25 papers · ranked by Valyu relevance
Jaroslaw Krzywanski, Marcin Sosnowski, Karolina Grabowska, Anna Zylka + 3 more
'Anna Zylka' 'Lukasz Lasek' 'Agnieszka Kijo-Kleczkowska' 'Bongju Kim'] This paper provides a comprehensive review of recent advancements in computational methods for modeling, simulation, and optimization of complex systems in materials engineering, mechanical engineering, and energy systems. We identified key trends…
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…
Jeannette M. Wing
Computational thinking will influence everyone in every field of endeavour. This vision poses a new educational challenge for our society, especially for our children. In thinking about computing, we need to be attuned to the three drivers of our field: science, technology and society. Accelerating technological…
Desmond J. Higham
I give a brief, non-technical, historical perspective on numerical analysis and optimization. I also touch on emerging trends and future challenges. This content is based on the short presentation that I made at the opening ceremony of The International Conference on Numerical Analysis and Optimization, which was held…
Rohan Chandraghatgi, Hai-Feng Ji, Gail L. Rosen, Bahrad A. Sokhansanj
Recent advances in computational methods provide the promise of dramatically accelerating drug discovery. While math-ematical modeling and machine learning have become vital in predicting drug-target interactions and properties, there is untapped potential in computational drug discovery due to the vast and complex…
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
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…
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…
Ulrich Rüde, Karen Willcox, Lois Curfman McInnes, Hans De Sterck + 29 more
'George Biros' 'Hans Bungartz' 'James Corones' 'Evin Cramer' 'James L. Crowley' 'Omar Ghattas' 'Max Gunzburger' 'Michael Hanke' 'Robert Harrison' 'Michael A. Heroux' 'Jan S. Hesthaven' 'Peter K. Jimack' 'Chris R. Johnson' 'Kirk E. Jordan' 'David E. Keyes' 'Rolf Krause' 'Vipin Kumar' 'Stefan Mayer' 'Juan M López Meza'…
David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-generation molecular simulation engine and associated libraries optimized for performance on fast, multicore central processor units (CPUs) and graphics processing units (GPUs) with independent memory and tens of thousands of threads. STORMM…
Philipp Bader, Sergio Blanes, Fernando Casas
The Schr¨odinger eigenvalue problem is solved with the imaginary time propagation technique. The separability of the Hamiltonian makes the problem suitable for the application of splitting methods. High order fractional time steps of order greater than two necessarily have negative steps and can not be used for this…
Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Giulia Capitoli + 4 more
Mathematical models of biochemical networks can largely facilitate the comprehension of the mechanisms at the basis of cellular processes, as well as the formulation of hypotheses that can then be tested with targeted laboratory experiments. However, two issues might hamper the achievement of fruitful outcomes. On the…
Chris Rackauckas, Yingbo Ma, Andreas Noack, Vaibhav Dixit + 10 more
Pharmacometric modeling establishes causal quantitative relationships between administered dose, tissue exposures, desired and undesired effects and patient’s risk factors. These models are employed to de-risk drug development and guide precision medicine decisions. However, pharmacometric tools have not been designed…
Clare Horsman, Susan Stepney, Rob C. Wagner, Viv Kendon
Computing is a high-level process of a physical system. Recent interest in non-standard computing systems, including quantum and biological computers, has brought this physical basis of computing to the forefront. There has been, however, no consensus on how to tell if a given physical system is acting as a computer or…
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…
Hesam Dashti, Jonathan R. Wedell, Gabriel Cornilescu, Charles D. Schwieters + 3 more
Computational molecular dynamics, energy minimization, and modeling of molecular interactions are widely used in studies involving natural products, metabolites, and drugs. Manually directed computational steps commonly utilize an evolving collection of experimental and computational data, to which new data sources are…
Ashar J. Malik, Chandra S. Verma
Quantum computers have demonstrated advantage in tackling problems considered hard for classical computers and hold promise for tackling complex problems in molecular mechanics such as mapping the conformational landscapes of biomolecules. This work attempts to explore a few ways in which classical data, relating to…
Claude Tadonki
The next frontier of high performance computing is the Exascale, and this will certainly stand as a noteworthy step in the quest for processing speed potential. In fact, we always get a fraction of the technically available computing power (so-called theoretical peak), and the gap is likely to go hand-to-hand with the…
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…
Yifan Wu, Aron Walsh, Alex Ganose
What is the minimum number of experiments, or calculations, required to find an optimal solution? Relevant chemical problems range from identifying a compound with target functionality within a given phase space to controlling materials synthesis and device fabrication conditions. A common feature in this application…
Simone Severini
This piece plays with the idea of the Computocene: an era defined not merely by the ubiquity of computers, but by their deepening role in how we observe, interpret, and make sense of the world. Rather than emphasizing automation, speed, scale, or intelligence, computation is reframed as a mode of attention—filtering…
Andrew Simmonett, Bernard Brooks, Thomas Darden
Evaluation of noncovalent electrostatic interactions is the dominant bottleneck in classical molecular dynamics simulations, and evaluation of Coulombic matrix elements similarly limits quantum mechanical self consistent field calculations. These difficulties are a result of the Coulomb operator’s slow decay, which…
Lorenzo Magnani
Eco-cognitive computationalism sees computation in context, exploiting the ideas developed in those projects that have originated the recent views on embodied, situated, and distributed cognition. Turing’s original intellectual perspective has already clearly depicted the evolutionary emergence in humans of…
Derek Groen, Jaroslaw Knap, Philipp Neumann, Diana Suleimenova + 2 more
In the last few decades, multiscale modelling has emerged as one of the dominant modelling paradigms in many areas of science and engineering. Its rise to dominance is primarily driven by advancements in computing power and the need to model systems of increasing complexity. The multiscale modelling paradigm is now…
Matti Tedre, Nella Moisseinen
Experiments play a central role in science. The role of experiments in computing is, however, unclear. Questions about the relevance of experiments in computing attracted little attention until the 1980s. As the discipline then saw a push towards experimental computer science, a variety of technically, theoretically…