Article
Mathematics, Interdisciplinary Applications
Sekar Elango, Bundit Unyong
Summary: This article investigates the use of two non-uniform meshes in the finite difference method for solving singularly perturbed mixed-delay differential equations. The multiplication of the second-order derivative by a small parameter creates boundary layers at x=0 and x=3, as well as strong interior layers at x=1 and x=2 due to the delay terms. It is proven that the method has almost first-order convergence on the Shishkin mesh and first-order convergence on the Bakhvalov-Shishkin mesh. Error estimates are derived in the discrete maximum norm, and practical examples are provided for validation.
FRACTAL AND FRACTIONAL
(2023)
Article
Mathematics, Applied
Ingeborg G. Gjerde, Kundan Kumar, Jan M. Nordbotten
Summary: In this work, we analyze the Poisson equation with a line source using a dual-mixed variational formulation. By making assumptions on the problem parameters, we split the solution into higher- and lower-regularity terms, and propose a singularity removal-based mixed finite element method to approximate the higher-regularity terms, which significantly improves the convergence rate compared to approximating the full solution.
SIAM JOURNAL ON NUMERICAL ANALYSIS
(2021)
Article
Engineering, Marine
Luka Grubisic, Domagoj Lacmanovic, Marin Palaversa, Pero Prebeg, Josip Tambaca
Summary: We present an algorithm for the fully automatic generation of a class-compliant mesh for ship structural analysis. The algorithm consists of automatic geometry refinement and a preconditioned Delaunay frontal quad dominant mesh generator. The main contribution of the paper is the automatic geometry refinement algorithm and the virtual stiffener procedure. The algorithm is implemented in Python using the open-source Gmsh system and the Open CASCADE kernel.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Mathematics, Applied
Nicolas Barnafi, Gabriel N. Gatica, Daniel E. Hurtado, Willian Miranda, Ricardo Ruiz-Baier
Summary: This work presents new primal and dual-mixed finite element methods for deformable image registration, considering the continuity of the similarity measure and ellipticity of the regularizer. By modifying the original model to incorporate additional degrees of freedom from the regularizer's kernel, ellipticity is granted on the entire solution space. The well-posedness of extended formulations and error estimates with convergence rates are proven, with numerical examples demonstrating the efficiency of the methods in registration tasks, particularly for translations and rotations.
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2021)
Article
Mathematics, Applied
Rui M. P. Almeida, Jose C. M. Duque, Belchior C. X. Mario
Summary: We present a new mixed finite element method for solving a class of parabolic equations with p-Laplacian and nonlinear memory. The applicability, stability, and convergence of the method are studied. The paper provides the numerical discretization process and the relation between the convergence order and the parameter p.
APPLIED NUMERICAL MATHEMATICS
(2022)
Article
Plant Sciences
Zhen Xiao, Nicolas Brunel, Chenwei Tian, Jingzhe Guo, Zhenbiao Yang, Xinping Cui
Summary: Polar cell growth is a crucial process in the growth, development, and reproduction of eukaryotic organisms. This paper introduces a mechanistic integro-differential equation and constrained semiparametric regression to quantitatively describe the interplay among different processes involved in the polar distribution of active ROP1 protein. The analysis reveals a stable equilibrium between positive and negative feedback loops, which defines the tip growth and polarity of pollen tubes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Mathematics
Todd Arbogast, Chuning Wang
Summary: This paper introduces new families of direct serendipity and direct mixed finite elements defined on general planar, strictly convex polygons. The finite elements provide optimal approximation while using the minimal degrees of freedom. The paper proposes alternative ways to construct supplemental functions on the element, resulting in better accuracy and robustness in numerical tests.
Article
Computer Science, Interdisciplinary Applications
Meng Fan, Yan Jin, Thomas Wick
Summary: A mixed-mode phase-field fracture model is developed in this work, utilizing a parallel-adaptive quasi-monolithic framework. The model is tested and compared with existing models on rock-like and masonry-like materials, demonstrating numerical robustness and physical soundness.
ENGINEERING WITH COMPUTERS
(2022)
Article
Mathematics, Applied
Sunil Kumar, Shashikant Kumar, Sumit
Summary: This article presents a numerical analysis of a class of singularly perturbed delay Volterra integro-differential equations with multiple boundary layers. The problem is discretized using an implicit difference scheme for the differential term and a composite numerical integration rule for the integral term. The analysis of the discrete scheme consists of two parts: an a priori error estimate for robust convergence on specific meshes, and a maximum norm a posteriori error estimate involving difference derivatives of the approximate solution. Numerical experiments confirm the theoretical findings.
NUMERICAL ALGORITHMS
(2023)
Article
Mathematics, Applied
Ritesh Kumar Dubey, Prabhat Mishra
Summary: This article presents an entirely new approach for constructing locally adaptive mesh to compute nonoscillatory solutions using representative second order schemes. The method uses modified equation analysis and a notion of data dependent stability of schemes to identify the solution regions for local mesh adaptation.
NUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS
(2023)
Article
Mathematics, Applied
Reuben Rauch, Manfred R. Trummer, J. F. Williams
Summary: A Chebyshev spectral collocation method is proposed for solving mixed functional differential equations involving delay, advance terms, or derivatives in boundary value problems. Despite the generally not very smooth solutions, the method allows for accurate evaluation of approximated solutions at points not on the grid. The study presents numerical results and examines convergence behavior related to smoothness.
APPLIED NUMERICAL MATHEMATICS
(2021)
Article
Mathematics, Applied
Todd Arbogast, Chuning Wang
Summary: This paper presents new families of direct serendipity and direct mixed finite elements on general planar, strictly convex polygons. These elements are H-1 and H(div) conforming, respectively, and achieve optimal accuracy for any order. They have the minimum number of degrees of freedom while satisfying conformity and accuracy constraints. The convergence properties of the finite elements are demonstrated under certain regularity assumptions and mild restrictions on the construction of supplemental functions. Numerical experiments on various meshes illustrate the performance of these new finite element families.
NUMERICAL ALGORITHMS
(2023)
Article
Mathematics, Applied
Huoyuan Duan, Junhua Ma, J. U. N. Zou
Summary: This paper presents a mixed finite element method for the Maxwell eigenproblem with modifications on the Kikuchi mixed formulation, resulting in efficient numerical solutions through discretization of the electric field and multiplier. In practical applications, the method shows superior performance on grids, with higher accuracy and reliability.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2021)
Article
Engineering, Multidisciplinary
Bhagyashree Prabhune, Krishnan Suresh
Summary: The finite element method requires tangle-free elements and convex quadrilateral and hexahedral elements. However, generating high-quality tangle-free meshes, especially 3D hexahedral meshes, is challenging. The tangled finite element method (TFEM) was proposed to handle concave quadrilateral elements but is computationally expensive and complex. Here, they present a computationally efficient isoparametric-TFEM (i-TFEM) framework for inverted quadrilateral and hexahedral elements, which is simple, efficient, and accurate with optimal convergence rate.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Computer Science, Interdisciplinary Applications
Modesar Shakoor
Summary: FEMS is a Finite Element Modeling Software that integrates mesh generation and adaption features to alleviate the difficulty of designing an FE mesh. It is targeted at engineers and scientists addressing localization problems in mechanics, with capabilities for handling internal interfaces in solid and fluid mechanics. FEMS automatically adapts the FE mesh during simulation to achieve the best accuracy for a prescribed number of nodes.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Review
Biotechnology & Applied Microbiology
Richard J. Weaver, Eric A. Blomme, Amy E. Chadwick, Ian M. Copple, Helga H. J. Gerets, Christopher E. Goldring, Andre Guillouzo, Philip G. Hewitt, Magnus Ingelman-Sundberg, Klaus Gjervig Jensen, Satu Juhila, Ursula Klingmuller, Gilles Labbe, Michael J. Liguori, Cerys A. Lovatt, Paul Morgan, Dean J. Naisbitt, Raymond H. H. Pieters, Jan Snoeys, Bob van de Water, Dominic P. Williams, B. Kevin Park
NATURE REVIEWS DRUG DISCOVERY
(2020)
Article
Pharmacology & Pharmacy
Giulio Giustarini, Suzanna Huppelschoten, Marco Barra, Angela Oppelt, Laura Wagenaar, Richard J. Weaver, Marianne Bol-Schoenmakers, Joost J. Smit, Bob van de Water, Ursula Klingmueller, Raymond H. H. Pieters
TOXICOLOGY AND APPLIED PHARMACOLOGY
(2020)
Article
Oncology
Soo-Zin Kim-Wanner, Yassen Assenov, Mridul B. Nair, Dieter Weichenhan, Axel Benner, Natalia Becker, Katharina Landwehr, Ruprecht Kuner, Holger Sultmann, Manel Esteller, Ina Koch, Michael Lindner, Michael Meister, Michael Thomas, Matthias Bieg, Ursula Klingmueller, Matthias Schlesner, Arne Warth, Benedikt Brors, Erhard Seifried, Halvard Boenig, Christoph Plass, Angela Risch, Thomas Muley
JOURNAL OF THORACIC ONCOLOGY
(2020)
Article
Multidisciplinary Sciences
Avlant Nilsson, Jurgen R. Haanstra, Martin Engqvist, Albert Gerding, Barbara M. Bakker, Ursula Klingmueller, Bas Teusink, Jens Nielsen
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Frederique Kok, Marcus Rosenblatt, Melissa Teusel, Tamar Nizharadze, Vladimir Goncalves Magalhaes, Christopher Daechert, Tim Maiwald, Artyom Vlasov, Marvin Waesch, Silvana Tyufekchieva, Katrin Hoffmann, Georg Damm, Daniel Seehofer, Tobias Boettler, Marco Binder, Jens Timmer, Marcel Schilling, Ursula Klingmueller
MOLECULAR SYSTEMS BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Niklas Gremke, Pierfrancesco Polo, Aaron Dort, Jean Schneikert, Sabrina Elmshauser, Corinna Brehm, Ursula Klingmuller, Anna Schmitt, Hans Christian Reinhardt, Oleg Timofeev, Michael Wanzel, Thorsten Stiewe
NATURE COMMUNICATIONS
(2020)
Article
Oncology
Sabine Wessels, Thomas Muley, Petros Christopoulos, Michael Meister, Ingrid Heinzmann-Groth, Arne Warth, Esther Herpel, Simone Hummler, Ursula Klingmuller, Jonas Kuon, Claus-Peter Heussel, Ralf Eberhardt, Felix J. F. Herth, Hauke Winter, Helge Bischoff, Albrecht Stenzinger, Martin Reck, Rudolf Maria Huber, Michael Thomas, Marc A. Schneider
TRANSLATIONAL LUNG CANCER RESEARCH
(2020)
Article
Immunology
Soumya R. Mohapatra, Ahmed Sadik, Suraj Sharma, Gernot Poschet, Hagen M. Gegner, Tobias V. Lanz, Philippe Lucarelli, Ursula Klingmueller, Michael Platten, Ines Heiland, Christiane A. Opitz
Summary: The liver plays a critical role in maintaining homeostatic levels of essential amino acids like tryptophan. Hypoxic conditions prompt significant rewiring of tryptophan metabolism in hepatocytes, leading to reduced expression of TDO2 and increased tryptamine production. This hypoxic adaptation may be linked to hallucinogenic responses and immunosuppressive activities, highlighting the importance of hypoxia in regulating tryptophan metabolism and potential implications for mental health.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Lorenza A. D'Alessandro, Ursula Klingmueller, Marcel Schilling
Summary: This article investigates the response of liver cells to cytokines and growth factors, with a specific focus on the regulation of growth factor receptors on the cell surface. The study suggests that mechanistic mathematical modeling based on quantitative data can help unravel these molecular-level interactions.
BIOCHEMICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Karolin Dehlke, Linda Krause, Silvana Tyufekchieva, Anastasia Murtha-Lemekhova, Philipp Mayer, Artyom Vlasov, Ursula Klingmueller, Nikola S. Mueller, Katrin Hoffmann
Summary: This study investigates the expression of cytokines and growth factors in post-hepatectomy regeneration and finds that certain expression trajectories are associated with liver failure, morbidity, and mortality. Regression models can predict mortality following major liver resection based on preoperative cytokine and growth factor signatures. Liquid-biopsy based risk profiling can predict postoperative liver failure and mortality on the first day after surgery.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Sajib Chakraborty, Geoffroy Andrieux, Philipp Kastl, Lorenz Adlung, Sandro Altamura, Martin E. Boehm, Luisa E. Schwarzmueller, Yomn Abdullah, Marie-Christine Wagner, Barbara Helm, Hermann-Josef Groene, Wolf D. Lehmann, Melanie Boerries, Hauke Busch, Martina U. Muckenthaler, Marcel Schilling, Ursula Klingmueller
Summary: The lack of erythropoietin receptor leads to a deficiency of hemoglobin in CFU-E cells in embryos, along with massive iron overload in the fetal liver, indicating a communication issue between the liver and placenta. Additionally, the reduction of related proteins also causes a metabolic shift. Balancing interactions between erythropoiesis, iron homeostasis regulation, and metabolic reprogramming is crucial for survival.
Article
Cell Biology
Natella I. I. Enukashvily, Nikita V. V. Ponomartsev, Avanee Ketkar, Roman Suezov, Anna V. V. Chubar, Andrey D. D. Prjibelski, Daria D. D. Shafranskaya, Sabrina Elmshaeuser, Corinna U. U. Keber, Vera N. N. Stefanova, Andrey L. L. Akopov, Ursula Klingmueller, Petra I. I. Pfefferle, Thorsten Stiewe, Matthias Lauth, Anna I. I. Brichkina
Summary: The abnormal tumor microenvironment significantly influences the response of cancer to chemo- and immuno-therapy. This study demonstrates the induction of pericentromeric satellite DNA (satDNA) transcription in cancer-associated fibroblasts (CAFs) of lung adenocarcinoma. The findings suggest that satellite long non-coding (lnc) RNAs in CAFs regulate inflammatory gene expression and can be secreted, potentially playing a role in cell-cell communication in the tumor microenvironment.
CELL DEATH & DISEASE
(2023)
Article
Biochemistry & Molecular Biology
Hagen M. Gegner, Thomas Naake, Aurelien Dugourd, Torsten Mueller, Felix Czernilofsky, Georg Kliewer, Evelyn Jaeger, Barbara Helm, Nina Kunze-Rohrbach, Ursula Klingmueller, Carsten Hopf, Carsten Mueller-Tidow, Sascha Dietrich, Julio Saez-Rodriguez, Wolfgang Huber, Rudiger Hell, Gernot Poschet, Jeroen Krijgsveld
Summary: Metabolomic and proteomic analyses of human plasma and serum samples have the potential to advance our understanding of disease biology. However, pre-analytical factors such as temperature and time can impact the integrity of the samples and there is a need for standardized operating procedures to ensure reliable data.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jana Samarin, Piotr Fabrowski, Roman Kurilov, Hana Nuskova, Johanna Hummel-Eisenbeiss, Hannelore Pink, Nan Li, Vivienn Weru, Hamed Alborzinia, Umut Yildiz, Laura Grob, Minerva Taubert, Marie Czech, Michael Morgen, Christina Brandstaedter, Katja Becker, Lianghao Mao, Ashok Kumar Jayavelu, Angela Goncalves, Ulrike Uhrig, Jeanette Seiler, Yanhong Lyu, Sven Diederichs, Ursula Klingmueller, Martina Muckenthaler, Annette Kopp-Schneider, Aurelio Teleman, Aubry K. Miller, Nikolas Gunkel
Summary: A study found a set of antioxidant-capacity biomarkers (ACB) in lung cancer cell lines, which are repressed by STAT3 and STAT5A/B in sensitive cells, making them susceptible to redox-targeting and ferroptosis-inducing drugs. Low ACB expression was associated with a high level of nitric oxide instead of reactive oxygen species (ROS), which is required for high replication rates. ACB expression pattern can help stratify cancer patients for clinical trials of ROS-inducing drugs.
Article
Hematology
Silvia Thoene, Tamoghna Mandal, Naidu M. Vegi, Leticia Quintanilla-Martinez, Reinhild Roesler, Sebastian Wiese, Klaus H. Metzeler, Tobias Herold, Torsten Haferlach, Konstanze Doehner, Hartmut Doehner, Luisa Schwarzmueller, Ursula Klingmueller, Christian Buske, Vijay P. S. Rawat, Michaela Feuring-Buske