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Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying atomic structure evolution, structural deformation, phase transitions, recrystallization as well as electron emission…
Heliospheric plasmas require multi-scale and multi-physics considerations. On one hand, MHD codes are widely used for global simulations of the solar-terrestrial environments, but do not provide the most elaborate physical description of…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Storing data is easy, but finding and using data is not. It is desirable that the data is stored in a structured format, which can be preserved and retrieved in future. Creating Metadata for the data is one way of creating structured data…
High-pressure research is a productive route to new structures and emergent properties. However, crucial high-pressure structural information remains highly fragmented across individual publications and heterogeneous computational…
Astrophysical research in recent decades has made significant progress thanks to the availability of various $N$-body simulation techniques. With the rapid development of high-performance computing technologies, modern simulations have been…
Developing an effective molecular generation framework even with a limited number of molecules is often important for its practical deployment, e.g., drug discovery, since acquiring task-related molecular data requires expensive and…
Federated learning is widely used in medical applications for training global models without needing local data access. However, varying computational capabilities and network architectures (system heterogeneity), across clients pose…
2D materials find promising applications in next-generation devices, however, large-scale, low-defect, and reproducible synthesis of 2D materials remains a challenging task. To assist in the selection of suitable substrates for the…
Exascale I/O initiatives will require new and fully integrated I/O models which are capable of providing straightforward functionality, fault tolerance and efficiency. One solution is the Distributed Asynchronous Object Storage (DAOS)…
Scientific applications produce a huge amount of data, which imposes serious management and analysis challenges. In particular, limitations in current database management systems prevent their adoption in simulation applications, in which…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Computational micromagnetics requires numerical solution of partial differential equations to resolve complex interactions in magnetic nanomaterials. The Virtual Micromagnetics project described here provides virtual machine simulation…
Horizon Run 5 (HR5) is a cosmological hydrodynamical simulation which captures the properties of the Universe on a Gpc scale while achieving a resolution of 1kpc. Inside the simulation box we zoom-in on a high-resolution cuboid region with…
The object of this article is to review the development of ultrahigh-density, nanoscale data storage, i.e., nanostorage. As a fundamentally new type of storage system, the recording mechanisms of nanostorage may be completely different to…
Hydrogen fuel cells are a key technology in the transition toward carbon-neutral energy systems, offering clean power with water as the only byproduct. Microfluidic fuel cells, which operate at the microliter scale, are an emerging variant…
To store information at extremely high-density and data-rate, we propose to adapt, integrate, and extend the techniques developed by chemists and molecular biologists for the purpose of manipulating biological and other macromolecules. In…