25 papers · ranked by Valyu relevance
Rodrigo F. Daguano, Leopoldo R. Yoshioka, Marcio L. Netto, Claudio L. Marte + 6 more
'Claudio L. Marte' 'Cassiano A. Isler' 'Max Mauro Dias Santos' 'João F. Justo' 'Ashish Khanna' 'Isabel De La Torre Díez' 'Jameel Ahamed'] Traffic simulations are valuable tools for urban mobility planning and operation, particularly in large cities. Simulation-based microscopic models have enabled traffic engineers to…
Satya N. V. Arjunan, Koichi Takahashi
As quantitative biologists get more measurements of spatially regulated systems such as cell division and polarization, simulation of reaction and diffusion of proteins using the data is becoming increasingly relevant to uncover the mechanisms underlying the systems. Spatiocyte is a lattice-based stochastic particle…
Stefan Hellander, Andreas Hellander
We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh, while others live on a coarse-grained mesh. By allowing molecules to transfer…
Michael T Klann, Alexei Lapin, Matthias Reuss
Background In this paper we apply a novel agent-based simulation method in order to model intracellular reactions in detail. The simulations are performed within a virtual cytoskeleton enriched with further crowding elements, which allows the analysis of molecular crowding effects on intracellular diffusion and…
Nicholas M. Boffi, Yipei Guo, Chris H. Rycroft, Ariel Amir
The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of…
Subhamoy Mahajan, Tian Tang
Fluorescence microscopy allows the visualization of live cells and their components, but even with advances in super- resolution microscopy, atomic resolution remains unattainable. On the other hand, molecular simulations (MS) can easily access atomic resolution, but comparison with experimental microscopy images has…
Stefan Hellander, Andreas Hellander, Linda Petzold
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or Green's Function Reaction Dynamics (GFRD) the RDME can be orders of magnitude faster…
Bowen Li, Denis Taniguchi, Jayathilake Pahala Gedara, Valentina Gogulancea + 6 more
We present NUFEB, a flexible, efficient, and open source software for simulating the 3D dynamics of microbial communities. The tool is based on the Individual-based Modelling (IbM) approach, where microbes are represented as discrete units and their behaviour changes over time due to a variety of processes. This…
Tihamér Geyer
Background Brownian Dynamics (BD) is a coarse-grained implicit-solvent simulation method that is routinely used to investigate binary protein association dynamics, but due to its efficiency in handling large simulation volumes and particle numbers it is well suited to also describe many-protein scenarios as they often…
Adam Noel, Dimitrios Makrakis
—In this paper, an algorithm is presented to calculate the transition rates between adjacent mesoscopic subvolumes in the presence of flow and diffusion. These rates can be integrated in stochastic simulations of reaction-diffusion systems that follow a mesoscopic approach, i.e., that partition the environment into…
Adam Husar, Mariam Ordyan, Guadalupe C. Garcia, Joel G. Yancey + 4 more
Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes and surfaces of scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularity stochastic behavior dominates, well-mixed continuum…
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…
Mengkun Wu, Ankui Hu, Shuai Zhou, Xianhui Mao + 1 more
When the Linear Parallel Bond Model (PBM) in Particle Flow Code is used to simulate intact rocks, a basic problem is how to determine the microscopic parameters that control the macroscopic properties of the modeled rocks. After simplifying the microscopic parameters of the PBM model, this study proposes a new method…
Authors not listed
Atomistic simulations provide essential mechanistic insights into chemical processes, yet many important phenomena in chemistry and materials science occur on timescales that are inaccessible to molecular dynamics. Existing computational approaches force a choice between atomic resolution on relatively short timescales…
Benjamin S. Hanson, Daniel J. Read
Many biophysical systems and proteins undergo mesoscopic conformational changes in order to perform their biological function. However, these conformational changes often result from a cascade of atomistic interactions within a much larger overall object. For simulations of such systems, the computational cost of…
Authors not listed
The rapid progress in Artificial Intelligence (AI) has led to extraordinary achievements across various domains, significantly impacting every aspect of daily life. This advancement is also revolutionizing research in numerous scientific areas, particularly within bioinformatics, chemistry, pharmaceuticals, and…
Andreas Zöttl
In this review we discuss the recent progress in the simulation of soft active matter systems and in particular the hydrodynamics of microswimmers using the method of multiparticle collision dynamics, which solves the hydrodynamic flows around active objects on a coarse-grained level. We first present a brief overview…
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…
Authors not listed
This study introduces an implementation of multiple Gaussian filters within the Hamiltonian hybrid particle-field (HhPF) theory, aimed at capturing phase coexistence phenomena in mesoscopic molecular simulations. By employing a linear combination of two Gaussians, we demonstrate that HhPF can generate potentials with…
Xhorxhina Shaulli, Rodrigo Rivas-Barbosa, Maxime J. Bergman, Chi Zhang + 3 more
Responsivity of Microgels and Its Interplay with a Solid Surface by Super-Resolution Microscopy and Numerical Simulations Authors: ['Xhorxhina Shaulli' 'Rodrigo Rivas-Barbosa' 'Maxime J. Bergman' 'Chi Zhang' 'Nicoletta Gnan' 'Frank Scheffold' 'Emanuela Zaccarelli'] Super-resolution microscopy has become a powerful tool…
Authors not listed
Soft matter is characterized by its relatively strong response to external and internal influences. A soft piece of rubber or biological tissue can be easily deformed between our fingers using muscle force, whereas a steel rod does not show visible deformations detectable by eye. We use theoretical calculations and…
Maximilian R. Bailey, Dmitry A. Fedosov, Federico Paratore, Fabio Grillo + 2 more
'Fabio Grillo' 'Gerhard Gompper' 'Lucio Isa'] The generation of fluid flows by autophoretic microswimmers has been proposed as a mechanism to enhance mass transport and mixing at the micro- and nanoscale. Here, we experimentally investigate the ability of model 2-D "active baths" of photocatalytic silica-titania Janus…
Ilham Essafri, Bappa Ghosh, Caroline Desgranges, Jérôme Delhommelle
Ilham Essafri1,2 , Bappa Ghosh1,2 , Caroline Desgranges2 and Jerome Delhommelle1, 2, 3, 4 1)Department of Biomedical Engineering, University of North Dakota, 243 Centennial Dr Stop 8155, Grand Forks, ND 58202, USA 2)MetaSimulation of Nonequilibrium Processes (MSNEP), Tech Accelerator, University of North Dakota, Suite…
Authors not listed
Polysiloxanes are versatile polymeric materials with widespread applications in industries ranging from electronics to biomedical devices due to their unique thermal and viscoelastic properties. Accurate molecular simulations of polysiloxanes are essential for understanding their broad applications from the microscopic…
Nils Edvin Richard Zimmermann, Gabriela Guevara-Carrion, Jadran Vrabec, Niels Hansen
The thermodiffusion behavior of binary Lennard-Jones mixtures in the liquid state was investigated by combining the individual strengths of non-equilibrium molecular dynamics (NEMD) and equilibrium molecular dynamics (EMD) simulations. On the one hand, boundarydriven NEMD simulations are useful to quickly predict Soret…