29 papers · ranked by Valyu relevance
Jiayi Du, Yu Zhou, Lihua Jin, Ke Sheng + 1 more
As a powerful but computationally intensive method, hybrid computational models study the dynamics of multicellular systems by evolving discrete cells in reacting and diffusing extracellular microenvironments. As the scale and complexity of studied biological systems continuously increase, the exploding computational…
Sairam Sri Vatsavai, Raees Khan, Kuan-Chieh Hsu, Ozgur O. Kilic + 23 more
Large-scale distributed computing infrastructures such as the Worldwide LHC Computing Grid (WLCG) require comprehensive simulation tools for evaluating performance, testing new algorithms, and optimizing resource allocation strategies. However, existing simulators suffer from limited scalability, hardwired algorithms…
Weiwei Fan, L. Jeff Hong, Guangxin Jiang, Jun Luo
Large-scale simulation optimization (SO) problems encompass both large-scale ranking-and-selection problems and high-dimensional discrete or continuous SO problems, presenting significant challenges to existing SO theories and algorithms. This paper begins by providing illustrative examples that highlight the…
Authors not listed
Machine Learning Interatomic Potentials (MLIPs), trained with Quantum Mechanics data, can model potential energy surfaces for molecular systems with very high accuracy and extreme speedups compared to reference quantum calculations, offering a powerful tool for studying complex chemical and biological systems. This…
Weiliang Chen, Erik De Schutter
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from…
Shenggan Cheng, Hao-Ran Yu, Derek Inman, Qiucheng Liao + 2 more
'James Lin'] Abstract—N-body simulations are essential tools in physical cosmology to understand the large-scale structure (LSS) formation of the universe. Large-scale simulations with high resolution are important for exploring the substructure of universe and for determining fundamental physical parameters like…
Marco Atzori, Wiebke Köpp, Steven W. D. Chien, Daniele Massaro + 9 more
'Fermín Mallor' 'Adam Peplinski' 'Mohamad Rezaei' 'Niclas Jansson' 'Stefano Markidis' 'Ricardo Vinuesa' 'Erwin Laure' 'Philipp Schlatter' 'Tino Weinkauf'] In situ visualization on high-performance computing systems allows us to analyze simulation results that would otherwise be impossible, given the size of the…
Lorenzo L. Pesce, Hyong C. Lee, Mark Hereld, Sid Visser + 3 more
'Rick L. Stevens' 'Albert Wildeman' 'Wim van Drongelen'] Our limited understanding of the relationship between the behavior of individual neurons and large neuronal networks is an important limitation in current epilepsy research and may be one of the main causes of our inadequate ability to treat it. Addressing this…
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…
Kaoruko Higuchi, Tomoki Kazawa, Buntaro Sakai, Shigehiro Namiki + 2 more
A major challenge in neurosciences is the elucidation of neural mechanisms in brains that are crucial for the processing of sensory information and the generation of adaptive behavior. In conjunction with the ever-growing body of experimental data, computational simulations have become crucial in integrating…
Alfons G. Hoekstra, Bastien Chopard, David Coster, Simon Portegies Zwart + 1 more
'Simon Portegies Zwart' 'Peter V. Coveney'] In this position paper, we discuss two relevant topics: (i) generic multiscale computing on emerging exascale high-performing computing environments, and (ii) the scaling of such applications towards the exascale. We will introduce the different phases when developing a…
Peter W. Gething, Anand P. Patil, Simon I. Hay, Mercedes Pascual
Risk maps estimating the spatial distribution of infectious diseases are required to guide public health policy from local to global scales. The advent of model-based geostatistics (MBG) has allowed these maps to be generated in a formal statistical framework, providing robust metrics of map uncertainty that enhances…
Dali Wang, Chen Wang, Qinglei Cao, Peter Schwartz + 8 more
'Jayesh Krishna' 'Danqing Wu' 'D. M. Ricciuto' 'Peter Thornton' 'Shih‐Chieh Kao' 'Michele Thornton' 'Kathryn Mohror'] Abstract—The development of a kilometer-scale E3SM Land Model (km-scale ELM) is an integral part of the E3SM project, which seeks to advance energy-related Earth system science research with…
Valentin Honoré, Tu Mai Anh, Loïc Pottier, Rafael Ferreira da Silva + 2 more
'Ewa Deelman' 'Frédéric Suter'] The amount of data generated by numerical simulations in various scientific domains such as molecular dynamics, climate modeling, biology, or astrophysics, led to a fundamental redesign of application workflows. The throughput and the capacity of storage subsystems have not evolved as…
Borja Bordel Sánchez, Ramón Alcarria, Álvaro Sánchez-Picot, Diego Sánchez-de-Rivera
'Diego Sánchez-de-Rivera'] Cyber-Physical Social Sensing (CPSS) is a new trend in the context of pervasive sensing. In these new systems, various domains coexist in time, evolve together and influence each other. Thus, application-specific tools are necessary for specifying and validating designs and simulating…
Mario Paolucci, Roberto Lo Conte, Jörn Kohlhammer, Martin Groß + 16 more
'Björn‐Ola Linnér' 'Panos Argyrakis' 'Bruce Edmonds' 'Steve Anderson' 'P Lukowicz' 'Petros Koumoutsakos' 'D. Kossman' 'Sara de Freitas' 'A.E. Blandford' 'Olga Sorkine' 'Robert W. Sumner' 'Natasha Gilbert' 'P Slusallek' 'Giulia Bonelli' 'D Helbing' 'Alexander Krause'] Mario Paolucci1,a , Donald Kossman2 , Rosaria Conte1…
Huebl, Axel, Arianna Formenti, Marco Garten + 1 more
In situ visualization is a tremendously powerful workflow to generate insight into the largest simulations run today. Recently, the 2022 Gordon Bell Prize-winning application WarpX [[2]] was used to run in situ visualization on 552 nodes of the Frontier supercomputer [[9]]. Immediate visualization of simulation…
Minna Palmroth, Urs Ganse, Yann Pfau-Kempf, Markus Battarbee + 6 more
This paper reviews Vlasov-based numerical methods used to model plasma in space physics and astrophysics. Plasma consists of collectively behaving charged particles that form the major part of baryonic matter in the Universe. Many concepts ranging from our own planetary environment to the Solar system and beyond can be…
Fabian Schuhmann, Jan A. Stevens, Neda Rahmani, Isabell Lindahl + 7 more
Molecular dynamics (MD) simulations excel at capturing biological processes at the molecular scale but rely on a well-defined initial structure. As MD simulations now extend to whole-cell-level modeling, new tools are needed to efficiently build initial structures. Here, we introduce TS2CG version 2, designed to…
Dileep Kishore, Srikiran Chandrasekaran
Biological systems are intrinsically noisy and this noise may determine the qualitative outcome of the system. In the absence of analytical solutions to mathematical models incorporating noise, stochastic simulation algorithms are useful to explore the possible trajectories of these systems. Algorithms used for such…
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…
Eva-Maria Kapfer, Paul Stapor, Jan Hasenauer
Mathematical models based on ordinary differential equations have been employed with great success to study complex biological systems. With soaring data availability, more and more models of increasing size are being developed. When working with these large-scale models, several challenges arise, such as high…
José Guadalupe Rosas Jiménez, Balázs Fábián, Gerhard Hummer
The need for short time steps currently limits routine atomistic molecular dynamics (MD) simulations to the microsecond timescale. For long time steps, the numerical integration of the equations of motion becomes unstable, resulting in catastrophic crashes. Here, we combine mass repartitioning and rescaling to…
Derek Groen, Stefan J. Zasada, Peter V. Coveney
—Multiscale and multiphysics applications are now commonplace, and many researchers focus on combining existing models to construct combined multiscale models. Here we present a concise review of multiscale applications and their source communities. We investigate the prevalence of multiscale projects in the EU and the…
Amjad Dabi, Daniel R. Schrider
Simulations are an essential tool in all areas of population genetic research, used in tasks such as the validation of theoretical analysis and the study of complex evolutionary models. Forward-in-time simulations are especially flexible, allowing for various types of natural selection, complex genetic architectures…
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…
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…
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…
Zhimian Hao, Chonghuan Zhang, Alexei Lapkin
We propose a workflow for reduction in the time required for data generation during generation of statistical digital twins. This methodology is particularly relevant for real-world engineering problems when data generation is expensive. A prerequisite for building surrogates is sufficient input/output data, whereas…