相关论文: Message-Passing Multi-Cell Molecular Dynamics on t…
Molecular dynamics (MD) simulations provide considerable benefits for the investigation and experimentation of systems at atomic level. Their usage is widespread into several research fields, but their system size and timescale are also…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Machine Learning and Data Mining (MLDM) algorithms are becoming increasingly important in analyzing large volume of data generated by simulations, experiments and mobile devices. With increasing data volume, distributed memory systems (such…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Reduction of communication and efficient partitioning are key issues for achieving scalability in hierarchical $N$-Body algorithms like FMM. In the present work, we propose four independent strategies to improve partitioning and reduce…
The application of distributed model predictive controllers (DMPC) for multi-agent systems (MASs) necessitates communication between agents, yet the consequence of communication data rates is typically overlooked. This work focuses on…
Cycle-level simulators such as gem5 are widely used in microarchitecture design, but they are prohibitively slow for large-scale design space explorations. We present Concorde, a new methodology for learning fast and accurate performance…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based…
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
Recent advances in computing architectures and networking are bringing parallel computing systems to the masses so increasing the number of potential users of these kinds of systems. In particular, two important technological evolutions are…
This paper takes a new look at Cell-free Massive MIMO (multiple-input multiple-output) through the lens of the dynamic cooperation cluster framework from the Network MIMO literature. The purpose is to identify and address scalability issues…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
Modeling plasma accelerators is a computationally challenging task and the quasi-static particle-in-cell algorithm is a method of choice in a wide range of situations. In this work, we present the first performance-portable, quasi-static,…
For 35 years, {\it ab initio} molecular dynamics (AIMD) has been the method of choice for modeling complex atomistic phenomena from first principles. However, most AIMD applications are limited by computational cost to systems with…
Communication at millimeter wave (mmWave) frequencies is one of the main novelties introduced in the 5th generation (5G) of cellular networks. The opportunities and challenges associated with such high frequencies have stimulated a number…
Massive machine type communication (mMTC) is one of the basic components of the future fifth generation (5G) wireless communication system. In mMTC, the information processing at the sensor nodes is required to be simple, low power…
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…