16 papers · ranked by Valyu relevance
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…
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…
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…
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…
Giulia Palermo, Alexandre M. J. J. Bonvin, Matteo Dal Peraro, Rommie E. Amaro + 1 more
Indeed, elements from system biology must be included when the level of simulation scales toward that of the cell. Widely used approaches in this case are those of Kinetic Master Equations (KME) connecting a set of cell elements. KME is used for instance in the representation of the whole complement cascade of the…
Junfeng Wang, Guohui Li
Computational chemistry methods are playing an increasingly pivotal role in chemical experiments. From quantum chemistry simulations to finite element simulations, researchers can always find an appropriate simulation method to elucidate the specific mechanisms at a certain resolution scale. However, in organic or…
Filippo Castiglione, Francesco Pappalardo, Carlo Bianca, Giulia Russo + 1 more
It is coming nowadays more clear that in order to obtain a unified description of the different mechanisms governing the behavior and causality relations among the various parts of a living system, the development of comprehensive computational and mathematical models at different space and time scales is required.…
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…
Martin O. Steinhauser, Stefan Hiermaier
This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed…
David Stephenson, James R. Kermode, Duncan A. Lockerby
We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-scale information…
Douglas Lin, Michael Martin
Introduction Bioreporters are genetically engineered cells that produce detectable responses in the presence of specific analytes, providing a cheap, mass-producible, and accurate method of analyte detection. Most research focuses on the single cell-level, where all engineering is concentrated on the interactions…
Michael Klann, Heinz Koeppl
Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of…
Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin + 1 more
'Herbert M. Sauro'] Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program.…
Thomas E. Gorochowski, Antoni Matyjaszkiewicz, Thomas Todd, Neeraj Oak + 7 more
'Neeraj Oak' 'Kira Kowalska' 'Stephen Reid' 'Krasimira T. Tsaneva-Atanasova' 'Nigel J. Savery' 'Claire S. Grierson' 'Mario di Bernardo' "Avi Ma'ayan"] Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to…
Till Köster, Philipp Henning, Adelinde M. Uhrmacher
Background To study cell biological phenomena which depend on diffusion, active transport processes, or the locations of species, modeling and simulation studies need to take space into account. To describe the system as a collection of discrete objects moving and interacting in continuous space, various particle-based…
Angran Li, Amir Barati Farimani, Yongjie Jessica Zhang
Neurons exhibit complex geometry in their branched networks of neurites which is essential to the function of individual neuron but also brings challenges to transport a wide variety of essential materials throughout their neurite networks for their survival and function. While numerical methods like isogeometric…