Related papers: Message-Passing Multi-Cell Molecular Dynamics on t…
Computational intensity and sequential nature of estimation techniques for Bayesian methods in statistics and machine learning, combined with their increasing applications for big data analytics, necessitate both the identification of…
Large-scale HPC simulations of plasma dynamics in fusion devices require efficient parallel I/O to avoid slowing down the simulation and to enable the post-processing of critical information. Such complex simulations lacking parallel I/O…
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
This short report describes the scaling, up to 1024 software processes and hardware cores, of a distributed simulator of plastic spiking neural networks. A previous report demonstrated good scalability of the simulator up to 128 processes.…
The auto differentiable simulation is a type of simulation that outputs of the simulation include not only the simulation result itself, but also their derivatives with respect to various input parameters. It provides an efficient method to…
We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics (MD) simulations [Skeel et al., J. Comput. Chem., 23, 673 (2002)], to handle dispersion…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
We leverage the Multiplicative Weight Update (MWU) method to develop a decentralized algorithm that significantly improves the performance of dynamic time division duplexing (D-TDD) in small cell networks. The proposed algorithm adaptively…
While load balancing in distributed-memory computing has been well-studied, we present an innovative approach to this problem: a unified, reduced-order model that combines three key components to describe "work" in a distributed system:…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
A machine learning (ML) design framework is proposed for dynamically adjusting clock frequency based on propagation delay of individual instructions. A Random Forest model is trained to classify propagation delays in real-time, utilizing…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
The need to use a short time step is a key limit on the speed of molecular dynamics (MD) simulations. Simulations governed by classical potentials are often accelerated by using a multiple-time-step (MTS) integrator that evaluates certain…
Quantum computers have the potential to simulate chemical systems beyond the capability of classical computers. Recent developments in hybrid quantum-classical approaches enable the determinations of the ground or low energy states of…
We propose a Distributed and Collaborative Monitoring system, DCM, with the following properties. First, DCM allow switches to collaboratively achieve flow monitoring tasks and balance measurement load. Second, DCM is able to perform…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
In this paper, we propose a series of novel coordination schemes for multi-cell downlink communication. Starting from full base station (BS) coordination, we first propose a fully-coordinated scheme to exploit beneficial effects of both…
Optical interconnect is a potential solution to attain the large bandwidth on-chip communications needed in high performance computers in a low power and low cost manner. Mode-division multiplexing (MDM) is an emerging technology that…
In this paper, a simple memory limited transmitter for molecular communication is proposed, in which information is encoded in the diffusion rate of the molecules. Taking advantage of memory, the proposed transmitter reduces the ISI problem…