25 papers · ranked by Valyu relevance
Henrik Podéus, Gustav Magnusson, Sasan Keshmiri, Kajsa Tunedal + 3 more
When modeling complex, hierarchical, and time-dynamic systems, such as biological systems, good computational tools are essential. Current tools, while powerful, often lack comprehensive frameworks for modular model composition, hierarchical system building, and time-dependent input handling, particularly within the…
Sebastian Knoll, Klara Silber, Jason D. Williams, Peter Sagmeister + 4 more
'Christopher A. Hone' 'C. Oliver Kappe' 'Martin Steinberger' 'Martin Horn'] This paper introduces a versatile, open-source MATLAB/Simulink toolbox for modeling and optimizing flow reactors. The toolbox features a modular architecture and an intuitive drag-and-drop interface, supporting a range of different modeling…
Daniel Schick
The udkm1Dsim toolbox is a collection of Python classes and routines to simulate the thermal, structural, and magnetic dynamics after laser excitation as well as the according X-ray scattering response in one-dimensional sample structures. The toolbox provides the capabilities to define arbitrary layered structures on…
Brian Drawert, Andreas Hellander, Ben Bales, Debjani Banerjee + 14 more
'Giovanni Bellesia' 'Bernie J. Daigle Jr.' 'Geoffrey Douglas' 'Mengyuan Gu' 'Anand Gupta' 'Stefan Hellander' 'Chris Horuk' 'Dibyendu Nath' 'Aviral Takkar' 'Sheng Wu' 'Per Lötstedt' 'Chandra Krintz' 'Linda R. Petzold' 'Andreas Prlic'] We present StochSS: Stochastic Simulation as a Service, an integrated development…
Stewart Heitmann, Matthew Aburn, Michael Breakspear
The Brain Dynamics Toolbox provides a graphical tool for simulating user-defined dynamical systems in matlab. It supports three classes of differential equations commonly used in computational neuroscience: Ordinary Differential Equations, Delay Differential Equations and Stochastic Differential Equations. The design…
Vipul Singhal, Zoltan A. Tuza, Zachary Z. Sun, Richard M. Murray
We introduce a MATLAB based simulation toolbox, called txtlsim, for an E. coli based Transcription-Translation (TX-TL) system. This toolbox accounts for several cell-free related phenomena, such as resource loading, consumption, and degradation, and in doing so, models the dynamics of TX-TL reactions for the entire…
Riccardo Mengacci, Grazia Zambella, Giorgio Grioli, Danilo Caporale + 2 more
'Manuel G. Catalano' 'Antonio Bicchi'] To enable the design of planning and control strategies in simulated environments before their direct application to the real robot, exploiting the Sim2Real practice, powerful and realistic dynamic simulation tools have been proposed, e.g., the ROS-Gazebo framework. However, the…
William R. P. Nourse, Clayton Jackson, Nicholas S. Szczecinski, Roger D. Quinn + 2 more
'Roger D. Quinn' 'Mingguo Zhao' 'Biao Hu'] One developing approach for robotic control is the use of networks of dynamic neurons connected with conductance-based synapses, also known as Synthetic Nervous Systems (SNS). These networks are often developed using cyclic topologies and heterogeneous mixtures of spiking and…
Mohammad Mahdi Moayeri, Mohammad Hemami, Jamal Amani Rad, Kourosh Parand
The study of synchronous or asynchronous in (stochastic) neuronal populations is an important concept both in theory and in practice in neuroscience. The NPDS toolbox provides an interactive simulation platform for exploring such processes in Matlab looking through the lens of nonlinear dynamical systems. NPDS includes…
Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak + 3 more
'Intawat Nookaew' 'Jens Nielsen' 'Costas D. Maranas'] We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive…
Anup Teejo Mathew, Ikhlas Ben Hmida, Costanza Armanini, Frédéric Boyer + 1 more
S oft robotics has been a trending topic within the robotics community for almost two decades. However, available tools for the modeling and analysis of soft robots are still limited. This article introduces a user-friendly MATLAB toolbox, Soft Robot Simulator (SoRoSim), that integrates the geometric variable-strain…
N. Ngada
The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for…
Sequoia Ploeg, Hyrum Gunther, Ryan M. Camacho
—We present Simphony, a free and open-source software toolbox for abstracting and simulating photonic integrated circuits, implemented in Python. The toolbox is both fast and easily extensible; plugins can be written to provide compatibility with existing layout tools, and device libraries can be easily created without…
Jan Sören Schwarz, Leonard Enrique Ramos Perez, Minh Cong Pham, Kai Heussen + 1 more
'Kai Heussen' 'Quoc Tuan Tran'] Abstract—In context of highly complex energy system experiments, sensitivity analysis is gaining more and more importance to investigate the effects changing parameterization has on the outcome. Thus, it is crucial how to design an experiment to efficiently use the available resources.…
Maria Pozzi, Gabriele Maria Achilli, Maria Cristina Valigi, Monica Malvezzi
'Monica Malvezzi'] Grasping and dexterous manipulation remain fundamental challenges in robotics, above all when performed with multifingered robotic hands. Having simulation tools to design and test grasp and manipulation control strategies is paramount to get functional robotic manipulation systems. In this paper, we…
Kirill Zinovjev, Marc W. van der Kamp
Motivation: Experimental structural data can allow detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than a static picture of protein-ligand interactions is obtained…
Kirill Zinovjev, Marc W. van der Kamp
X-ray crystallography allows detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. However, crystal structures provide little more than a static picture of proteinligand interactions, whereas dynamical…
João P.G. Santos, Kadri Pajo, Daniel Trpevski, Andrey Stepaniuk + 5 more
Neuroscience incorporates knowledge from a range of scales from molecular dynamics to neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a variety of different software tools in the model building and analysis…
João P. G. Santos, Kadri Pajo, Daniel Trpevski, Andrey Stepaniuk + 5 more
'Olivia Eriksson' 'Anu G. Nair' 'Daniel Keller' 'Jeanette Hellgren Kotaleski' 'Andrei Kramer'] Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two…
Kevin Maik Jablonka, Michaël Zasso, Luc Patiny, Nicola Marzari + 3 more
Nowadays, computer simulations and experiments are closely interlocked. However, the data and analysis workflows are often barred into "silos" of knowledge — even for routine simulations. Here, we show how a typical electronic laboratory notebook (ELN) environment can be seamlessly integrated with a computational…
Anupam Ojha, Lane Votapka, Gary Huber, Shang Gao + 1 more
SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) is a powerful and versatile software tool designed to computationally estimate the kinetics and thermodynamics of complex molecular processes, particularly emphasizing the process of receptor-ligand binding and unbinding. We present a suite of tutorials for…
Kazuhiro Maeda, Fred C. Boogerd, Hiroyuki Kurata
Kinetic modeling is essential in understanding the dynamic behavior of biochemical networks, such as metabolic and signal transduction pathways. However, parameter estimation remains a major bottleneck in the development of kinetic models. We present RCGAToolbox, software for real-coded genetic algorithms (RCGAs)…
Authors not listed
We have developed Aitomia – a platform powered by AI to assist in performing AI-driven atomistic and quantum chemical (QC) simulations. This evolving intelligent assistant platform is equipped with chatbots and AI agents to help experts and guide non-experts in setting up and running atomistic simulations, monitoring…
Authors not listed
Electrochemiluminescence (ECL) is a vital analytical technique widely used in immunosensing and emerging applica-tions in biological imaging. Traditional ECL simulations rely on finite element methods, which provide valuable insights into reaction dynamics and spatial distribution of species. However, such methods are…
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…