25 papers · ranked by Valyu relevance
Bilal Shaikh, Lucian P Smith, Dan Vasilescu, Gnaneswara Marupilla + 71 more
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example…
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…
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla + 67 more
'Michael A. Wilson' 'Eran Agmon' 'Henry Agnew' 'Steven S. Andrews' 'Azraf Anwar' 'Moritz Emanuel Beber' 'Frank Bergmann' 'David J. Brooks' 'Lutz Brusch' 'Laurence Calzone' 'Kiri Choi' 'Joshua Cooper' 'John Detloff' 'Brian Drawert' 'Michel Dumontier' 'G. Bard Ermentrout' 'James R. Faeder' 'Andrew P. Freiburger' 'Fabian…
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…
Nadja Damij, Pavle Boškoski, Marko Bohanec, Biljana Mileva Boshkoska + 1 more
'Matjaz Perc'] The omnipresent need for optimisation requires constant improvements of companies’ business processes (BPs). Minimising the risk of inappropriate BP being implemented is usually performed by simulating the newly developed BP under various initial conditions and “what-if” scenarios. An effectual business…
Kael Dai, Sergey L. Gratiy, Yazan N. Billeh, Richard Xu + 8 more
Experimental studies in neuroscience are producing data at a rapidly increasing rate, providing exciting opportunities and formidable challenges to existing theoretical and modeling approaches. To turn massive datasets into predictive quantitative frameworks, the field needs software solutions for systematic…
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…
Tianxiao Zhao, Katherine Zhang, Michelle Hollenberg, Wen Zhou + 1 more
Tissue function is tightly linked to the spatial organization, and our knowledge of the relationship between tissue structure and function has increased due to the rapid technological development of spatial transcriptomics approaches. A bottle-neck is, however, the analysis of the complex and high-dimensional spatial…
Thaleia Ntiniakou, James Osborne, Jieling Zhao, Jules Dichamp + 30 more
The emergence of virtual human twins (VHT) in biomedical research has sparked interest in multiscale in silico modelling frameworks, particularly in their application bridging cellular to tissue levels. Among the diverse array of multiscale modelling tools, off-lattice center-based agent-based models (CBM) offer a…
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…
Seyed Mahdi Javadi, Seyed Jafar Sadjadi, Ahmad Makui
In manufacturing systems, simulation modeling plays an important role in creating some changes instead of working on real systems. Manipulation in a real system is more costly than manipulation in a simulated model. In this research, we tried to use a simulation approach to recognize and minimize bottlenecks of a…
Iñaki Ucar, Bart Smeets
The simmer package brings discrete-event simulation to R. It is designed as a generic yet powerful process-oriented framework. The architecture encloses a robust and fast simulation core written in C++ with automatic monitoring capabilities. It provides a rich and flexible R API that revolves around the concept of…
Masoud Jamei, Steve Marciniak, Duncan Edwards, Kris Wragg + 3 more
'Kairui Feng' 'Adrian Barnett' 'Amin Rostami-Hodjegan'] Developing a user-friendly platform that can handle a vast number of complex physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models both for conventional small molecules and larger biologic drugs is a substantial challenge. Over the last decade…
Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis + 9 more
Computer simulation is an indispensable tool for studying complex biological systems. In particular, agent-based modeling is an attractive method to describe biophysical dynamics. However, two barriers limit faster progress. First, simulators do not always take full advantage of parallel and heterogeneous hardware.…
Brenno Lemos Melquiades dos Santos, Diego Augusto Silva Castro, Sávio Francisco Cirino da Paz, Davi Jannotti Coelho Pinheiro + 4 more
'Sávio Francisco Cirino da Paz' 'Davi Jannotti Coelho Pinheiro' 'Bárbara de Melo Quintela' 'Marcelo Lobosco' 'Alexandre Bittencourt Pigozzo' 'Teddy Lazebnik'] Mathematical and computational modeling are transforming biological research by enabling detailed exploration of complex systems. However, building computational…
Robert Clewley, Andreas Prlic
The PyDSTool software environment is designed to develop, simulate, and analyze dynamical systems models, particularly for biological applications. Unlike the engineering application focus and graphical specification environments of most general purpose simulation tools, PyDSTool provides a programmatic environment…
Authors not listed
Agentic artificial intelligence (AI) is poised to redefine how science is conducted, automating not just data analysis but the entire research lifecycle, from hypothesis generation to validation. Yet most current AI agents remain domain-bound, tailored to specific applications such as materials synthesis or quantum…
Breno Bernard Nicolau de França, Dietmar Pfahl, Valdemar Vicente Graciano Neto, Nauman bin Ali
Engineering Authors: ['Breno Bernard Nicolau de França' 'Dietmar Pfahl' 'Valdemar Vicente Graciano Neto' 'Nauman bin Ali'] Abstract The chapter supports educators and postgraduate students in understanding the role of simulation in software engineering research based on the authors' experience. This way, it includes a…
Panagiotis Sakagiannis, Hannes Rapp, Tijana Jovanic, Martin Paul Nawrot
Behavioral modeling supports theory building and evaluation across disciplines. Leveraging advances in motion-tracking and computational tools, we present a virtual laboratory for Drosophila larvae that integrates agent-based modeling with multiscale neural control and supports analysis of both simulated and…
Xuan Jiang, Yuhan Tang, Zhiyi Tang, Junzhe Cao + 3 more
U rbanization projects indicate that by 2050, more than 70% Europeans and 80% North Americans will call cities home. In developed regions, where nearly 80% of the population is expected to be urbanized [1], such rapid growth has also brought a host of problems including issues with mobility, infrastructure, congestion…
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…
Raquel Lopez-Rios de Castro, Alejandro Santana-Bonilla, Robert M. Ziolek, Christian D. Lorenz
Molecular dynamics simulations have become an essential tool in the study of soft matter and biological macromolecules. The large amount of high-dimensional data produced by such simulations does not immediately elucidate the atomistic mechanisms that underlie complex materials and molecular processes. Analysis of…
Kael Dai, Juan Hernando, Yazan N. Billeh, Sergey L. Gratiy + 12 more
Increasing availability of comprehensive experimental datasets in neuroscience and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational network models. To support construction and simulation, as well as sharing of such large-scale models, a…
Wassja Kopp, Can Huang, Yuqing Zhao, Peiyang Yu + 3 more
Automatic potential energy surface (PES) exploration is important to better understand reaction mechanisms. Existing automatic PES mapping tools usually rely on predefined knowledge or on computationally expensive on-the-fly quantum-chemical calculations. In this work, we have developed a method for discovering novel…
Alan Aspuru-Guzik, Roland Lindh, Markus Reiher
To date, the program for the development of methods and models for atomistic and continuum simulation directed toward chemicals and materials has reached an incredible degree of sophistication and maturity. Currently, one can witness an increasingly rapid emergence of advances in computing, artificial intelligence, and…