Article
Zoology
Sriram Chandrasekaran, Nicole Danos, Uduak Z. George, Jin-Ping Han, Gerald Quon, Rolf Muller, Yinphan Tsang, Charles Wolgemuth
Summary: The biological challenges facing humanity are complex, multi-factorial, and crucial for the future of health, welfare, and the environment. Tackling these issues requires integrating diverse datasets, developing new frameworks, and promoting transparency in models and interdisciplinary collaboration.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Mingle Li, Kalayou Hiluf Gebremedhin, Dandan Ma, Zhongji Pu, Tao Xiong, Yunjie Xu, Jong Seung Kim, Xiaojun Peng
Summary: The article introduces a conditionally activatable photoredox catalysis method, which achieves more effective tumor treatment through site-specific photoredox. This approach enables control of photoresponsivity while ensuring biocompatibility and safety.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Claire Miller, Edmund Crampin, James M. Osborne
Summary: Maintenance of epidermal thickness is crucial for the skin's barrier function. This paper combines a subcellular model of desquamation with a multicellular model to investigate the role of cell adhesion degradation in maintaining tissue thickness. The model shows how disruptions to desquamation can lead to reduced tissue thickness and investigates the impact of different treatment scenarios on tissue response.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Jianbo Gao, Bo Xu
Summary: This article proposes the synergistic use of machine learning and multiscale approaches to study complex systems and emergence. The multiscale approaches are helpful in identifying key parameters for system evolution and designing more accurate unsupervised machine learning schemes.
APPLIED SCIENCES-BASEL
(2021)
Article
Neurosciences
Jennifer Rollo, John Crawford, John Hardy
Summary: Alzheimer's disease is a complex pathology that requires non-linear dynamical systems modeling and community-wide participation to understand and predict its dynamics. A new methodology is proposed to integrate intuition and test system-level hypotheses and interventions.
Article
Chemistry, Physical
You Lu, Kakali Sen, Chin Yong, David S. D. Gunn, John A. Purton, Jingcheng Guan, Alec Desmoutier, Jamal Abdul Nasir, Xingfan Zhang, Lei Zhu, Qing Hou, Joe Jackson-Masters, Sam Watts, Rowan Hanson, Harry N. Thomas, Omal Jayawardena, Andrew J. Logsdail, Scott M. Woodley, Hans M. Senn, Paul Sherwood, C. Richard A. Catlow, Alexey A. Sokol, Thomas W. Keal
Summary: Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are powerful tools for studying catalysis, providing an accurate description of reactions in complex electrostatic environments. ChemShell, a scriptable computational chemistry environment, is a leading software package for QM/MM calculations, offering a flexible and high-performance framework for biomolecular and materials catalysis. This article gives an overview of recent applications of ChemShell in catalysis, as well as new functionality introduced in the Python-based version to support catalytic modeling.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Chemistry, Physical
Jacob Fish, Gregory J. Wagner, Sinan Keten
Summary: Multiscale modelling is a powerful tool for simulating materials behavior across different length and time scales. It aims to simulate continuum-scale behavior using information from computational models of finer scales, rather than relying on empirical constitutive models. Various methods have been developed to bridge multiple length and time scales, including techniques integrating new fields such as machine learning and material design.
Review
Mathematics, Interdisciplinary Applications
Lourenco Corte Vieira, Rafael S. Costa, Duarte Valerio
Summary: Cancer, as a complex disease, has a significant impact on global mortality. Mathematical techniques, including fractional calculus, have been increasingly used in cancer modelling to study its intricate phenomena and improve understanding. This review provides an overview of the main trends and categories in cancer research, highlighting the growing application of fractional calculus in mathematical modelling. The review also outlines key research questions, challenges, and future perspectives.
FRACTAL AND FRACTIONAL
(2023)
Article
Biochemistry & Molecular Biology
Pankaj Bhatt, Kanika Sethi, Saurabh Gangola, Geeta Bhandari, Amit Verma, Muhammad Adnan, Yashpal Singh, Shshank Chaube
Summary: Atrazine is a widely used herbicide in agriculture, but its increased environmental concentration can have toxic effects on non-target species. This study investigated the ability of bacteria to biodegrade atrazine and examined its impact on environmental systems. A model was constructed to analyze the biochemistry and physiology of atrazine in different cellular networks. Topological analysis confirmed the nodes and edges involved in atrazine degradation. The results showed overall biomagnification of atrazine in different environmental systems.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Food Science & Technology
Clement Kehinde Ajani, Zhiwei Zhu, Da-Wen Sun
Summary: Spoilage of agrifood produce is a major issue in the industry, and cooling is an effective technique to extend shelf life. The porous medium approach is commonly used due to difficulties in directly solving wide spatial and temporal scales, but improvements and modeling at wider scales are needed. Multiscale CFD modeling approaches have been developed to tackle these challenges and enhance understanding of cooling processes and systems.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2021)
Article
Biology
Linnea Gyllingberg, Abeba Birhane, David J. T. Sumpter
Summary: We criticize mathematical biology in view of the rapid advancements in modern machine learning. We argue that researchers in the field have been excessively focused on analyzing models (activity 2) at the expense of formulating models (activity 1). To counter this trend, we suggest adopting a pluralistic approach that considers multiple perspectives when modeling biological phenomena. Using fish locomotion as an example, we demonstrate the pitfalls, such as universalism and creating models of models, that hinder progress in mathematical biology. Finally, we discuss the rediscovery of the lost art of creative mathematical modeling.
MATHEMATICAL BIOSCIENCES
(2023)
Article
Multidisciplinary Sciences
Fan Zheng, Marcus R. Kelly, Dana J. Ramms, Marissa L. Heintschel, Kai Tao, Beril Tutuncuoglu, John J. Lee, Keiichiro Ono, Helene Foussard, Michael Chen, Kari A. Herrington, Erica Silva, Sophie N. Liu, Jing Chen, Christopher Churas, Nicholas Wilson, Anton Kratz, Rudolf T. Pillich, Devin N. Patel, Jisoo Park, Brent Kuenzi, Michael K. Yu, Katherine Licon, Dexter Pratt, Jason F. Kreisberg, Minkyu Kim, Danielle L. Swaney, Xiaolin Nan, Stephanie Fraley, J. Silvio Gutkind, Nevan J. Krogan, Trey Ideker
Summary: This study successfully created a comprehensive map of cancer protein systems called NeST and identified 395 specific systems under mutational selection, contributing to the understanding of how disparate tumor mutations converge on protein assemblies at different scales.
Article
Automation & Control Systems
Renjie Zhou, Xiao Wang, Jian Wan, Naixue Xiong
Summary: Sample entropy technologies are widely used in diagnosing faults in industrial systems, but they have limitations in distance measurement and similarity evaluation. A new method called Euclidean distance based multiscale fuzzy entropy is proposed for better accuracy in measuring signal complexity and detecting bearing faults.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2021)
Article
Green & Sustainable Science & Technology
Andrea Mio, Serena Bertagna, Luca Cozzarini, Erik Laurini, Vittorio Bucci, Alberto Marino, Maurizio Fermeglia
Summary: This study focuses on using multiscale molecular modeling to generate life cycle inventory data for complex nanostructured materials, with a particular emphasis on nanocomposite formulations. By comparing nanocomposite materials with traditional aluminum, it was found that the reuse of aluminum covers can reduce the need for primary metal, providing environmental benefits in terms of footprint. The study demonstrates the potential of in-silico techniques in contributing to ecodesign improvements by considering the entire product lifecycle.
SUSTAINABLE MATERIALS AND TECHNOLOGIES
(2021)
Article
Biochemical Research Methods
Fei Liu, Wujie Sun, Monika Heiner, David Gilbert
Summary: The study introduces a method called Fuzzy Continuous Petri Nets for integrated modelling of biological systems, which combines continuous Petri nets with fuzzy inference systems to address uncertainties in the modeling process.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Mathematics, Applied
Bouchra Aylaj, Nicola Bellomo, Livio Gibelli, Alessandro Reali
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2020)
Article
Mathematics, Applied
N. Bellomo, F. Brezzi, J. Soler
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2020)
Editorial Material
Multidisciplinary Sciences
Nicola Bellomo, Damian A. Knopoff, Pietro Terna
Article
Mathematics, Applied
Nicola Bellomo, Richard Bingham, Mark A. J. Chaplain, Giovanni Dosi, Guido Forni, Damian A. Knopoff, John Lowengrub, Reidun Twarock, Maria Enrica Virgillito
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2020)
Article
Mathematics, Applied
Nicola Bellomo, Giovanni Dosi, Damian A. Knopoff, Maria Enrica Virgillito
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2020)
Article
Mathematics, Applied
N. Bellomo, Y. Tao, M. Winkler
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2020)
Article
Automation & Control Systems
Nicola Bellomo, Seung-Yeal Ha, Nisrine Outada
ESAIM-CONTROL OPTIMISATION AND CALCULUS OF VARIATIONS
(2020)
Article
Mathematics, Applied
N. Bellomo, F. Brezzi, J. Soler
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2020)
Article
Mathematics, Applied
N. Bellomo, F. Brezzi
Summary: This editorial paper introduces the articles published in a special issue focusing on active particle methods applied to modeling, qualitative analysis, and simulation of large systems of interacting living entities in science and society. The paper discusses the modeling approach, applications, and proposes a critical analysis of the overall contents of the issue to provide research perspectives.
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2021)
Article
Mathematics, Applied
Nicola Bellomo, Diletta Burini, Giovanni Dosi, Livio Gibelli, Damian Knopoff, Nisrine Outada, Pietro Terna, Maria Enrica Virgillito
Summary: This paper discusses the mathematical modeling of living systems composed of many interacting entities in order to describe their collective behaviors. The approach is developed within the framework of the kinetic theory of active particles, with the presentation divided into three parts: deriving mathematical tools, applying the method to case studies, and looking forward to future research directions.
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2021)
Review
Multidisciplinary Sciences
Diletta Burini, Nadia Chouhad, Nicola Bellomo
Summary: This paper presents advanced concepts and research perspectives on the dynamics of systems of many interacting living entities using a philosophical-mathematical approach. The first part introduces the general conceptual framework, followed by a critical analysis of existing literature relating to a multiscale view of mathematics in living organisms. The paper aims to understand how distant the current state-of-the-art is from achieving this challenging objective. The overall study identifies research perspectives and provides possible hints to address them.
Review
Mathematics
B. Aylaj, N. Bellomo, N. Chouhad, D. Knopoff
Summary: This paper discusses the potential contributions of mathematical sciences to modeling complex systems, specifically those composed of interacting living entities with nonlocal and nonlinear interactions. It addresses the specific features of living systems, reviews known modeling strategies, and presents open problems with suggestions for tackling them, along with speculations on the interplay between soft and hard sciences.
VIETNAM JOURNAL OF MATHEMATICS
(2021)
Article
Mathematics, Interdisciplinary Applications
Nicola Bellomo, Sarah De Nigris, Damian Knopoff, Matteo Morini, Pietro Terna
NETWORKS AND HETEROGENEOUS MEDIA
(2020)
Article
Mathematics, Applied
Nicola Bellomo, Youshan Tao
DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS-SERIES S
(2020)
Article
Mathematics, Applied
Nicola Bellomo, Livio Gibelli, Nisrine Outada
KINETIC AND RELATED MODELS
(2019)
Article
Mathematics, Applied
Kevin J. Painter, Thomas Hillen, Jonathan R. Potts
Summary: The use of nonlocal PDE models in describing biological aggregation and movement behavior has gained significant attention. These models capture the self-organizing and spatial sorting characteristics of cell populations and provide insights into how animals perceive and respond to their surroundings. By deriving and analyzing these models, we can better understand biological movement behavior and provide a basis for explaining sociological phenomena.
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2024)
Article
Mathematics, Applied
Nicola Bellomo, Massimo Egidi
Summary: This paper focuses on Herbert A. Simon's visionary theory of the Artificial World and proposes a mathematical theory to study the dynamics of organizational learning, highlighting the impact of decomposition and recombination of organizational structures on evolutionary changes.
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2024)
Article
Mathematics, Applied
Tayfun E. Tezduyar, Kenji Takizawa, Yuri Bazilevs
Summary: This paper provides an overview of flows with moving boundaries and interfaces (MBI), which include fluid-particle and fluid-structure interactions, multi-fluid flows, and free-surface flows. These problems are frequently encountered in engineering analysis and design, and pose computational challenges that require core computational methods and special methods. The paper focuses on isogeometric analysis, complex geometries, incompressible-flow Space-Time Variational Multiscale (ST-VMS) and Arbitrary Lagrangian-Eulerian VMS (ALE-VMS) methods, and special methods developed in connection with these core methods.
MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES
(2024)
