Article
Mathematics, Applied
D. Crisan, D. D. Holm, P. Korn
Summary: A generic approach to stochastic climate modelling is developed for an idealised Atmosphere-Ocean model by incorporating stochasticity into the atmospheric component using stochastic Lie transport. The resulting stochastic model, SALT, preserves circulation like the underlying deterministic climate model. A variant of SALT called LA-SALT replaces the drift velocity of the stochastic vector field with its expected value, and its higher moments are governed by deterministic equations. The modelling approach is substantiated by establishing local existence results for the deterministic and stochastic models.
Article
Engineering, Environmental
Stephen E. Obrike, Stuart L. Barr, Pauline E. Miller, Goodluck K. Anudu
Summary: An evidential reasoning multi-source geospatial integration approach was developed to recognize and predict landslide susceptibility in transport corridors. By integrating airborne laser scanning, digital map datasets, and imagery data, along with a novel method for characterizing soil moisture distribution, numeric measures of slope instability were spatially characterized.
BULLETIN OF ENGINEERING GEOLOGY AND THE ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Yukti Hari-Gupta, Natalia Fili, Alia dos Santos, Alexander W. Cook, Rosemarie E. Gough, Hannah C. W. Reed, Lin Wang, Jesse Aaron, Tomas Venit, Eric Wait, Andreas Grosse-Berkenbusch, J. Christof M. Gebhardt, Piergiorgio Percipalle, Teng-Leong Chew, Marisa Martin-Fernandez, Christopher P. Toseland
Summary: This study reveals the crucial role of nuclear myosin VI (MVI) in the spatial organization of RNA polymerase II (RNAPII). MVI acts as a molecular anchor to maintain high-density clusters of RNAPII. Perturbation of MVI disrupts RNAPII localization, chromatin organization, and gene expression.
NATURE COMMUNICATIONS
(2022)
Article
Engineering, Environmental
Xuneng Tong, Mui-Choo Jong, Jingjie Zhang, Luhua You, Karina Yew-Hoong Gin
Summary: The study found that wind significantly influences the transport of floating plastics in coastal waters, and the model predicted that plastic waste can swiftly move seaward under specific wind conditions in Singapore. Climate change and increasing plastic usage will exacerbate plastic pollution and accelerate its spread.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Geosciences, Multidisciplinary
Sebastian Mueller, Lennart Schueler, Alraune Zech, Falk Hesse
Summary: Geostatistics is a subfield of statistics that deals with spatial correlations in applications such as earth sciences. This article introduces GSTools, a user-friendly software suite based on Python that can solve various geostatistical problems, including random field generation, kriging, and variogram estimation. The capabilities of this software suite are demonstrated through example applications.
GEOSCIENTIFIC MODEL DEVELOPMENT
(2022)
Article
Computer Science, Interdisciplinary Applications
Nathaniel J. L. MacFadden, Ara N. Knaian
Summary: This article presents a new method for simulating particle transport through aerosols efficiently. By voxelizing the aerosol and generating 'droplets' voxel-by-voxel only when necessary, significant reductions in simulation time and memory usage can be achieved. The presented model demonstrates a decrease in simulation time of 1-2 orders of magnitude and a decrease in simulation memory of about 1 order of magnitude when compared to the benchmark method.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Environmental Sciences
Jingchen Yin, Haitao Chen, Yuqiu Wang, Lifeng Guo, Guoguang Li, Puzhou Wang
Summary: This paper estimates the load and delivery of ammonium nitrogen (NH4+-N) in the Poyang Lake Basin and Haihe River Basin using SPARROW. It suggests measures such as enhancing point source management and reducing chemical fertilizer usage to improve water quality.
Article
Biology
C. White, V Rottschafer, L. J. Bridge
Summary: In this paper, a mathematical model representing the binding of VEGF to VEGFR and the subsequent ligand-induced dimerisation is presented. The qualitative and quantitative effect of binding cooperativity is a key factor in this work. The ordinary differential equation system is analyzed at equilibrium, and numerical methods are used to study time-course dynamics. Perturbation analysis is employed to understand the complexities of the behaviors. The simulation results validate the model by showing an excellent fit to experimental data.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Environmental Sciences
Christophe L. Folly, Garyfallos Konstantinoudis, Antonella Mazzei-Abba, Christian Kreis, Benno Bucher, Reinhard Furrer, Ben D. Spycher
Summary: This study constructed a map of terrestrial radiation for Switzerland using airborne gamma-spectrometry measurements, a Bayesian mixed-effects model, and Integrated Nested Laplace Approximation for inference. The predicted higher ambient dose rates in the alpine regions and Ticino compared to the western and northern parts of Switzerland can be used for exposure assessment in epidemiological studies and as a baseline for potential contamination assessment.
JOURNAL OF ENVIRONMENTAL RADIOACTIVITY
(2021)
Article
Mathematics
Haneen Hamam, Ali Raza, Manal M. Alqarni, Jan Awrejcewicz, Muhammad Rafiq, Nauman Ahmed, Emad E. Mahmoud, Witold Pawlowski, Muhammad Mohsin
Summary: Evolutionary approaches play a critical role in various disciplines and are particularly important for the design and solution of stochastic models. Standard and nonstandard evolutionary methods differ in terms of efficiency and cost, with the proposed method being efficient, cost-effective, and meeting the desired feasibility properties.
Article
Chemistry, Physical
M. P. Rosseto, L. R. Evangelista, E. K. Lenzi, R. S. Zola, R. R. Ribeiro de Almeida
Summary: The research aims to investigate the interaction between free and bound charge densities and their influence on permittivity and impedance profiles by modifying the Poisson-Nernst-Planck model.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Motoki Miura, Fumika Sakaue, Hirokazu Matsuno, Kento Morita, Akiko Yoshida, Rintaro Iwata Hara, Ren Nishimura, Yurika Nishida, Mariko Yokogawa, Masanori Osawa, Takanori Yokota
Summary: This study reveals two mechanisms for modulating the solubility of TDP-43 through RNA binding: N-terminal domain dimerization and spatial separation of TDP-43 molecules. These findings provide new insights into the regulation of TDP-43 solubility.
Article
Multidisciplinary Sciences
Chukiat Tantiwong, Joanne L. Dunster, Rachel Cavill, Michael G. Tomlinson, Christoph Wierling, Johan W. M. Heemskerk, Jonathan M. Gibbins
Summary: Agent-based models (ABMs) were developed to explore the extent of GPVI dimerization, showing that confined domains with glycolipid enriched raft-like structures decrease receptor diffusivity and increase dimerization rates. Crowding of receptors by other membrane proteins was also an important determinant of GPVI dimerization.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Marije F. W. Semmelink, Anton Steen, Liesbeth M. Veenhoff
Summary: This review discusses the crucial role of nuclear transport in neurodegenerative diseases, the diversity in outcomes of transport assays in disease models, and the challenges in interpreting their results. Using ALS caused by mutations in C9orf72 as an example, it demonstrates the complexity in determining whether the kinetics of nucleocytoplasmic transport are altered. Answering this question has implications for the widespread mislocalization of proteins, beyond the reported mislocalization of transport reporters, and presents a challenge for future research efforts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Materials Science, Multidisciplinary
Philip Townsend, Emanuel Larsson, Tomas Karlson, Stephen A. Hall, Malin Lundman, Per Bergstrom, Charlotta Hanson, Niklas Loren, Tobias Geback, Aila Sarkka, Magnus Roding
Summary: The research explores the relationship between fiber structure and properties using a virtual fiber model as a replacement for real material. 3D image data sets of a sample fibrous material are obtained via X-ray microtomography to estimate parameters for generating virtual fiber structures. Experimental results demonstrate good agreement between the virtual structure and physical material in terms of permeability.
COMPUTATIONAL MATERIALS SCIENCE
(2021)
Article
Engineering, Biomedical
Ruirui Liu, Kathryn A. Higley, Maciej H. Swat, Mark A. J. Chaplain, Gibin Powathil, James A. Glazier
Summary: The paper discusses the importance of understanding and designing clinical radiation therapy in oncological treatments. A computational platform was introduced to build a sophisticated multicellular model to simulate how radiation affects living tissue biology. By coupling Geant4 and CompuCell3D, the study developed a tool to simulate the dynamics of biological tissue in the presence of ionizing radiation for quantifying the biological consequences of radiation therapy.
PHYSICS IN MEDICINE AND BIOLOGY
(2021)
Article
Chemistry, Physical
Adrien Coulier, Stefan Hellander, Andreas Hellander
Summary: Spatial stochastic models of single cell kinetics are crucial in capturing fluctuations in molecular numbers and spatial dependencies, but the computational cost is a limiting factor. Further approximation of spatial dynamics is necessary for improving computational efficiency in practical applications.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biology
Chiara Villa, Mark A. J. Chaplain, Alf Gerisch, Tommaso Lorenzi
Summary: Mechanical and mechanochemical models of pattern formation in biological tissues, considering different stress-strain constitutive equations for the ECM, reveal that fluid-like constitutive models such as Maxwell and Jeffrey models have higher pattern formation potential compared to solid-like models like Kelvin-Voigt and standard linear solid models. This finding suggests the importance of acquiring detailed quantitative information on the mechanical properties of ECM components in various biological tissues to improve the accuracy of mechanical models in representing tissue rheology.
BULLETIN OF MATHEMATICAL BIOLOGY
(2021)
Article
Biology
Sara Hamis, James Yates, Mark A. J. Chaplain, Gibin G. Powathil
Summary: The study successfully simulated the treatment responses of LoVo cells to the anti-cancer drug AZD6738 by combining a systems pharmacology approach with an agent-based modelling approach, showing the potential of agent-based models in bridging the gap between in vitro and in vivo research in preclinical drug development.
BULLETIN OF MATHEMATICAL BIOLOGY
(2021)
Article
Biology
Linnea C. Franssen, Nikolaos Sfakianakis, Mark A. J. Chaplain
Summary: A three-dimensional hybrid atomistic-continuum model is developed to describe the invasive growth dynamics of individual cancer cells in tissue, accounting for phenotypic variation and transitions between epithelial-like and mesenchymal-like cell phenotypes. The model consists of partial and stochastic differential equations considering matrix-degrading enzyme concentrations and extracellular matrix density, calibrated to an in vitro invasion assay experiment of oral squamous cell carcinoma cells through parameter estimation and sensitivity analysis. This model provides a new theoretical basis for studying the invasion mechanisms of cancer cells.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yunchen Xiao, Len Thomas, Mark A. J. Chaplain
Summary: Two different methods were proposed to estimate parameters within a partial differential equation model of cancer invasion, one based on approximate Bayesian computation and the other on a two-stage gradient matching method using a generalized additive model. Both methods performed well on simulated data, but the ability to estimate some model parameters deteriorated rapidly in the presence of simulated measurement error.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Oncology
Sara J. Hamis, Yury Kapelyukh, Aileen McLaren, Colin J. Henderson, C. Roland Wolf, Mark A. J. Chaplain
Summary: The study developed a mechanistic mathematical model to describe the synergistic action of dabrafenib and trametinib on ERK activity in BRAFV600E-mutant melanoma cells, elucidating the molecular mechanism underlying vertical inhibition of the BRAF-MEK-ERK cascade.
BRITISH JOURNAL OF CANCER
(2021)
Editorial Material
Biology
Philip K. Maini, Mark A. J. Chaplain, Mark A. Lewis, Jonathan A. Sherratt
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Biology
Chiara Villa, Alf Gerisch, Mark A. J. Chaplain
Summary: The formation of new vascular networks is crucial for tissue development and regeneration. Cluster-based vasculogenesis, a new mechanism involving the mobilization of cells from the bone marrow, plays a key role in connecting distant blood vessels in vivo. We propose a mathematical model to study the dynamics of cluster formation and investigate the effects of endogenous chemotaxis and matrix degradation through numerical and parametric analysis.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Richard Jiang, Prashant Singh, Fredrik Wrede, Andreas Hellander, Linda Petzold
Summary: In this work, a data-driven method is presented to infer the underlying biochemical reaction system governing a set of observed species concentrations over time. The method utilizes sparse Bayesian inference to produce robust, interpretable biochemical reaction networks, along with uncertainty estimates of parameters.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Mathematics, Applied
N. Bellomo, F. Brezzi, M. A. J. Chaplain
Summary: This editorial proposes modeling and simulation of mutating virus pandemics in a globally connected world. It is divided into three parts: a general framework that goes beyond deterministic population dynamics, the contents of the papers in this issue, and a critical analysis of research perspectives.
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2022)
Article
Biochemical Research Methods
Adrien Coulier, Prashant Singh, Marc Sturrock, Andreas Hellander
Summary: Quantitative stochastic models of gene regulatory networks are important tools for studying cellular regulation. Determining model fidelity is a practical challenge, as it affects the accuracy and computation cost of the results. Inference of true model parameters is often approximate and requires difficult choices, such as summary statistics selection and data quantity.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biology
Dimitrios Katsaounis, Mark A. J. Chaplain, Nikolaos Sfakianakis
Summary: This paper addresses the question of identifying the migratory pattern and spread of individual cancer cells or small clusters of cancer cells when the macroscopic evolution of the cancer cell colony is determined by a specific partial differential equation (PDE). The authors demonstrate that the traditional understanding of the diffusion and advection terms of the PDE as responsible for random and biased motion of solitary cancer cells, respectively, is imprecise. Instead, they show that the drift term of the correct stochastic differential equation scheme should also take into account the divergence of the PDE diffusion. Numerical experiments and computational simulations are used to support their claims.
JOURNAL OF MATHEMATICAL BIOLOGY
(2023)
Article
Mathematics, Applied
Chiara Villa, Mark A. Chaplain, Tommaso Lorenzi
Summary: This study investigates the emergence of phenotypic heterogeneity in vascularized tumors through mathematical modeling and numerical simulations. The results provide a theoretical basis for the empirical evidence that the phenotypic properties of cancer cells in vascularized tumors vary with the distance from the blood vessels, and establish a relation between the degree of tumor tissue vascularization and the level of intratumor phenotypic heterogeneity.
SIAM JOURNAL ON APPLIED MATHEMATICS
(2021)
Article
Mathematics
Chiara Villa, Mark A. J. Chaplain, Tommaso Lorenzi
Summary: This study investigates the evolutionary dynamics of tumour cells in vascularised tumours under chemotherapy using a mathematical model and numerical simulations. Findings suggest that tumour cell phenotypic properties vary with distance from blood vessels, hypoxic regions may support intra-tumour phenotypic heterogeneity, and hypoxia may favor the selection for chemoresistant phenotypic variants prior to treatment.
VIETNAM JOURNAL OF MATHEMATICS
(2021)