26 papers · ranked by Valyu relevance
Martin O. Steinhauser, Stefan Hiermaier
This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed…
Marcos D. Caballero, M. Hjorth‐Jensen
In this contribution we discuss how to develop a physics curriculum for undergraduate students that includes computing as a central element. Our contribution starts with a definition of computing and pertinent learning outcomes and assessment studies and programs. We end with a discussion on how to implement computing…
Tor Ole B. Odden, Elise Lockwood, Marcos D. Caballero
Tor Ole B. Odden1 , Elise Lockwood2 , and Marcos D. Caballero1,3 1 Center for Computing in Science Education, University of Oslo, Oslo, Norway 2 Department of Mathematics, Oregon State University, Corvallis, OR 3 Department of Physics and Astronomy & CREATE for STEM Institute, Michigan State University, East Lansing…
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…
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…
Chi-Ning Chou
Two transformative waves of computing have redefined the way we approach science. The first wave came with the birth of the digital computer, which enabled scientists to numerically simulate their models and analyze massive datasets. This technological breakthrough led to the emergence of many sub-disciplines bearing…
Małgorzata Borówko
Molecular simulation is one of the fastest growing fields in science. This is connected with the rapid increase of computer efficiency and with the appearance of new, sophisticated simulation methods enabling the modeling of complex systems while seamlessly bridging different length and time scales. Now, it is possible…
Authors not listed
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…
Barry I. Schneider
Over the past 40 years there has been remarkable progress in the quantitative treatment of complex many-body problems in atomic and molecular physics (AMP). This has happened as a consequence of the development of new and powerful numerical methods, translating these algorithms into practical software and the…
Matthias Möller, C. Vuik
Quantum computing technologies have become a hot topic in academia and industry receiving much attention and financial support from all sides. Building a quantum computer that can be used practically is in itself an outstanding challenge that has become the 'new race to the moon'. Next to researchers and vendors of…
Yasar Y. Atas, Jinglei Zhang, Randy Lewis, Amin Jahanpour + 2 more
'Jan F. Haase' 'Christine A. Muschik'] Quantum computers have the potential to create important new opportunities for ongoing essential research on gauge theories. They can provide simulations that are unattainable on classical computers such as sign-problem afflicted models or time evolutions. In this work, we…
Vaitea Opuu, Young Joo Sun, Titus Hou, Nicolas Panel + 2 more
A powerful approach to understand protein structure and evolution is to perform computer simulations that mimic aspects of evolution. In particular, structure-based computational protein design (CPD) can address the inverse folding problem, exploring a large space of amino acid sequences and selecting ones predicted to…
Billy J. Fournier, Bryant Wyatt
We have two basic methods of modeling matter. We can treat matter as a continuum and solve differential equations or we can treat it discretely and solve massive N-body problems. The differential equations produced by meaningful problems can be extremely difficult to formulate and much more difficult to solve, if not…
Alexander J. Bryer, Juan R. Perilla
Dimensionality reduction via coarse grain modeling has positioned itself as an indispensable tool for decades, particularly for biomolecular simulations where atomic systems encompass hundreds of millions of atoms. While distinct flavors of coarse grain modeling exist, those occupying the coarse end of the spectrum are…
Chitrak Gupta, John Kevin Cava, Daipayan Sarkar, Eric Wilson + 4 more
Molecular dynamics (MD) simulations have emerged to become the back-bone of today’s computational biophysics. Simulation tools such as, NAMD, AMBER and GROMACS have accumulated more than 100,000 users. Despite this remarkable success, now also bolstered by compatibility with graphics processor units (GPUs) and exascale…
Christopher Myers, Ken Miyazaki, Thomas Trepl, Christine Isborn + 1 more
GPU-accelerated on-the-fly nonadiabatic dynamics is enabled by interfacing the linearized semiclassical dynamics approach with the TeraChem electronic structure program. We describe the computational workflow of the "PySCES" code interface, a Python code for semiclassical dynamics with on-the-fly electronic structure…
Mads Bertelsen, Peter K. Willendrup, Sunyoung Yoo, Adriano Meligrana + 4 more
Monte Carlo neutron ray-tracing simulations of time-of-flight (TOF)-Laue neutron macromolecular crystal diffraction (n-MX) using the McStas software package were done for the upcoming NMX Macromolecular Diffractometer at the European Spallation Source. Splitting neutron rays that arrive at the crystal lead to dramatic…
Authors not listed
For decades, computational theoretical chemistry has provided critical insights into molecular behavior, often anticipating experimental discoveries. This review surveys twenty notable examples from the past fifteen years in which computational chemistry successfully predicted molecular structures, reaction mechanisms…
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…
Liangzhu Leon Wang, Huiheng Liu, Honghao Fu, Zhipeng Deng + 2 more
Quantum computing is a new approach to computation that utilizes superposition, entanglement, interference, and tunneling to solve problems too complex for classical computers. This paper discusses the basic concepts and development of quantum computing, exploring its potential applications in the built environment and…
Authors not listed
Nonadiabatic dynamics simulations complement time-resolved experiments by revealing ultrafast excited-states mechanistic information in photochemical reactions. Understanding the relaxation mechanisms of photo-excited molecules finds application in energy, material, and medicinal research. However, with substantial…
Mårten Skogh, Phalgun Lolur, Werner Dobrautz, Christopher Warren + 5 more
There is currently no combination of quantum hardware and algorithms that can provide an advantage over conventional calculations of molecules or materials. However, if or when such a point is reached, new strategies will be needed to verify predictions made using quantum devices. We propose that the electron density…
David Thompson, Johan Gielis
Our understanding of quantum phenomena often begins with simple particle-in-a-box style problems, the solutions of which introduce the student to foundational quantum concepts such as degeneracy and quantization. Simple model geometries of confinement afford analytic solutions, which are readily derivable, easily…
Fergus R. Cooper, Ruth E. Baker, Alexander G. Fletcher
Mathematical modelling provides a useful framework within which to investigate the organization of biological tissues. With advances in experimental biology leading to increasingly detailed descriptions of cellular behaviour, models that consider cells as individual objects are becoming a common tool to study how…
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…
Viv Kendon
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of speed. Other types of computation using radically different architectures…