28 papers · ranked by Valyu relevance
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…
Abdon Atangana, Seda İğret Araz
Using the existing collected data from European and African countries, we present a statistical analysis of forecast of the future number of daily deaths and infections up to 10 September 2020. We presented numerous statistical analyses of collected data from both continents using numerous existing statistical…
Sonja Mathias, Adrien Coulier, Anass Bouchnita, Andreas Hellander
Centre-based, or cell-centre models are a framework for the computational study of multicellular systems with widespread use in cancer modelling and computational developmental biology. At the core of these models are the numerical method used to update cell positions and the force functions that encode the pairwise…
Denys Dutykh
This article is devoted to Feller's diffusion equation which arises naturally in probabilities and physics (e.g. wave turbulence theory). If discretized naively, this equation may represent serious numerical difficulties since the diffusion coefficient is practically unbounded and most of its solutions are weakly…
Lionel Dupuy, Matthias Mimault, Mariya Ptashnyk
Movement is critical for bacterial species inhabiting soils because nutrient availability is limited and heterogeneously distributed both in space and time. Recent live microscopy experiments show that bacteria form flocks when navigating through porous medium, and complex cell-cell interactions may be required to…
Yongho Kim, Yongho Choi
Simulation speed depends on code structures, hence it is crucial how to build a fast algorithm. We solve the Allen–Cahn equation by an explicit finite difference method, so it requires grid calculations implemented by many for-loops in the simulation code. In terms of programming, many for-loops make the simulation…
Shejie Qin, Yu Yang, Yongxiang Huang, Xinyu Mei + 2 more
small enough grid spacing and time-step definitely reliable/correct? Authors: ['Shejie Qin' 'Yu Yang' 'Yongxiang Huang' 'Xinyu Mei' 'Lipo Wang' 'Shijun Liao'] Turbulence is strongly associated with the vast majority of fluid flows in nature and industry. Traditionally, results given by the direct numerical simulation…
Chang F Quo, May D Wang
Background This article provides guidelines for selecting optimal numerical solvers for biomolecular system models. Because various parameters of the same system could have drastically different ranges from 10-15 to 1010, the ODEs can be stiff and ill-conditioned, resulting in non-unique, non-existing, or…
Ming Yang, Louis Z. Yang
What values of relative numerical tolerance should be chosen in simulation of a deterministic model of a biochemical reaction is unclear, which impairs the modeling effort since the simulation outcomes of a model may depend on the relative numerical tolerance values. In an attempt to provide a guideline to selecting…
Wenqiang Guo, Mikhail Sheremet, Tianbai Xiao, Yuan Hu + 1 more
In this work, the Simpson method is proposed to calculate the interface flux of a discrete unified gas kinetic scheme (DUGKS) according to the distribution function at the node and the midpoint of the interface, which is noted by Simpson-DUGKS. Moreover, the optimized DUGKS and Simpson-DUGKS considering the force term…
Enran Hou, Fuzhang Wang, Essam Roshdy El-Zahar, Umar Nazir + 2 more
'Muhammad Sohail' 'Jinyuan Qian'] Engineers, scientists and mathematicians are greatly concerned about the thermal stability/instability of any physical system. Current contemplation discusses the role of the Soret and Dufour effects in hydro-magnetized Carreau-Yasuda liquid passed over a permeable stretched surface.…
Authors not listed
As a prove of concept for experimental geochemistry, an advanced 3D numerical framework, here and after called Digital Twin (DT), of a diffusion experiment conducted at a synchrotron beamline, has been implemented using in-situ measurements data, physics-based modelling, a machine learning (ML) model, and parameter…
A. Abbasi Goodarzi, Maryam Rahimi, MohammadJavad Valizadeh, Fakhteh Ghanbarnejad
'Fakhteh Ghanbarnejad'] Abstract— In dealing with nonlinear systems, it is common to use numerical solutions. Unlike the careful behavior towards the numerical results in chaotic regions, the validity of numerical results in regions of transient chaos might not always be taken into consideration. This article…
Fergus R. Cooper, Ruth E. Baker, Alexander G. Fletcher
Mathematical modelling provides a useful framework within which to investigate the organization of biological tissues. With advances in experimental biology leading to increasingly detailed descriptions of cellular behaviour, models that consider cells as individual objects are becoming a common tool to study how…
Vladimir Mladenovic, Danijela Milosevic, Miroslav Lutovac, Yigang Cen + 1 more
'Yigang Cen' 'Matjaz Debevc'] This paper presents a method for shortening the computation time and reducing the number of math operations required in complex calculations for the analysis, simulation, and design of processes and systems. The method is suitable for education and engineering applications. The efficacy of…
Małgorzata Borówko
Molecular simulation is one of the fastest growing fields in science. This is connected with the rapid increase of computer efficiency and with the appearance of new, sophisticated simulation methods enabling the modeling of complex systems while seamlessly bridging different length and time scales. Now, it is possible…
Koki Ide, Tetsuro Tsuji, Takayuki Suzuki, Kenji Setoura
Microscale thermophoresis (MST) has garnered significant attention as a manipulation method for chemical species ranging from nanometers to micrometers in liquids. Despite the substantial increase in experimental reports on MST, a comprehensive theoretical model remains elusive due to its intricate mechanism.…
Walter Boscheri, Giacomo Dimarco
In this work, we present a family of time and space high order finite volume schemes for the solution of the full Boltzmann equation. The velocity space is approximated by using a discrete ordinate approach while the collisional integral is solved by spectral methods. The space reconstruction is realized by integrating…
T.J. Sego, James P. Sluka, Herbert M. Sauro, James A. Glazier
Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular…
Dagmar Zakova, Peter Frolkovic
This study investigates numerical methods to solve nonlinear transport problems characterized by various sorption isotherms with a focus on the Freundlich type of isotherms. We describe and compare second order accurate numerical schemes, focusing on implicit methods, to effectively model transport phenomena without…
C. Gadd, W. Xing, M. Mousavi Nezhad, A. A. Shah
In this paper, we develop a surrogate modelling approach for capturing the output field (e.g. the pressure head) from groundwater flow models involving a stochastic input field (e.g. the hydraulic conductivity). We use a Karhunen-Loève expansion for a log-normally distributed input field and apply manifold learning…
Authors not listed
The present study investigates the transient 3D numerical prediction of the significance of passive control techniques, using triangular and rectangular span-wise pimples, placed at cambered section at the location 32% chord length from of the nose of the hydrofoil, and combined with a modified finite trailing edge…
Ali Ahmad Malik
- Digital twin has emerged as the next wave in the simulation technology to answer the growing complexities of manufacturing systems. - The exactitude of the virtual models defines the accuracy of predicted behavior obtained from the experimentation on the digital twin. - The lack of frameworks often makes it difficult…
Jianan Zeng, Yanbing Zhang, Lei Wu
Multiscale rarefied gas flows with moving boundaries pose significant challenges to the numerical simulation, where the primary difficulties involve robustly managing the mesh movement and ensuring computational efficiency across all flow regimes. Build upon recent advancements of the general synthetic iterative scheme…
Yuanfei Xue, Jia-Ning Wang, Wenxin Hu, Jun Zheng + 6 more
Path integral molecular dynamics (PIMD) is becoming a routinely applied method for the incorporation of the nuclear quantum effect in computer simulations. However, direct PIMD simulations at an ab initio level of theory are formidably expensive. Using the protonated 1,8-bis(dimethylamino)naphthalene molecule as an…
Daniel T. Birdsell, Benjamin M. Adams, Jonathan D. Ogland-Hand, Jeffrey M. Bielicki + 2 more
Geothermal electricity generation may play a role in reducing greenhouse gas emissions and addressing climate change in a cost-effective manner. Reservoir equations for pressure and temperature must be coupled to a power cycle model to calculate electricity generation from a geothermal power plant. This work focuses on…
Authors not listed
Rapid and robust simulation of chemical processes is critical to conduct process design, optimization, techno-economic analysis, and sustainability analysis. Yet, efficiently solving simulation models remains a challenge due to the highly coupled and nonlinear nature of the underlying algebraic equations that capture…
Authors not listed
Cavitation, a transient and dynamic phenomenon, significantly impacts the characteristics and performance of hydrofoils across various applications, necessitating effective passive control strategies. This study employs transient numerical simulations to investigate the effectiveness of passive controllers of varying…