20 papers · ranked by Valyu relevance
Huandong Wang, Huan Yan, Can Rong, Yuan Yuan + 5 more
'Zhenyu Han' 'Hongjie Sui' 'Depeng Jin' 'Yong Li'] Complex system simulation has been playing an irreplaceable role in understanding, predicting, and controlling diverse complex systems. In the past few decades, the multi-scale simulation technique has drawn increasing attention for its remarkable ability to overcome…
Derek Groen, Jaroslaw Knap, Philipp Neumann, Diana Suleimenova + 2 more
In the last few decades, multiscale modelling has emerged as one of the dominant modelling paradigms in many areas of science and engineering. Its rise to dominance is primarily driven by advancements in computing power and the need to model systems of increasing complexity. The multiscale modelling paradigm is now…
Adam Noel, Karen C. Cheung, Robert Schober
—Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic simulations partition the environment into subvolumes, track when molecules move…
Cameron A. Smith, Christian A. Yates
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as partial differential equations are typically fast to simulate, they lack the…
Jan Hasenauer, Nick Jagiella, Sabrina Hroß, Fabian J. Theis
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual…
Mahnoor Naseer Gondal, Safee Ullah Chaudhary
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built on top of this data have the potential to provide specific insights…
Pariksheet Nanda, Maral Budak, Christian T. Michael, Kathryn Krupinsky + 1 more
Although infectious disease dynamics are often analyzed at the macro-scale, increasing numbers of drug-resistant infections highlight the importance of within-host modeling that simultaneously solves across multiple scales to effectively respond to epidemics. We review multiscale modeling approaches for complex…
Yongguo Mei, Vida Abedi, Adria Carbo, Xiaoying Zhang + 6 more
'Casandra Philipson' 'Raquel Hontecillas' 'Stefan Hoops' 'Nathan Liles' 'Josep Bassaganya-Riera'] Computational modeling techniques are playing increasingly important roles in advancing a systems-level mechanistic understanding of biological processes. Computer simulations guide and underpin experimental and clinical…
Jiale Linghu, Hao Dong, Junzhi Cui, Yufeng Nie
The direct deep learning simulation for multi-scale problems remains a challenging issue. In this work, a novel higher-order multi-scale deep Ritz method (HOMS-DRM) is developed for thermal transfer equation of authentic composite materials with highly oscillatory and discontinuous coefficients. In this novel HOMS-DRM…
Alexander G. Fletcher, James M. Osborne
The growth and dynamics of multicellular tissues involve tightly regulated and coordinated morphogenetic cell behaviors, such as shape changes, movement, and division, which are governed by subcellular machinery and involve coupling through short- and long-range signals. A key challenge in the fields of developmental…
Yang, Sirui, Zhong, Chengwen + 10 more
The hypersonic flow around near-space vehicles constitutes a multi-scale flow problem. Due to insufficient molecular collisions to achieve equilibrium, rarefied gas effects are present in the flow field. Thus, numerical methods capable of accurately resolving multi-scale flows are required. Furthermore…
Emad Alamoudi, Yannik Schälte, Robert Müller, Jörn Starruß + 4 more
Biological tissues are dynamic and highly organized. Multi-scale models are helpful tools to analyze and understand the processes determining tissue dynamics. These models usually depend on parameters that need to be inferred from experimental data to achieve a quantitative understanding, to predict the response to…
Oriol Canela-Xandri, Samira Anbari, Javier Buceta
This document is an extended version of the main text where some details and results are fleshed out. Further details can be also found in the manual of the code and at TiFoSi’s website: http://tifosi.thesimbiosys.com. Emerging phenomena in developmental biology and tissue engineering are the result of feedbacks…
Richard Oliver Matzko, Laurentiu Mierla, Savas Konur, Francisco Ortuño + 5 more
'Francisco Ortuño' 'Alfredo Benso' 'Jean-Marc Schwartz' 'Alexandre G. de Brevern' 'Ignacio Rojas' 'Olga Valenzuela'] The elevation of Synthetic Biology from single cells to multicellular simulations would be a significant scale-up. The spatiotemporal behavior of cellular populations has the potential to be prototyped…
Authors not listed
Machine Learning Interatomic Potentials (MLIPs), trained with Quantum Mechanics data, can model potential energy surfaces for molecular systems with very high accuracy and extreme speedups compared to reference quantum calculations, offering a powerful tool for studying complex chemical and biological systems. This…
Authors not listed
Accurate extrapolation in data-scarce scientific systems remains a central challenge for machine intelligence. In microbial bioprocessing, kinetic parameters change non-monotonically with reactor volume due to interacting hydrodynamic, oxygen-transfer, and mixing effects, rendering classical empirical scaling laws…
James M. Osborne
In recent years, multi–cellular models, where cells are represented as individual interacting entities, are becoming ever popular. This has led to a proliferation of novel methods and simulation tools. The first aim of this paper is to review the numerical methods utilised by multi–cellular modelling tools and to…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Pauli Losoi, Jukka Konttinen, Ville Santala
Tall vessels equipped with multiple impellers, such as many gas-liquid contactors in bioprocessing, often suffer from poor macromixing of feeds, which leads to heterogeneities and complicates the scale-up. Here, a diffusion equation was used as a simple model of macromixing in multi-impeller tanks, and the model fitted…
Sterling G. Baird, Taylor D. Sparks
In scientific disciplines, benchmarks play a vital role in driving progress forward. For a benchmark to be effective, it must closely resemble real-world tasks. If the level of difficulty or relevance is inadequate, it can impede progress in the field. Moreover, benchmarks should have low computational overhead to…