Article
Polymer Science
Antonio Lamura
Summary: The dynamical response of a tethered semiflexible polymer with self-attractive interactions under an external force field was numerically investigated by varying stiffness and self-interaction strength. Different parameters led to various transitions and morphological changes in the polymer chain. The study showed that the external force had significant effects on the conformation and deformation of the polymer chain.
Review
Construction & Building Technology
Katerina Ioannidou, Christophe Labbez, Enrico Masoero
Summary: This manuscript reviews the current state of the art in coarse-grained and mesoscale simulations of C-S-H, and highlights opportunities for future research.
CEMENT AND CONCRETE RESEARCH
(2022)
Article
Biophysics
Graham T. Johnson, Eran Agmon, Matthew Akamatsu, Emma Lundberg, Blair Lyons, Wei Ouyang, Omar A. Quintero-Carmona, Megan Riel-Mehan, Susanne Rafelski, Rick Horwitz
Summary: Cell science faces challenges in integrating vast amounts of information and making data and methods more accessible. This paper proposes the concept of constructing next-generation virtual cells by integrating information from diverse sources, which can simulate real cells accurately, bridge the gap between theory and experiments, and facilitate collaboration among researchers across different fields.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Plaboni Sen, Suchandra Roy Acharyya, Arisha Arora, Siddhartha Sankar Ghosh
Summary: WIF1, a potent tumour suppressor gene, is epigenetically silenced in various malignancies. In this study, computational methods were used to investigate the role of WIF1 protein and its interactions with Wnt pathway molecules. The results provide insights into the potential role of WIF1 in inhibiting Wnt pathways in different types of cancer.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Green & Sustainable Science & Technology
Padmalalitha Thennal VenkatesaNarayanan, Rajeswari Thirunavukkarasu, Vijaya M. Sunder
Summary: This study examines the relationship between dimensions of learning organization, green supply chain practices, and corporate performance, highlighting the indispensable link between environmentalism and learning.
JOURNAL OF CLEANER PRODUCTION
(2021)
Editorial Material
Anesthesiology
Thomas Heidegger, Takashi Asai
Summary: Despite the availability of new technologies, recent evidence has shown that fibreoptic intubation remains an essential technique for managing difficult airways. It is our responsibility as anaesthesia societies and practitioners to offer this technique to patients in appropriate situations.
BRITISH JOURNAL OF ANAESTHESIA
(2023)
Article
Mechanics
Tingting Guo, Xiuyan Liu, Dalei Song
Summary: This paper proposes a new sliding negative pressure adsorption mechanism (SNPAM) for underwater climbing adsorption robots. The robot can generate a maximum adsorption force of 600 kgf at a gap height of 12 mm in adsorption mode, and can maintain a maximum force of 363 kgf at a gap height of 28 mm in locomotion mode. The mathematical model allows the robot to adjust both the gap height and adsorption force according to various adsorbate surface conditions. Application experiments confirm the SNPAM's ability to help an underwater climbing robot to perform adsorption and locomotion.
Article
Engineering, Biomedical
Roni Sverdlov Arzi, Maya Davidovich-Pinhas, Noy Cohen, Alejandro Sosnik
Summary: Nanonization of poorly water-soluble drugs improves their oral bioavailability by increasing drug dissolution rate and adhesion to gastrointestinal mucus. This study synthesized mucin hydrogels to mimic freshly excised porcine mucin and investigated the effects of particle size, concentration, and hydrogel crosslinking density on particle penetration. The results showed that drug nanonization significantly increased oral bioavailability and half-life. This research provides a basis for the rational design of nano-drug delivery systems for mucosal administration.
ACTA BIOMATERIALIA
(2023)
Article
Cell Biology
Karina Barreiro, Abigail C. Lay, German Leparc, Van Du T. Tran, Marcel Rosler, Lusyan Dayalan, Frederic Burdet, Mark Ibberson, Richard J. M. Coward, Tobias B. Huber, Bernhard K. Kraemer, Denis Delic, Harry Holthofer
Summary: Extracellular vesicles (EV) are membrane particles secreted by cells and found in body fluids. The contents of EV, including RNA species, proteins, lipids and metabolites, reflect the physiological status of their parent cells. In this study, EV from different human kidney cells were analyzed and compared to EV in human urine to identify potential biomarkers for kidney disease.
JOURNAL OF EXTRACELLULAR VESICLES
(2023)
Article
Meteorology & Atmospheric Sciences
Mathias W. Rotach, Stefano Serafin, Helen C. Ward, Marco Arpagaus, Ioana Colfescu, Joan Cuxart, Stephan F. J. De Wekker, Vanda Grubisic, Norbert Kalthoff, Thomas Karl, Daniel J. Kirshbaum, Manuela Lehner, Stephen Mobbs, Alexandre Paci, Elisa Palazzi, Adriana Bailey, Jurg Schmidli, Christoph Wittmann, Georg Wohlfahrt, Dino Zardi
Summary: This essay discusses the challenges faced by the atmospheric community in adequately treating flows over mountains and their implications for numerical weather prediction, climate simulations, and impact modeling. It emphasizes the need for further research and understanding of the mountain boundary layer (MoBL), as the current parameterizations overlook its many differences from the boundary layer over flat terrain, potentially leading to inaccurate model outputs.
BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY
(2022)
Article
Clinical Neurology
George D. Price, Michael V. Heinz, Daniel Zhao, Matthew Nemesure, Franklin Ruan, Nicholas C. Jacobson
Summary: This study analyzed passive data collected from wearable sensors to investigate behavioral differences between individuals with schizophrenia, major depressive disorder (MDD), and controls. The findings suggest that unsupervised clustering can effectively differentiate behavioral differences between diagnostic groups, and depressed individuals show the highest behavioral variability.
JOURNAL OF AFFECTIVE DISORDERS
(2022)
Article
Clinical Neurology
Christiaan H. Vinkers, Erika Kuzminskaite, Femke Lamers, Erik J. Giltay, Brenda W. J. H. Penninx
Summary: Patients with depressive and anxiety disorders consistently exhibit dysregulation across the HPA-axis, immune system, and ANS, particularly during current episodes. An integrated approach using cumulative stress indices within and across biological stress systems is crucial for understanding stress system functionality in affective disorders.
JOURNAL OF AFFECTIVE DISORDERS
(2021)
Article
Chemistry, Physical
Aleksander E. P. Durumeric, Gregory A. Voth
Summary: Bottom-up CG molecular dynamics models, parameterized using complex effective Hamiltonians, are often optimized to approximate high dimensional data from atomistic simulations. However, human validation of these models may not differentiate between the CG model and the atomistic simulations. We propose using classification to estimate high dimensional errors and utilizing explainable machine learning to convey this information to scientists. This approach is demonstrated using Shapley additive explanations and two CG protein models, and may be valuable for assessing the accuracy of allosteric effects in CG models at the atomistic level.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Plant Sciences
Kai Hao, Yun Wang, Zhanpin Zhu, Yu Wu, Ruibing Chen, Lei Zhang
Summary: This review summarizes the recent progress on the contributions of the miR160-ARF module to important traits of plants and the role of miR160-centered gene regulatory network in coordinating growth with endogenous and environmental factors. Manipulation of miR160-guided gene regulation may provide a new method to engineer plants with improved adaptability and yield.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Chemistry, Analytical
Vanessa Takeshita, Gustavo Vinicios Munhoz-Garcia, Anderson Espirito Santo Pereira, Valdemar Luiz Tornisielo, Leonardo Fernandes Fraceto
Summary: Nanopesticides are a promising alternative to conventional pesticides in agriculture, but thorough evaluation of their environmental impact and efficacy is necessary before their commercialization. The use of radiometric techniques can help track active ingredients of nanopesticides in biological and environmental systems, in addition to other characterization techniques for nanomaterials. This article provides a perspective on using radiolabeled pesticides to monitor nanoformulations and discusses the advantages and challenges associated with this approach.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Cell Biology
Weria Pezeshkian, Siewert J. Marrink
Summary: Biological membranes exhibit diversity in their shapes and complexity in chemical compositions that are linked to many cellular functions. Simulation studies using a diverse range of computational techniques are able to capture this complexity at increasing levels of realism and connect the microscopic view on protein-lipid interactions to cellular morphologies at the level of entire organelles. Recent advances highlight the understanding of this complexity, identify current bottlenecks, and sketch possible ways ahead.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Article
Chemistry, Physical
Yang Liu, Alex H. de Vries, Weria Pezeshkian, Siewert J. Marrink
Summary: Research on lateral organization in plasma membranes remains a challenging issue, with simplified models often used. While coarse-grained models have shown success in capturing phase separation, achieving the same with all-atom models is more difficult. By applying the virtual site hybrid method, researchers were able to accelerate and guide phase separation in a ternary membrane.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Senthil Arumugam, Stefanie Schmieder, Weria Pezeshkian, Ulrike Becken, Christian Wunder, Dan Chinnapen, John Hjort Ipsen, Anne K. Kenworthy, Wayne Lencer, Satyajit Mayor, Ludger Johannes
Summary: The study reveals that the acyl chain structure of GM1 determines the establishment of nanodomains when actively clustered by actin.
NATURE COMMUNICATIONS
(2021)
Review
Food Science & Technology
Weria Pezeshkian, Julian C. Shillcock, John H. Ipsen
Summary: The investigation of bacterial toxin entry mechanism remains challenging, but computer simulations serve as robust complementary tools for exploring biological processes in detail. Recent developments in the study of toxin endocytosis have significantly advanced our understanding, with implications for nanoparticle design and protein phase separation at membrane surfaces. The discussed methods also show promise for future development in this field.
Review
Biochemistry & Molecular Biology
Victoria Thusgaard Ruhoff, Guillermo Moreno-Pescador, Weria Pezeshkian, Poul Martin Bendix
Summary: Continuous reshaping of the plasma membrane is critical for cellular functions. Recent studies have shown that protein crowding can bend membranes by generating spontaneous vesicle formation and tubular morphologies. However, the in vivo impact of protein crowding is still under investigation.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Chemistry, Multidisciplinary
Nicola De Franceschi, Weria Pezeshkian, Alessio Fragasso, Bart M. H. Bruininks, Sean Tsai, Siewert J. Marrink, Cees Dekker
Summary: The shape of cellular membranes determines their structure and function. A DNA-nanotechnology-based approach, called the synthetic membrane shaper (SMS), can stabilize the shape of cellular membranes and is compatible with protein reconstitution. This method provides a general tool for studying protein binding to complex membrane geometries.
Article
Chemistry, Physical
Fabian Grunewald, Mats H. Punt, Elizabeth E. Jefferys, Petteri A. Vainikka, Melanie Koenig, Valtteri Virtanen, Travis A. Meyer, Weria Pezeshkian, Adam J. Gormley, Maarit Karonen, Mark S. P. Sansom, Paulo C. T. Souza, Siewert J. Marrink
Summary: The study develops a consistent strategy to accurately parametrize carbohydrate molecules within the framework of Martini 3 model and demonstrates the validity and transferability of this approach through various test cases.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Review
Biochemistry & Molecular Biology
Victoria Thusgaard Ruhoff, Poul Martin Bendix, Weria Pezeshkian
Summary: Biomembranes are crucial for our understanding of the basic building blocks of life – cells. A key characteristic of membranes is their ability to adopt various shapes that are essential for cellular function. In this article, we review different mechanisms by which membranes can change shape, with a special focus on how membrane proteins induce local curvature and rigidity, resulting in emerging forces and large-scale membrane deformations. We also argue that considering changes in membrane rigidity moduli is necessary to fully understand the interaction between rigid proteins and biomembranes.
EMERGING TOPICS IN LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Weria Pezeshkian, Fabian Grunewald, Oleksandr Narykov, Senbao Lu, Valeria Arkhipova, Alexey Solodovnikov, Tsjerk A. Wassenaar, Siewert J. Marrink, Dmitry Korkin
Summary: Despite efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains unknown. This study developed a computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail and focused on the understudied M protein. Molecular dynamics simulations revealed the agglomeration of M dimers into large macromolecular assemblies with distinct patterns, in agreement with experimental data, demonstrating a versatile approach for de novo virus structure modeling.
Meeting Abstract
Biophysics
Mayank P. Pandey, Weria Pezeshkian, Himanshu Khandelia
BIOPHYSICAL JOURNAL
(2023)
Article
Engineering, Biomedical
Aida Nonn, Balint Kiss, Weria Pezeshkian, Thomas Tancogne-Dejean, Albert Cerrone, Miklos Kellermayer, Yuanli Bai, Wei Li, Tomasz Wierzbicki
Summary: A methodology combining experimental and simulation techniques was proposed to investigate the internal structure and mechanical properties of SARS-CoV-2. The elastic properties and fracture strength of the viral membrane were estimated, and the results showed a close association between membrane proteins and ribonucleoproteins. These findings provide valuable knowledge for the development of novel prevention and treatment methods.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Maria Lyngby Karlsen, Dennis S. Bruhn, Weria Pezeshkian, Himanshu Khandelia
Summary: The study reveals that cholesterol is predominantly located in the outer leaflet of asymmetric lipid membranes, with longer chain sphingomyelin depleting more cholesterol from the inner leaflet. In complex asymmetric membranes, the higher chain saturation of the outer leaflet compensates for the effect of longer chain sphingomyelin.
Article
Physics, Fluids & Plasmas
Weria Pezeshkian, John H. Ipsen
Summary: The study of properties of freestanding tensionless interfaces and membranes at low bending rigidity kappa reveals three different regimes, which are important for describing soft interface systems.
Article
Chemistry, Physical
Christoffer Dam Florentsen, Alexander Kamp-Sonne, Guillermo Moreno-Pescador, Weria Pezeshkian, Ali Asghar Hakami Zanjani, Himanshu Khandelia, Jesper Nylandsted, Poul Martin Bendix
Summary: The plasma membrane of eukaryotic cells is a crowded environment with a high diversity of proteins in a complex lipid matrix. The lateral organization of membrane proteins in the plasma membrane is closely related to biological functions such as endocytosis. Annexin A4 (ANXA4), a key player in various biological functions, is involved in plasma membrane repair and is activated by Ca2+ influx. ANXA4 is found to be a sensor of negative membrane curvatures and the trimer structure of ANXA4 generates membrane curvature upon binding, with an affinity for highly curved membrane regions only within a defined curvature window.
