic response to nanoparticles has hampered the understanding of the mechanism of action. Here, by performing a meta-analysis of a large collection of transcriptomics data from various engineered nanoparticle exposure studies, we identify common patterns of gene regulation that impact the transcriptomic response. Analysis identifies deregulation of immune functions as a prominent response across different exposure studies. Looking at the promoter regions of these genes, a set of binding sites for zinc finger transcription factors C2H2, involved in cell stress responses, protein misfolding and chromatin remodelling and immunomodulation, is identified. The model can be used to explain the outcomes of mechanism of action and is observed across a range of species indicating this is a conserved part of the innate immune system.
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Affiliation(s)
- G Del Giudice
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - A Serra
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere, Finland
| | - L A Saarimäki
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - K Kotsis
- School of Physics, University College Dublin, Dublin, Ireland
| | - I Rouse
- School of Physics, University College Dublin, Dublin, Ireland
| | - S A Colibaba
- School of Physics, University College Dublin, Dublin, Ireland
| | - K Jagiello
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - A Mikolajczyk
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - M Fratello
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - A G Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
- Novamechanics Ltd, Nicosia, Cyprus
| | - N Sanabria
- National Institute for Occupational Health, National Health Laboratory Services, Johannesburg, South Africa
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - M E Annala
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - J Morikka
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - P A S Kinaret
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland
| | | | - G Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece
| | | | - K Tämm
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - T Puzyn
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - M Gulumian
- National Institute for Occupational Health, National Health Laboratory Services, Johannesburg, South Africa
- Haematology and Molecular Medicine Department, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Water Research Group, Unit for Environmental Sciences and Management, North West University, Potchefstroom, South Africa
| | - V Lobaskin
- School of Physics, University College Dublin, Dublin, Ireland
| | - I Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - A Federico
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere, Finland
| | - D Greco
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland.
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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4
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Subbotina J, Lobaskin V. Multiscale Modeling of Bio-Nano Interactions of Zero-Valent Silver Nanoparticles. J Phys Chem B 2022; 126:1301-1314. [PMID: 35132861 PMCID: PMC8859825 DOI: 10.1021/acs.jpcb.1c09525] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Understanding the
specifics of interaction between the protein
and nanomaterial is crucial for designing efficient, safe, and selective
nanoplatforms, such as biosensor or nanocarrier systems. Routing experimental
screening for the most suitable complementary pair of biomolecule
and nanomaterial used in such nanoplatforms might be a resource-intensive
task. While a range of computational tools are available for prescreening
libraries of proteins for their interactions with small molecular
ligands, choices for high-throughput screening of protein libraries
for binding affinities to new and existing nanomaterials are very
limited. In the current work, we present the results of the systematic
computational study of interaction of various biomolecules with pristine
zero-valent noble metal nanoparticles, namely, AgNPs, by using the UnitedAtom multiscale approach. A set of blood plasma and
dietary proteins for which the interaction with AgNPs was described
experimentally were examined computationally to evaluate the performance
of the UnitedAtom method. A set of interfacial descriptors
(log PNM, adsorption affinities, and adsorption
affinity ranking), which can characterize the relative hydrophobicity/hydrophilicity/lipophilicity
of the nanosized silver and its ability to form bio(eco)corona, was
evaluated for future use in nano-QSAR/QSPR studies.
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Affiliation(s)
- Julia Subbotina
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
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Hatami A, Salahshoori I, Rashidi N, Nasirian D. The effect of ZIF-90 particle in Pebax/Psf composite membrane on the transport properties of CO2, CH4 and N2 gases by Molecular Dynamics Simulation method. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2019.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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6
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Adsorption behavior of β-cyclodextrin onto gold nanoparticles. J Mol Graph Model 2020; 94:107483. [DOI: 10.1016/j.jmgm.2019.107483] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/28/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022]
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7
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Jiménez-Serratos G, Cárdenas H, Müller EA. Extension of the effective solid-fluid Steele potential for Mie force fields. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1669836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Harry Cárdenas
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Erich A. Müller
- Department of Chemical Engineering, Imperial College London, London, UK
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8
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Dasetty S, Barrows JK, Sarupria S. Adsorption of amino acids on graphene: assessment of current force fields. SOFT MATTER 2019; 15:2359-2372. [PMID: 30789189 DOI: 10.1039/c8sm02621a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields-Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid-graphene interactions are favorable irrespective of the force field. While the magnitudes of ΔAads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. ΔAads positively correlates with amino acid-graphene and negatively correlates with graphene-water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that the force fields studied will give qualitatively consistent relative strength of adsorption across proteins but different structural preferences in the graphene adsorbed state.
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Affiliation(s)
- Siva Dasetty
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA.
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9
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10
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Kyrychenko A, Blazhynska MM, Slavgorodska MV, Kalugin ON. Stimuli-responsive adsorption of poly(acrylic acid) onto silver nanoparticles: Role of polymer chain length and degree of ionization. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.130] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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11
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Blazhynska MM, Kyrychenko A, Kalugin ON. Molecular dynamics simulation of the size-dependent morphological stability of cubic shape silver nanoparticles. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1469751] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
| | - Alexander Kyrychenko
- School of Chemistry, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - Oleg N. Kalugin
- School of Chemistry, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
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12
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Kyrychenko A, Pasko DA, Kalugin ON. Poly(vinyl alcohol) as a water protecting agent for silver nanoparticles: the role of polymer size and structure. Phys Chem Chem Phys 2018; 19:8742-8756. [PMID: 28217797 DOI: 10.1039/c6cp05562a] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical modification of silver nanoparticles (AgNPs) with a stabilizing agent, such as poly(vinyl alcohol) (PVA), plays an important role in shape-controlled seeded-growth and colloidal stability. However, theoretical aspects of the stabilizing mechanism of PVA are still poorly understood. To gain a better understanding of the role of PVA in water protecting effects for silver nanoparticles, we developed an atomistic model of a AgNP grafted with single-chain PVA of various lengths. Our model, designed for classical molecular dynamics (MD) simulations, approximates the AgNP as a quasi-spherical silver nanocrystal with 3.9 nm diameter and uses a united-atom representation for PVA with its polymer chain length varying from 220 up to 1540 repeating units. We found that PVA adsorbs onto the AgNP surface through multiple non-covalent interactions, among which non-covalent bonding of the hydroxyl groups plays a key role. The analysis of adsorption isotherms by using the Hill, Scatchard, and McGhee & von Hippel models exhibits evidence for positive binding cooperativity with the cooperativity parameter varying from 1.55 to 2.12. Our results indicate that the size of the PVA polymer rather than its structure plays a crucial role in providing water protecting effects for the AgNP core, varying from 40% up to 91%. The water-protecting efficiency was well approximated by the Langmuir-Freundlich equation, allowing us to predict that the saturated coverage of the nanoparticle of a given diameter of 3.9 nm should occur when the PVA molecular weight approaches 115 kDa, which corresponds to the number of vinyl alcohol monomers being equal to 3100 units.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv 61022, Ukraine. and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv 61022, Ukraine
| | - Dmitry A Pasko
- School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv 61022, Ukraine
| | - Oleg N Kalugin
- School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv 61022, Ukraine
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13
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Krause KD, Roy S, Hore DK. Interplay between adsorbed peptide structure, trapped water, and surface hydrophobicity. Biointerphases 2017; 12:02D407. [PMID: 28506069 PMCID: PMC5432376 DOI: 10.1116/1.4983408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 01/05/2023] Open
Abstract
Atomistic molecular dynamics simulations were used to study the influence of interfacial water on the orientation and conformation of a facewise amphipathic α-helical peptide adsorbed to hydrophilic and hydrophobic substrates. Water behavior beneath the peptide adsorbed to a hydrophilic surface was observed to vary with the height of the peptide above the surface. In general, the orientation of water close to the peptide (with the oxygen atom pointing up toward the peptide) was complementary to that observed near the hydrophilic surface in the absence of peptide. That is, no change in orientation of water trapped between the peptide and a hydrophilic surface is required as the peptide approaches the surface. The adsorption of the peptide to the hydrophilic surface was observed to be mediated by a layer of ordered water. Water was found to be largely excluded on adsorption to the hydrophobic surface. However, the small amount of water present was observed to be highly ordered. At the closest point of contact to the hydrophobic surface, the peptide was observed to make direct contact. These findings shed light on the fundamental driving forces of peptide adsorption to hydrophobic and hydrophilic surfaces in aqueous environments.
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Affiliation(s)
- Katherine D Krause
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Sandra Roy
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Dennis K Hore
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
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14
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Maharana J, Vats A, Gautam S, Nayak BP, Kumar S, Sendha J, De S. POP1 might be recruiting its type-Ia interface for NLRP3-mediated PYD-PYD interaction: Insights from MD simulation. J Mol Recognit 2017; 30. [PMID: 28370480 DOI: 10.1002/jmr.2632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 02/14/2017] [Accepted: 02/23/2017] [Indexed: 11/12/2022]
Abstract
Inflammasomes are multiprotein caspase-activating complexes that enhance the maturation and release of proinflammatory cytokines (IL-1β and IL-18) in response to the invading pathogen and/or host-derived cellular stress. These are assembled by the sensory proteins (viz NLRC4, NLRP1, NLRP3, and AIM-2), adaptor protein (ASC), and effector molecule procaspase-1. In NLRP3-mediated inflammasome activation, ASC acts as a mediator between NLRP3 and procaspase-1 for the transmission of signals. A series of homotypic protein-protein interactions (NLRP3PYD :ASCPYD and ASCCARD :CASP1CARD ) propagates the downstream signaling for the production of proinflammatory cytokines. Pyrin-only protein 1 (POP1) is known to act as the regulator of inflammasome. It modulates the ASC-mediated inflammasome assembly by interacting with pyrin domain (PYD) of ASC. However, despite similar electrostatic surface potential, the interaction of POP1 with NLRP3PYD is obscured till date. Herein, to explore the possible PYD-PYD interactions between NLRP3PYD and POP1, a combined approach of protein-protein docking and molecular dynamics simulation was adapted. The current study revealed that POP1's type-Ia interface and type-Ib interface of NLRP3PYD might be crucial for 1:1 PYD-PYD interaction. In addition to type-I mode of interaction, we also observed type-II and type-III interaction modes in two different dynamically stable heterotrimeric complexes (POP1-NLRP3-NLRP3 and POP1-NLRP3-POP1). The inter-residual/atomic distance calculation exposed several critical residues that possibly govern the said interaction, which need further investigation. Overall, the findings of this study will shed new light on hitherto concealed molecular mechanisms underlying NLRP3-mediated inflammasome, which will have strong future therapeutic implications.
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Affiliation(s)
- Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Ashutosh Vats
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
| | - Santwana Gautam
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Bibhu Prasad Nayak
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Sushil Kumar
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
| | - Jasobanta Sendha
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Sachinandan De
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
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16
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Atomistic Modelling of Confined Polypropylene Chains between Ferric Oxide Substrates at Melt Temperature. Polymers (Basel) 2016; 8:polym8100361. [PMID: 30974636 PMCID: PMC6431934 DOI: 10.3390/polym8100361] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 11/30/2022] Open
Abstract
The interactions and conformational characteristics of confined molten polypropylene (PP) chains between ferric oxide (Fe2O3) substrates were investigated by molecular dynamics (MD) simulations. A comparative analysis of the adsorbed amount shows strong adsorption of the chains on the high-energy surface of Fe2O3. Local structures formed in the polymer film were studied utilizing density profiles, orientation of bonds, and end-to-end distance of chains. At interfacial regions, the backbone carbon-carbon bonds of the chains preferably orient in the direction parallel to the surface while the carbon-carbon bonds with the side groups show a slight tendency to orient normal to the surface. Based on the conformation tensor data, the chains are compressed in the normal direction to the substrates in the interfacial regions while they tend to flatten in parallel planes with respect to the surfaces. The orientation of the bonds as well as the overall flattening of the chains in planes parallel to the solid surfaces are almost identical to that of the unconfined PP chains. Also, the local pressure tensor is anisotropic closer to the solid surfaces of Fe2O3 indicating the influence of the confinement on the buildup imbalance of normal and tangential pressures.
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Ramakrishnan SK, Zhu J, Gergely C. Organic-inorganic interface simulation for new material discoveries. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sathish Kumar Ramakrishnan
- Nanobiology Institute; Yale University; West Haven CT USA
- Laboratoire Charles Coulomb (L2C); UMR 5221 CNRS-Université de Montpellier; Montpellier France
| | - Jie Zhu
- Nanobiology Institute; Yale University; West Haven CT USA
| | - Csilla Gergely
- Laboratoire Charles Coulomb (L2C); UMR 5221 CNRS-Université de Montpellier; Montpellier France
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18
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Buehler MJ, Genin GM. Integrated multiscale biomaterials experiment and modelling: a perspective. Interface Focus 2016; 6:20150098. [PMID: 28981126 DOI: 10.1098/rsfs.2015.0098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Advances in multiscale models and computational power have enabled a broad toolset to predict how molecules, cells, tissues and organs behave and develop. A key theme in biological systems is the emergence of macroscale behaviour from collective behaviours across a range of length and timescales, and a key element of these models is therefore hierarchical simulation. However, this predictive capacity has far outstripped our ability to validate predictions experimentally, particularly when multiple hierarchical levels are involved. The state of the art represents careful integration of multiscale experiment and modelling, and yields not only validation, but also insights into deformation and relaxation mechanisms across scales. We present here a sampling of key results that highlight both challenges and opportunities for integrated multiscale experiment and modelling in biological systems.
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Affiliation(s)
- Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guy M Genin
- Department of Mechanical Engineering and Materials Science, and Department of Neurological Surgery, Washington University, St Louis, MO 63130, USA
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