29 papers · ranked by Valyu relevance
Muffy Calder, Claire Craig, Dave Culley, Richard de Cani + 15 more
'Christl A. Donnelly' 'Rowan Douglas' 'Bruce Edmonds' 'Jonathon Gascoigne' 'Nigel Gilbert' 'Caroline Hargrove' 'Derwen Hinds' 'David C. Lane' 'Dervilla Mitchell' 'Giles Pavey' 'David Robertson' 'Bridget Rosewell' 'Spencer Sherwin' 'Mark Walport' 'Alan Wilson'] In order to deal with an increasingly complex world, we…
Jessica S. Yu, Blair Lyons, Susanne Rafelski, Julie A. Theriot + 2 more
Iterating between data-driven research and generative computational models is a powerful approach for emulating biological systems, testing hypotheses, and gaining a deeper understanding of these systems. We developed a hybrid agent-based model (ABM) that integrates a Cellular Potts Model (CPM) designed to investigate…
Marvin van Aalst, Oliver Ebenhöh, Anna Matuszyńska
Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies and disease evolution or transmission. Unfortunately, despite community efforts leading to the development of…
Mark Burgin, Gordana Dodig-Crnković
We need much better understanding of information processing and computation as its primary form. Future progress of new computational devices capable of dealing with problems of big data, internet of things, semantic web, cognitive robotics and neuroinformatics depends on the adequate models of computation. In this…
Konrad Hinsen
Computational techniques have revolutionized many aspects of scientific research over the last few decades. Experimentalists use computation for data analysis, processing ever bigger data sets. Theoreticians compute predictions from ever more complex models. However, traditional articles do not permit the publication…
Bhanwar Lal Puniya, Meghna Verma, Chiara Damiani, Shaimaa Bakr + 2 more
In 2016, a community was founded for the Computational Modeling of Biological Systems (SysMod) as a Community of Special Interest (COSI) of the International Society for Computational Biology (ISCB) (, , ). The goal was to bring together members focusing on computational modeling and analysis of biological systems.…
Shuvra S. Bhattacharyya, Marilyn C. Wolf
—Heterogeneous computing is widely used at all levels of computing from data center to edge due to its power/performance characteristics. However, heterogeneity presents challenges. Interoperability—the management of workloads across heterogeneous resources—requires more careful design than is the case for homogeneous…
Yasmin Z. Paterson, David Shorthouse, Markus W. Pleijzier, Nir Piterman + 3 more
In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards systems biology and computational modelling to help unravel the complexities of gene and protein regulatory networks. In particular, the use of discrete modelling allows generation of…
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…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Maja Rudolph, Stefan Kurz, Barbara Rakitsch
Design patterns provide a systematic way to convey solutions to recurring modeling challenges. This paper introduces design patterns for hybrid modeling, an approach that combines modeling based on first principles with data-driven modeling techniques. While both approaches have complementary advantages there are often…
Beatrix C. Hiesmayr, Marc‐Thorsten Hütt
A recent trend in mathematical modeling is to publish the computer code together with the research findings. Here we explore the formal question, whether and in which sense a computer implementation is distinct from the mathematical model. We argue that, despite the convenience of implemented models, a set of implicit…
Szymon Wasik, Tomasz Prejzendanc, Jacek Blazewicz
Computational modeling is an important element of systems biology. One of its important applications is modeling complex, dynamical, and biological systems, including viral infections. This type of modeling usually requires close cooperation between biologists and mathematicians. However, such cooperation often faces…
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…
Erickson Fajiculay, Chao-Ping Hsu
Modeling biochemical systems can provide insights into behaviors that are difficult to observe or understand. It requires software, programming, and understanding of the system to build a model and study it. Softwares exist for systems biology modeling, but most support only certain types of modeling tasks. Desirable…
Patrik Christen, Olivier Del Fabbro
Many computer models have been developed and successfully applied. However, in some cases, these models might be restrictive on the possible solutions or their solutions might be difficult to interpret. To overcome this problem, we outline a new approach, the so-called allagmatic method, that automatically programs and…
Marcello Pompa, Simona Panunzi, Alessandro Borri, Laura D’Orsi + 2 more
Large volumes of data are these days collected and archived from patients in a variety of clinical settings. This phenomenon is the product of the evolution of analysis systems and the appearance of new diagnostic techniques . The physician has thus in many cases observations of the clinical status of the patient at…
Mark R. Davies, Ken Wang, Gary R. Mirams, Antonello Caruso + 6 more
'Denis Noble' 'Antje Walz' 'Thierry Lavé' 'Franz Schuler' 'Thomas Singer' 'Liudmila Polonchuk'] Title: Highlights 1. • Modelling and simulation can streamline decision making in drug safety testing. 2. • Computational cardiac electrophysiology is a mature technology with a long heritage. 3. • There are many challenges…
Patrik Christen, Olivier Del Fabbro
Mathematical modelling heavily employs differential equations to describe the macroscopic or global behaviour of systems. The dynamics of complex systems is in contrast more efficiently described by local rules and thus in an algorithmic and local or microscopic manner. The theory of such an approach has to be…
Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran + 2 more
Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in…
Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti + 3 more
We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. This allows exploiting the…
Andreas Tolk, Saikou Y. Diallo, José J. Padilla, Ross Gore
Epistemology is the branch of philosophy that deals with gaining knowledge. It is closely related to ontology. The branch that deals with questions like "What is real?" and "What do we know?" as it provides these components. When using modeling and simulation, we usually imply that we are doing so to either apply…
Ilya Korsunsky, Kathleen McGovern, Tom LaGatta, Loes Olde Loohuis + 3 more
'Terri Grosso-Applewhite' 'Nancy Griffeth' 'Bud Mishra'] A systems-biology approach to complex disease (such as cancer) is now complementing traditional experience-based approaches, which have typically been invasive and expensive. The rapid progress in biomedical knowledge is enabling the targeting of disease with…
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…
Peter V. Coveney, Roger R. Highfield
Title: Highlights 1. • When machine learning is applied in ignorance of fundamental laws of nature, it is likely to deliver unreliable answers. 2. • With his colleagues, Peter Coveney has described the computational algorithms best suited for deployment on exascale architectures. 3. • In the exascale era, we will…
Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
Reproducible, understandable models that can be reused and combined to true multi-scale systems are required to solve the present and future challenges of systems biology. However, many mathematical models are still built for a single purpose and reusing them in a different context can be challenging due to an…
Sachini P. Kadaoluwa Pathirannahalage, Nastaran Meftahi, Aaron Elbourne, Alessia C. G. Weiss + 8 more
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions, mixtures, and materials settings. It therefore forms the basis for all molecular dynamics simulations of biological phenomena, as well as for many chemical, industrial, and materials investigations. Over the years, many water…
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…
Samantha Durdy, Cameron J. Hargreaves, Mark Dennison, Benjamin Wagg + 5 more
The discovery of new materials often requires collaboration between experimental and computational chemists. Web based platforms allow more flexibility in this collaboration by giving access to computational tools without the need for access to computational researchers. We present Liverpool Materials Discovery Server…