Article
Multidisciplinary Sciences
Roland R. Netz, William A. Eaton
Summary: Researchers have achieved success in theoretically simulating parts of biological systems on the molecular level, but there are doubts about the feasibility of modeling whole cells due to their complexity. They have established approximate equations to estimate computation times for simulating highly simplified cell models, setting limits on the complexity that can be understood theoretically. While a molecular kinetics description of simple bacterial cells may soon be possible, theoretical descriptions for multicellular systems like the human brain may not be achievable for many decades, if at all, even with quantum computing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Gilberto M. Nakamura, Alinne C. C. Souza, Francisco C. M. Souza, Renato F. Bulcao-Neto, Alexandre S. Martinez, Alessandra A. Macedo
Summary: Symmetries greatly reduce computational efforts in evaluating system properties. This paper proposes two methods to simplify the analysis of disease spreading in an agent-based epidemic model using spin symmetries, and the efficiency gains are measured through simulations.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Engineering, Electrical & Electronic
Teng Wang, Pere L. Gilabert
Summary: The proposed MeS method, when combined with dimensionality reduction techniques, can significantly reduce training data and decrease the computational complexity of parameter identification.
IEEE MICROWAVE AND WIRELESS COMPONENTS LETTERS
(2021)
Review
Chemistry, Multidisciplinary
Stuart T. Johnston, Matthew Faria, Edmund J. Crampin
Summary: Understanding the interactions between nano-engineered particles and cells is crucial for designing particles for therapeutic, diagnostic, and imaging purposes. Quantitative models, both mathematical and computational, are powerful tools for elucidating this relationship and understanding the underlying mechanisms. Different types of mathematical and computational models have been used to examine particle-cell interactions and internalization, highlighting the benefits and limitations associated with each type of model.
NANOSCALE ADVANCES
(2021)
Article
Engineering, Electrical & Electronic
Mohamed Elsayed, Ahmad A. Aziz El-Banna, Octavia A. Dobre, Wanyi Shiu, Peiwei Wang
Summary: This article proposes two novel hybrid-layer neural network architectures, HCRNN and HCRDNN, for low-complexity self-interference cancellation. These cancelers achieve the same cancellation performance as polynomial and state-of-the-art neural network-based cancelers while reducing computational complexity through the use of convolutional and recurrent layers to extract features and learn temporal behavior.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Daniel J. Rosenkrantz, Anil Vullikanti, S. S. Ravi, Richard E. Stearns, Simon Levin, H. Vincent Poor, Madhav Marathe
Summary: The ongoing COVID-19 pandemic highlights the importance of reliable forecasting models for decision makers. However, forecasting contagion dynamics remains challenging due to complex behavioral responses, data uncertainty, stochastic processes, and the sensitivity of disease parameters to environmental changes. This study offers a rigorous explanation of the difficulty in short-term forecasting on networked populations using computational complexity concepts and develops efficient algorithms or approximation algorithms for restricted versions of forecasting problems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Analytical
Mercedes Vetrab, Gabor Gosztolya
Summary: The field of computational paralinguistics deals with non-verbal content in human speech and its applications, such as emotion recognition and sleepiness detection. Two main technical challenges are handling varying-length utterances and training models on small corpora. This study presents a method that combines automatic speech recognition and paralinguistic approaches to address these challenges. Experimental results show that the proposed method outperforms the baseline approach and is competitive and resource-efficient for various paralinguistic tasks, depending on the aggregation techniques and neural network layers used.
Article
Economics
Sebastiaan Tieleman
Summary: This paper discusses a methodology for validating macroeconomic agent-based models, focusing on the foundation of model validation, model classification, and the relationship between model structure and validation in practice. By connecting these three elements, two key characteristics of MABM validation are identified: mechanisms at different levels are validated independently, and the mechanisms of MABMs are directly validated at the agent level, making them more realistic compared to DSGE models.
COMPUTATIONAL ECONOMICS
(2022)
Article
Mathematics, Applied
Anna Ivagnes, Giovanni Stabile, Andrea Mola, Traian Iliescu, Gianluigi Rozza
Summary: In this paper, hybrid data-driven ROM closures for fluid flows are proposed. These closures combine two fundamentally different strategies: purely data-driven closures and physically based, eddy viscosity data-driven closures. The hybrid model is applied to investigate a two-dimensional flow past a circular cylinder at Re = 50,000, and the numerical results show that it is more accurate than both the purely data-driven ROM and the eddy viscosity ROM.
APPLIED MATHEMATICS AND COMPUTATION
(2023)
Article
Mathematics, Interdisciplinary Applications
Iveta Jancigova, Alzbeta Bohinikova, Michal Mulik, Ivan Cimrak
Summary: Comparative studies on the metastatic potential of tumor cell clusters and single tumor cells in microcirculation have demonstrated the significant contribution of clusters to metastasis, with the presence of cancer cells near vessel walls conditioning the metastatic potential. A biomechanical model of cell clusters capable of simulating both strong and weak adhesion among cells in various spatial configurations has been developed, and its validity has been confirmed through cell separation experiments. Computational results suggest that more elastic clusters and clusters of weakly adhesive cells exhibit decreased cluster-wall contact compared to more rigid clusters or clusters composed of strongly adhesive cells, while more spherical cluster shapes tend to drift away from the walls, reducing wall contact time.
COMPUTATIONAL PARTICLE MECHANICS
(2023)
Article
Computer Science, Artificial Intelligence
Manuel Contero, David Perez-Lopez, Pedro Company, Jorge D. Camba
Summary: Digital product data quality and reusability are crucial for efficient design and redesign of products in the Model-Based Enterprise. The ability to edit or reuse a history-based parametric CAD model depends on the part's geometric complexity and the construction procedure. This paper examines the concept of perceived CAD modeling complexity and proposes a method to integrate expert pairwise comparisons into a single metric. The study also explores quantitative metrics derived from geometric characteristics and graph structure, showing a strong correlation between perceived CAD modeling complexity and graph-based metrics.
ADVANCED ENGINEERING INFORMATICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Cristina Ruiz-Martin, Gabriel A. Wainer, Laouen Belloli
Summary: The study introduces a new method to translate SBML specifications into formal specifications for analysis and simulation by defining a generic biological model architecture that can be instantiated with different parameters for different types of cells and at different levels of detail. The research discusses the architecture, a prototype implementation, and various examples of application with synthetic and E. Coli models.
SIMULATION MODELLING PRACTICE AND THEORY
(2022)
Article
Multidisciplinary Sciences
Veerle de Goederen, Roman Vetter, Katie McDole, Dagmar Iber
Summary: This study investigates the biomechanical mechanism of mammalian neural tube formation using a mechanical finite element model. The researchers achieved neural tube closure by simulating mesoderm expansion, nonneural ectoderm expansion, and neural plate adhesion to the notochord. They propose that the biomechanical force for dorsolateral hinge point formation comes from zippering.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemical Research Methods
Karthik Nagarajan, Congjian Ni, Ting Lu
Summary: This review provides a comprehensive overview of recent advances in agent-based modeling of microbial communities, including algorithms for simulating intracellular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments, as well as applications of agent-based modeling. It also discusses challenges and potential mitigation strategies.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Alexis N. Prybutok, Jessica S. Yu, Joshua N. Leonard, Neda Bagheri
Summary: CAR T-cell therapy shows promise for treating both liquid cancers and solid tumors. However, testing all possible design choices for treatment is expensive and time-consuming. To address this, researchers extended a modeling framework to investigate the impact of different design choices on treatment outcomes, ultimately aiming to accelerate the development of effective treatment strategies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Letter
Biology
Himanshu Kaul, Yiannis Ventikos
JOURNAL OF THEORETICAL BIOLOGY
(2015)
Article
Cell & Tissue Engineering
Himanshu Kaul, Yiannis Ventikos
TISSUE ENGINEERING PART B-REVIEWS
(2015)
Article
Multidisciplinary Sciences
Himanshu Kaul, Brian K. Hall, Chris Newby, Yiannis Ventikos
SCIENTIFIC REPORTS
(2015)
Article
Engineering, Chemical
Himanshu Kaul, Yiannis Ventikos, Zhanfeng Cui
CHINESE JOURNAL OF CHEMICAL ENGINEERING
(2016)
Article
Orthopedics
Alex C. McLaren, Matt Nugent, Kostas Economopoulos, Himanshu Kaul, Brent L. Vernon, Ryan McLemore
CLINICAL ORTHOPAEDICS AND RELATED RESEARCH
(2009)
Article
Multidisciplinary Sciences
Himanshu Kaul, Zhanfeng Cui, Yiannis Ventikos
Article
Cell Biology
Ruth Saunders, Himanshu Kaul, Rachid Berair, Sherif Gonem, Amisha Singapuri, Amanda J. Sutcliffe, Latifa Chachi, Michael S. Biddle, Davinder Kaur, Michelle Bourne, Ian D. Pavord, Andrew J. Wardlaw, Salman H. Siddiqui, Richard A. Kay, Bindi S. Brook, Rod H. Smallwood, Christopher E. Brightling
SCIENCE TRANSLATIONAL MEDICINE
(2019)
Letter
Respiratory System
Latifa Chachi, Sarah Diver, Himanshu Kaul, Marlon C. Rebelatto, Anmarie Boutrin, Patricia Nisa, Paul Newbold, Christopher Brightling
EUROPEAN RESPIRATORY JOURNAL
(2019)
Editorial Material
Biochemical Research Methods
Himanshu Kaul
Meeting Abstract
Respiratory System
Ruth Saunders, Himanshu Kaul, Rachid Berair, Amisha Singapuri, Igor Chernyavsky, Latifa Chachi, Michael Biddle, Amanda Sutcliffe, Marie Laurencin, Gerald Bacher, Michelle Bourne, Ian D. Pavord, Andrew J. Wardlaw, Salman H. Siddiqui, Richard Kay, Bindi S. Brook, Rod Smallwood, Chris E. Brightling
EUROPEAN RESPIRATORY JOURNAL
(2017)
Meeting Abstract
Respiratory System
Himanshu Kaul, Chris Brightling, Rod Smallwood
EUROPEAN RESPIRATORY JOURNAL
(2017)
Meeting Abstract
Respiratory System
Ruth M. Saunders, Alessandra Sandrini, Himanshu Kaul, Rachid Berair, Amisha Singapuri, Igor Chernyavsky, Latifa Chachi, Michael Biddle, Amanda Sutcliffe, Marie Laurencin, Gerald Bacher, Michelle Bourne, Ian D. Pavord, Andrew J. Wardlaw, Salman H. Siddiqui, Richard Kay, Bindi S. Brook, Rod Smallwood, Christopher E. Brightling
Meeting Abstract
Critical Care Medicine
R. M. Saunders, H. Kaul, R. Berair, A. Singapuri, I. Chernyaysky, L. Chachi, M. Biddle, A. Sutcliffe, M. Laurencin, G. Bacher, M. Bourne, I. D. Pavord, A. Wardlaw, S. Siddiqui, R. Kay, B. S. Brook, R. Smallwood, C. E. Brightling
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2017)