24,764 research outputs found
Data-driven modelling of biological multi-scale processes
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 spatial scales and how they are integrated into holistic models.
We discuss the relation between spatial and temporal scales and the implication
of that on multi-scale modelling. Based upon this overview over
state-of-the-art modelling approaches, we formulate key challenges in
mathematical and computational modelling of biological multi-scale and
multi-physics processes. In particular, we considered the availability of
analysis tools for multi-scale models and model-based multi-scale data
integration. We provide a compact review of methods for model-based data
integration and model-based hypothesis testing. Furthermore, novel approaches
and recent trends are discussed, including computation time reduction using
reduced order and surrogate models, which contribute to the solution of
inference problems. We conclude the manuscript by providing a few ideas for the
development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and
Multiscale Dynamics (American Scientific Publishers
Virtual Delamination Testing through Non-Linear Multi-Scale Computational Methods: Some Recent Progress
This paper deals with the parallel simulation of delamination problems at the
meso-scale by means of multi-scale methods, the aim being the Virtual
Delamination Testing of Composite parts. In the non-linear context, Domain
Decomposition Methods are mainly used as a solver for the tangent problem to be
solved at each iteration of a Newton-Raphson algorithm. In case of strongly
nonlinear and heterogeneous problems, this procedure may lead to severe
difficulties. The paper focuses on methods to circumvent these problems, which
can now be expressed using a relatively general framework, even though the
different ingredients of the strategy have emerged separately. We rely here on
the micro-macro framework proposed in (Ladev\`eze, Loiseau, and Dureisseix,
2001). The method proposed in this paper introduces three additional features:
(i) the adaptation of the macro-basis to situations where classical
homogenization does not provide a good preconditioner, (ii) the use of
non-linear relocalization to decrease the number of global problems to be
solved in the case of unevenly distributed non-linearities, (iii) the
adaptation of the approximation of the local Schur complement which governs the
convergence of the proposed iterative technique. Computations of delamination
and delamination-buckling interaction with contact on potentially large
delaminated areas are used to illustrate those aspects
Proceedings for the ICASE Workshop on Heterogeneous Boundary Conditions
Domain Decomposition is a complex problem with many interesting aspects. The choice of decomposition can be made based on many different criteria, and the choice of interface of internal boundary conditions are numerous. The various regions under study may have different dynamical balances, indicating that different physical processes are dominating the flow in these regions. This conference was called in recognition of the need to more clearly define the nature of these complex problems. This proceedings is a collection of the presentations and the discussion groups
Modeling the effect of soil meso- and macropores topology on the biodegradation of a soluble carbon substrate
Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion Lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it
Multilayer Networks
In most natural and engineered systems, a set of entities interact with each
other in complicated patterns that can encompass multiple types of
relationships, change in time, and include other types of complications. Such
systems include multiple subsystems and layers of connectivity, and it is
important to take such "multilayer" features into account to try to improve our
understanding of complex systems. Consequently, it is necessary to generalize
"traditional" network theory by developing (and validating) a framework and
associated tools to study multilayer systems in a comprehensive fashion. The
origins of such efforts date back several decades and arose in multiple
disciplines, and now the study of multilayer networks has become one of the
most important directions in network science. In this paper, we discuss the
history of multilayer networks (and related concepts) and review the exploding
body of work on such networks. To unify the disparate terminology in the large
body of recent work, we discuss a general framework for multilayer networks,
construct a dictionary of terminology to relate the numerous existing concepts
to each other, and provide a thorough discussion that compares, contrasts, and
translates between related notions such as multilayer networks, multiplex
networks, interdependent networks, networks of networks, and many others. We
also survey and discuss existing data sets that can be represented as
multilayer networks. We review attempts to generalize single-layer-network
diagnostics to multilayer networks. We also discuss the rapidly expanding
research on multilayer-network models and notions like community structure,
connected components, tensor decompositions, and various types of dynamical
processes on multilayer networks. We conclude with a summary and an outlook.Comment: Working paper; 59 pages, 8 figure
Phase-field-crystal models for condensed matter dynamics on atomic length and diffusive time scales: an overview
Here, we review the basic concepts and applications of the
phase-field-crystal (PFC) method, which is one of the latest simulation
methodologies in materials science for problems, where atomic- and microscales
are tightly coupled. The PFC method operates on atomic length and diffusive
time scales, and thus constitutes a computationally efficient alternative to
molecular simulation methods. Its intense development in materials science
started fairly recently following the work by Elder et al. [Phys. Rev. Lett. 88
(2002), p. 245701]. Since these initial studies, dynamical density functional
theory and thermodynamic concepts have been linked to the PFC approach to serve
as further theoretical fundaments for the latter. In this review, we summarize
these methodological development steps as well as the most important
applications of the PFC method with a special focus on the interaction of
development steps taken in hard and soft matter physics, respectively. Doing
so, we hope to present today's state of the art in PFC modelling as well as the
potential, which might still arise from this method in physics and materials
science in the nearby future.Comment: 95 pages, 48 figure
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