Article
Engineering, Mechanical
Sankhadeep Bhattacharyya, Md Rushdie Ibne Islam, Puneet Kumar Patra
Summary: This manuscript investigates the fracture crack propagation in graphene sheets using a sequential multiscaling technique. By coupling continuum-scale smoothed particle hydrodynamics (SPH) with atomistic scale molecular dynamics (MD) simulations through proper constitutive modelling, the authors accurately reproduce the atomistic scale stress-strain behavior until failure. The study reveals the influence of notch orientation on crack propagation and the changes in stress-strain behavior caused by randomly oriented cracks in graphene sheets.
THEORETICAL AND APPLIED FRACTURE MECHANICS
(2022)
Article
Biochemical Research Methods
Alican Gulsevin, Jens Meiler
Summary: The AmphiScan protocol is a tool developed to predict the interaction of amphipathic helices with membranes, with features of fast, accurate, and highly customizable.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Giacomo Buccella, Andrea Villa, Davide Ceresoli, Luca Barbieri, Roberto Malgesini, Andres R. Leon-Garzon
Summary: This study compares two different models for the deterioration process of polyethylene exposed to reactive plasma. The first model successfully reproduces the experimentally detected oxidation of the polyethylene surface, while the second model explains the presence of nitrogen on the sample surface.
APPLIED SURFACE SCIENCE
(2021)
Article
Food Science & Technology
K. Kevion Darmawan, C. Tom Karagiannis, G. Jeff Hughes, M. Darryl Small, Andrew Hung
Summary: The study shows that acidic pH weakens interactions between lactoferrin and other proteins, but some contacts are maintained. This property could be used for developing novel food materials and indicates the potential antibacterial capability of apo-lactoferrin.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Rauoof Wani, Ajaz Mir, Farida Batool, Sanat Tiwari
Summary: Rayleigh-Taylor instability (RTI) in strongly coupled plasmas is studied using two-dimensional molecular dynamics simulations. The growth rate of RTI decreases with increasing coupling strength due to the suppression effect of the caging mechanism. However, the presence of background charges enhances the growth rate of the instability. Additionally, an increase in the Atwood number leads to a stronger growth of the instability.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Estefania Diaz Lopez, Aleix Comas-Vives
Summary: This study evaluated Rh(111)-catalyzed dry reforming of methane (DRM) using density functional theory and kinetic Monte Carlo simulations. The results showed that the catalytic system displayed Arrhenius behavior with CO2 activation identified as the dominant step.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Alessandro Berselli, Fabio Benfenati, Luca Maragliano, Giulio Alberini
Summary: Claudins (Cldns) are transmembrane proteins that play a major role in tight junction integrity and tissue selectivity. Computational methodologies have been used to investigate the properties of Cldn and provide valuable insights for improving the characterization of Cldn and designing strategies for controlling paracellular transport.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Alessandro Berselli, Fabio Benfenati, Luca Maragliano, Giulio Alberini
Summary: Claudins are transmembrane proteins that play a crucial role in tight junction integrity and tissue selectivity. They form barriers or ion-selective channels between cells in the paracellular space. Computational methodologies have helped to elucidate the properties of Claudins and could be useful for designing strategies to control the transport of drugs or molecules.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biophysics
Gabriel C. A. da Hora, John D. M. Nguyen, Jessica M. J. Swanson
Summary: This study investigates the association and permeation of Mycolactone through models of the mammalian endoplasmic reticulum (ER) and plasma membranes (PMs). The research reveals that Mycolactone exhibits different binding and permeation mechanisms in the ER membrane compared to the PMs. Increased order and interactions with unsaturated lipid tails stabilize the toxin in the ER membrane, while disruption of lipid packing destabilizes it in the PMs.
BIOPHYSICAL JOURNAL
(2022)
Article
Physics, Applied
R. M. Flanagan, M. A. Meyers, S. J. Fensin
Summary: This study systematically investigates the effect of size and concentration of He bubbles in Cu on ejecta production using molecular dynamics simulations. The presence of defects leads to non-planarities in the shock wave itself, resulting in the formation of ejecta as the front reaches the flat free surface.
JOURNAL OF APPLIED PHYSICS
(2021)
Article
Biophysics
Yuliang Sun, Zhixiong Deng, Xukai Jiang, Bing Yuan, Kai Yang
Summary: The study revealed that PMB has a preference for specific lipid species in its interaction with different membrane systems, leading to complex membrane interaction states. These findings provide insights into the action mechanism of PMB at a membrane level, laying the foundation for developing novel and safer polymyxin strategies for better clinical use.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Nililla Nisoh, Viwan Jarerattanachat, Mikko Karttunen, Jirasak Wong-ekkabut
Summary: This study uses coarse-grained molecular dynamic simulations to investigate the interactions between carbon nanoparticles (CNPs) and biological membranes. It demonstrates that CNPs can spontaneously penetrate plasma membranes and preferentially locate themselves in regions enriched with highly unsaturated lipids. The findings suggest that by adjusting the lipid composition, CNPs can be loaded inside the plasma membrane, which has potential applications in drug carrier liposome design.
Article
Chemistry, Physical
Natasha H. Rhys, David J. Barlow, M. Jayne Lawrence, Christian D. Lorenz
Summary: This study used molecular dynamics simulations to investigate the interactions between different diols with varying carbon chain lengths and hydroxylation patterns and a DMPC monolayer, finding that shorter diols can penetrate deeper into the lipid monolayer and disrupt its structure, while all diols studied formed hydrogen-bonded networks with DMPC head groups.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Tanusree Mookherjee, Angshuman Bagchi, Rita Ghosh
Summary: This study reveals a possible molecular mechanism of how the peptide circPPP1R12A can promote cancer by interfering with the Mst pathway. The peptide was found to bind to Mst1/2 proteins, preventing their interactions with Sav1 and inhibiting the activation of the Mst pathway.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Jan-Michael Y. Carrillo, Zhan Chen, Uvinduni I. Premadasa, Christian Steinmetz, E. Bryan Coughlin, Benjamin Doughty, Thomas P. Russell, Bobby G. Sumpter
Summary: By conducting experimental and simulation studies, this research addresses the issues of assembly, reconfiguration, and equilibrium conformation of charged star block copolymers at the oil-water interface, with implications for the development of novel surfactants or amphiphiles.
Article
Physics, Applied
Maksudbek Yusupov, Debbie Dewaele, Pankaj Attri, Umedjon Khalilov, Frank Sobott, Annemie Bogaerts
Summary: This study unravels the possible mechanisms of oligosaccharide oxidation induced by cold atmospheric plasma (CAP), providing atomic-level insight into the onset of plasma-induced removal of biofilms.
PLASMA PROCESSES AND POLYMERS
(2023)
Article
Physics, Fluids & Plasmas
I Tsonev, J. Boothroyd, St Kolev, A. Bogaerts
Summary: This study developed a 2D axisymmetric model to investigate the influence of the two cathode emission mechanisms on the cathode region and the positive column in a plasma discharge in flowing nitrogen gas. The results show that the electron emission mechanism greatly affects the size and temperature of the cathode region, but has no significant impact on the discharge column at atmospheric pressure. Additionally, it was found that the discharge contraction is enhanced with increasing flow velocity due to increased convective heat loss.
PLASMA SOURCES SCIENCE & TECHNOLOGY
(2023)
Article
Physics, Fluids & Plasmas
Omar Biondo, Ashley Hughes, Alex van de Steeg, Stein Maerivoet, Bjoern Loenders, Gerard van Rooij, Annemie Bogaerts
Summary: We investigate the discharge contraction in a microwave plasma at sub-atmospheric pressure in CO2 and CO2/CH4 mixtures, which intensifies the gas heating in the plasma core. The overall mechanism, including plasma contraction and chemical kinetics, is described by power concentration. Thermodynamic calculations and experimental observations are coupled for model validation and understanding of reactor performance in dry reforming of methane.
PLASMA SOURCES SCIENCE & TECHNOLOGY
(2023)
Article
Physics, Fluids & Plasmas
Patrick Vanraes, Syam Parayil Venugopalan, Matthieu Besemer, Annemie Bogaerts
Summary: Various strategies have been developed to cope with aspect ratio dependent etching (ARDE) in chip manufacturing, but they have their own limitations. In this study, we investigated the neutral transport mechanisms in ARDE by conducting experiments and simulations. Our findings suggest that the underlying mechanisms of ARDE involve shadowing and diffuse reflection of neutrals. We also explored different methods to regulate ARDE, with promising results obtained by adjusting the initial hardmask sidewall angle.
PLASMA SOURCES SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Elise Vervloessem, Mikhail Gromov, Nathalie De Geyter, Annemie Bogaerts, Yury Gorbanev, Anton Nikiforov
Summary: The current global energy crisis emphasizes the importance of understanding nonfossil fuel nitrogen fixation pathways for synthetic fertilizer production. This study investigates NH3 gas phase formation from humid N2 and air, demonstrating that adding water vapor increases nitrogen fixation capacity. However, a significant loss mechanism was identified, where HNO2 reacts with NH3 to form NH4NO2, which rapidly decomposes. Approaches to prevent this loss mechanism are discussed, such as in-line removal of HNO2 or direct solvation in liquid.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Rani Vertongen, Annemie Bogaerts
Summary: In this study, we evaluated new electrode configurations in a gliding arc plasmatron (GAP) reactor for CO2 conversion. The reactor design had limited influence on performance, with only slightly higher CO2 conversion compared to the basic GAP reactor design. Surprisingly, we found that different plasma reactors operating at atmospheric pressure showed similar performance, indicating potential performance limits. Further improvements should focus on aspects such as the post-plasma region to maximize the industrial potential of warm plasma technology.
JOURNAL OF CO2 UTILIZATION
(2023)
Article
Chemistry, Physical
Jinxin Wang, Kaimin Zhang, Myrjam Mertens, Annemie Bogaerts, Vera Meynen
Summary: This study provides new insights into the effect of (sub)micrometer particle sized materials on plasma-based CO2CH4 reforming. SiO2 spheres with varying particle sizes, including supported metal, were used. The optimal performance was achieved using 740 nm 5 wt% Ni loaded SiO2, significantly improving CO2 and CH4 conversion and energy yield in a fully packed reactor. These findings highlight the importance of selecting a suitable particle size and can guide the rational design of catalysts for plasma-based reactions.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2023)
Article
Chemistry, Physical
Amugul Esbergenova, Maksudbek Yusupov, Maryam Ghasemitarei, Rivojiddin Jalolov, Mirabbos Hojamberdiev, Ulugbek Shaislamov
Summary: The particle morphology of ZnO nanostructures significantly influences their photocatalytic activity. ZnO nanostructures with a nanostar-like morphology exhibit the highest photocatalytic activity due to the presence of a large number of oxygen vacancy-related defects on the (1 0 1) facet of ZnO.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2023)
Article
Chemistry, Applied
Bart Wanten, Rani Vertongen, Robin De Meyer, Annemie Bogaerts
Summary: This critical review provides a comprehensive guideline for authors in the field of plasma-based CO2 conversion, addressing the inconsistent reporting of performance metrics and providing correct definitions for gas conversion in plasma reactors. The paper discusses the importance of considering the change in volumetric flow rate and highlights inconsistencies in reporting energy efficiency. The authors also provide recommendations and good practices to stimulate the further development of this technology.
JOURNAL OF ENERGY CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Sean Kelly, Elizabeth Mercer, Robin De Meyer, Radu-George Ciocarlan, Sara Bals, Annemie Bogaerts
Summary: We investigated the conversion of CO2 and CH4 in atmospheric pressure microwave plasma, focusing on reaction performance and carbon formation. The energy costs were promising, with the best performance to date for plasma-based dry reforming of methane. The conversion rates for CO2 and CH4 were in the range of 46-49% and 55-67% respectively, producing primarily syngas with H2/CO ratios of 0.6-1.
JOURNAL OF CO2 UTILIZATION
(2023)
Review
Biochemistry & Molecular Biology
Maryam Ghasemitarei, Tayebeh Ghorbi, Maksudbek Yusupov, Yuantao Zhang, Tong Zhao, Parisa Shali, Annemie Bogaerts
Summary: Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), has shown versatile applications in various biological aspects. Reactive oxygen and nitrogen species (RONS) generated during CAP treatment play a crucial role in the therapeutic effects. Non-reactive molecular dynamics (MD) simulations provide valuable insights into the effects of CAP and nitro-oxidative stress on cellular components.
Article
Materials Science, Biomaterials
Francesco Tampieri, Albert Espona-Noguera, Cedric Labay, Maria-Pau Ginebra, Maksudbek Yusupov, Annemie Bogaerts, Cristina Canal
Summary: Non-thermal plasma has been extensively studied for biomedical applications, including tissue decontamination, regeneration, skin treatment, and tumor therapies. Plasma treatment of biopolymer solutions can enhance the generation of reactive oxygen and nitrogen species, making them ideal for indirect treatments of biological targets. The effects of plasma treatment on alginate solutions and the mechanisms responsible for enhanced reactive species generation were investigated using size exclusion chromatography, rheology, scanning electron microscopy, chromatography coupled with mass spectrometry, and molecular dynamics simulations. The active role of biopolymer chemistry during plasma treatment was highlighted, demonstrating its potential for targeted therapies using biocompatible hydrogels as vehicles for storing and delivering reactive species.
BIOMATERIALS SCIENCE
(2023)
Article
Physics, Fluids & Plasmas
Fahim Faraji, Mehdi Neek-Amal, Erik C. Neyts, Francois M. Peeters
Summary: Molecular dynamics simulations were conducted to investigate the influence of different cations on the permeation of charged polymers through narrow capillaries. It was discovered that Li+, Na+, and K+ cations, despite being monovalent, have distinct effects on polymer permeation and subsequent transmission speed. This phenomenon was attributed to the interplay between cations' hydration free energies and the hydrodynamic drag experienced by the polymer. Additionally, alkali cations exhibited surface-to-bulk preferences in small water clusters under an external electric field. The paper presents a new approach to controlling the speed of charged polymers in confined spaces using cations.
Article
Chemistry, Multidisciplinary
Omar Biondo, Cas F. A. M. Van Deursen, Ashley Hughes, Alex van de Steeg, Waldo Bongers, M. C. M. van de Sanden, Gerard van Rooij, Annemie Bogaerts
Summary: This study utilizes a microwave plasma in reverse vortex flow configuration to address the issue of solid carbon deposition in CO2/CH4 plasmas, achieving high reactor performance. The research demonstrates that by changing the gas flow configuration, greenhouse gases can be converted into value-added compounds without solid carbon, making significant strides in green chemistry.