Search results for "Scale model"
showing 10 items of 64 documents
Statistical Reconstruction of Microstructures Using Entropic Descriptors
2018
We report a multiscale approach of broad applicability to stochastic reconstruction of multiphase materials, including porous ones. The approach devised uses an optimization method, such as the simulated annealing (SA) and the so-called entropic descriptors (EDs). For a binary pattern, they quantify spatial inhomogeneity or statistical complexity at discrete length-scales. The EDs extract dissimilar structural information to that given by two-point correlation functions (CFs). Within the SA, we use an appropriate cost function consisting of EDs or comprised of EDs and CFs. It was found that the stochastic reconstruction is computationally efficient when we begin with a preliminary synthetic…
Multiscale modelling of structure formation of C$_{60}$ on insulating CaF$_2$ substrates
2021
Morphologies of adsorbed molecular films are of interest in a wide range of applications. To study the epitaxial growth of these systems in computer simulations requires access to long time and length scales, and one typically resorts to kinetic Monte Carlo (KMC) simulations. However, KMC simulations require as input transition rates and their dependence on external parameters (such as temperature). Experimental data allow only limited and indirect access to these rates, and models are often oversimplified. Here, we follow a bottom-up approach and aim at systematically constructing all relevant rates for an example system that has shown interesting properties in experiments, buckminsterfull…
Towards human cell simulation
2019
The faithful reproduction and accurate prediction of the phe-notypes and emergent behaviors of complex cellular systems are among the most challenging goals in Systems Biology. Although mathematical models that describe the interactions among all biochemical processes in a cell are theoretically feasible, their simulation is generally hard because of a variety of reasons. For instance, many quantitative data (e.g., kinetic rates) are usually not available, a problem that hinders the execution of simulation algorithms as long as some parameter estimation methods are used. Though, even with a candidate parameterization, the simulation of mechanistic models could be challenging due to the extr…
Insights into the summer diurnal cycle over Eastern South Africa.
2018
Abstract Adopting a state-of-the-art numerical model system, we investigate how the diurnal variations in precipitation and local breeze systems are characterized by lower-boundary conditions related to the Drakensberg highland and warm SST associated with the Agulhas Current. A control simulation can simulate the hydrometeorological climates in the region realistically, but the terrestrial rainfall is overestimated. During daytime, the precipitation is confined to the Drakensberg highland, and there is an onshore local breeze, while during midnight to morning, the rainfall is confined to the Agulhas Current, and the breeze is offshore. These variations are captured by the numerical simulat…
A multiphase multiobjective dynamic genome-scale model shows different redox balancing among yeast species of the saccharomyces genus in fermentation
2021
Yeasts constitute over 1,500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications, and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts’ metabolic specificity in batch cultures. Here, we propose a multiphase multiobjective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kinetic …
Modeling Drug Effects on Personalized 3D Models of the Heart: A Simulation Study
2010
[EN] The use of anti-arrhythmic drugs is common to treat heart rhythm disorders. Computational modeling and simulation are powerful tools that can be used to investigate the effects of specific drugs on cardiac electrophysiology. In this work a patient-specific anatomical heart model is built to study the effects of dofetilide, a drug that affects IKr current in cardiac cells. We study the multi-scale effects of the drug, from cellular to organ level, by simulating electrical propagation on tissue coupled cellular ion kinetics for several heart beats. Different cell populations configurations namely endocardial, midmyocardial and epicardial are used to test the effect of tissue heterogeneit…
The on-line coupled atmospheric chemistry model system MECO(n) – Part 5: Expanding the Multi-Model-Driver (MMD v2.0) for 2-way data exchange includin…
2018
Abstract. As part of the Modular Earth Submodel System (MESSy), the Multi-Model-Driver (MMD v1.0) was developed to couple online the regional Consortium for Small-scale Modeling (COSMO) model into a driving model, which can be either the regional COSMO model or the global European Centre Hamburg general circulation model (ECHAM) (see Part 2 of the model documentation). The coupled system is called MECO(n), i.e., MESSy-fied ECHAM and COSMO models nested n times. In this article, which is part of the model documentation of the MECO(n) system, the second generation of MMD is introduced. MMD comprises the message-passing infrastructure required for the parallel execution (multiple programme mul…
A simulation tool for analysis and design of reverse electrodialysis using concentrated brines
2015
Abstract Reverse electrodialysis (SGP-RE or RED) represents a viable technology for the conversion of the salinity gradient power into electric power. A comprehensive model is proposed for the RED process using sea or brackish water and concentrated brine as feed solutions. The goals were (i) reliably describing the physical phenomena involved in the process and (ii) providing information for optimal equipment design. For such purposes, the model has been developed at two different scales of description: a lower scale for the repeating unit of the system (cell pair), and a higher scale for the entire equipment (stack). The model was implemented in a process simulator, validated against orig…
Stormwater infiltration trenches: a conceptual modelling approach.
2009
In recent years, limitations linked to traditional urban drainage schemes have been pointed out and new approaches are developing introducing more natural methods for retaining and/or disposing of stormwater. These mitigation measures are generally called Best Management Practices or Sustainable Urban Drainage System and they include practices such as infiltration and storage tanks in order to reduce the peak flow and retain part of the polluting components. The introduction of such practices in urban drainage systems entails an upgrade of existing modelling frameworks in order to evaluate their efficiency in mitigating the impact of urban drainage systems on receiving water bodies. While s…
The fractal model of non-local elasticity with long-range interactions
2010
The mechanically-based model of non-local elasticity with long-range interactions is framed, in this study, in a fractal mechanics context. Non-local interactions are modelled introducing long-range central body forces between non-adjacent volume elements of the elastic continuum. Such long-range interactions are modelled as proportional to the product of interacting volumes, to the relative displacements of the centroids and to a distance-decaying function that is monotonically-decreasing with the distance. The choice of the decaying function is a key aspect of the model and it has been proved that any continuous function, strictly positive, is thermodynamically consistent and it leads to …