27 papers · ranked by Valyu relevance
Ian Foster, David C. Parkes, Stephan Zheng
Fifty years ago, weather forecasters struggled to do better than predicting that tomorrow's weather would be the same as today. Today, weather forecasts are often accurate a week or more into the future, allowing individuals and societies to prepare for what is no longer unforeseen. This remarkable transformation is…
Michael Levitt
Computer simulation is an important research tool in today’s scientific world. Computers allow us to perform computations that mimic the behavior of complex (biological) systems in ways that we could not otherwise achieve. You could think of these simulations as a computer game, in which a virtual world is created that…
Guillaume Lamé, Mary Dixon-Woods
Simulation can offer researchers access to events that can otherwise not be directly observed, and in a safe and controlled environment. How to use simulation for the study of how to improve the quality and safety of healthcare remains underexplored, however. We offer an overview of simulation-based research (SBR) in…
Evangelos Katsamakas
The simulation hypothesis suggests that we live in a computer simulation. That notion has attracted significant scholarly and popular interest. This article explores the simulation hypothesis from a business perspective. Due to the lack of a name for a universe consistent with the simulation hypothesis, we propose the…
Alexey Turchin, Michael Batin, David Denkenberger, Roman V. Yampolskiy
'Roman V. Yampolskiy'] The goal of the article is to explore what is the most probable type of simulation in which humanity lives (if any) and how this affects simulation termination risks. We firstly explore the question of what kind of simulation in which humanity is most likely located based on pure theoretical…
Małgorzta Borówko
Rapid advances are taking place in the application of molecular simulations to study complex systems. Molecular simulations are widely used in physics, chemistry, biology, material science, engineering, and even medicine. Each study conducted in a purely theoretical manner can be treated as a simulation. The behavior…
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…
Janina Wellmann
Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most…
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…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Jean Cury, Benjamin C. Haller, Guillaume Achaz, Flora Jay
Simulation of genomic data is a key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate how to simulate bacterial populations with SLiM, a forward-in-time…
Ishita Dasgupta, Kevin A. Smith, Eric Schulz, Joshua B. Tenenbaum + 1 more
People can learn about the effects of their actions either by performing physical experiments or by running mental simulations. Physical experiments are reliable but risky; mental simulations are unreliable but safe. We investigate how people negotiate the balance between these strategies. Participants attempted to…
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…
Alexander Paz, Naveen Veeramisti, Romesh Khaddar, Hanns de la Fuente-Mella + 1 more
'Hanns de la Fuente-Mella' 'Luiza Modorcea'] This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i) motion-based driving…
Rishi Rajalingham, Aida Piccato, Mehrdad Jazayeri
Primates can richly parse sensory inputs to infer latent information, and adjust their behavior accordingly. It has been hypothesized that such flexible inferences are aided by simulations of internal models of the external world. However, evidence supporting this hypothesis has been based on behavioral models that do…
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…
Harold Fellermann, Ben Shirt-Ediss, Jerzy W. Koryza, Matthew Linsley + 2 more
Our PCR Simulator is a web-based application designed to introduce concepts of multi-factorial experimental design and support teaching of the polymerase chain reaction. Learners select experimental settings and receive results of their simulated reactions quickly, allowing rapid iteration between data generation and…
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…
Gopal Sarma, Victor Faúndez
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale…
Timo M Deist, Andrew Patti, Zhaoqi Wang, David Krane + 3 more
We introduce simulation as a pre-processing step in a machine learning pipeline, in particular, as a way to include expert prior knowledge. One can consider simulation as a technique which regularizes data or as a specialized feature extraction method. In either view, the SimKern methodology offers a decomposition of…
Ignacio Erazo
Increased data availability has stimulated the interest in studying sports prediction problems via analytical approaches; in particular, with machine learning and simulation. We characterize several models that have been proposed in the literature, all of which suffer from the same drawback: they cannot incorporate…
Janine Egert, Clemens Kreutz
In systems biology, the analysis of complex nonlinear systems faces many methodological challenges. However, the performance evaluation of competing methods is limited by the small amount of publicly available data from biological experiments. Therefore, simulation studies with a realistic representation of the data…
Authors not listed
Computing the free energy of protein-ligand binding by employing molecular dynamics (MD) simulations is becoming a valuable tool in the early stages of drug discovery. However, the cost and complexity of such simulations are often prohibitive for high-throughput studies. We present an automated workflow for the…
M. E. Johnson, A. Chen, J. R. Faeder, P. Henning + 6 more
Most of the fascinating phenomena studied in cell biology emerge from interactions among highly organized multi-molecular structures and rapidly propagating molecular signals embedded into complex and frequently dynamic cellular morphologies. For the exploration of such systems, computational simulation has proved to…
Florian Cogoni, David Bernard, Roxana Kazhen, Salvatore Valitutti + 2 more
Agent-based models are commonly used in biology to study tissue-scale phenomena by reproducing the individual behavior of the cells. They offer the possibility to study cellular biology at the individual cell scale to explore the basic behavior of cells which are responsible of the emergence of more complex phenomena…
Authors not listed
Integrating machine learning (ML) into drug discovery has ushered in a new era of innovation, dramatically enhancing the efficiency and precision of identifying and developing new therapeutics. This review provides a comprehensive analysis of the current applications of machine learning in drug discovery, focusing on…
Authors not listed
Deriving versatile and robust mechanistic models from experimental data is a key challenge in engineering and natural sciences. This is especially true in chemical reaction engineering, where reactor manufacturers and operators increasingly pursue the development and maintenance of digital twins that rely on frequent…