Related papers: tinyMD: A Portable and Scalable Implementation for…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
Ligand coated nanoparticles are complex objects consisting of a metallic or semiconductor core with organic ligands grafted on their surface. These organic ligands provide stability to a nanoparticle suspension. In solutions, the effective…
We present the W-SLDA Toolkit, a general-purpose software package for simulating ultracold Fermi gases within the framework of density functional theory and its time-dependent extensions. The toolkit enables fully microscopic studies of…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
The development of cost-effective highperformance parallel computing on multi-processor supercomputers makes it attractive to port excessively time consuming simulation software from personal computers (PC) to super computes. The power…
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…
The goal of this paper is the experimental validation of a gray-box equivalent modeling approach applied to microgrids. The main objective of the equivalent modeling is to represent the dynamic response of a microgrid with a simplified…
The proliferation of smart and autonomous systems has motivated a shift toward executing intelligence directly on edge devices. This shift becomes particularly challenging for zero-energy devices (ZEDs), where severe constraints on memory,…
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…
The concept of scalability analysis of numerical parallel applications has been revisited, with the specific goals defined for the performance estimation of research applications. A series of Community Climate Model System (CCSM) numerical…
The landscape of miniaturized wireless biomedical devices (MWBDs) is rapidly expanding as proactive mobile healthcare proliferates. MWBDs are diverse and include various injectable, ingestible, implantable, and wearable devices. While the…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…
The numerical simulation of multiphase flows involving dispersed components with large scale disparities, such as the collisions between millimeter-sized bubbles and micron-sized mineral particles in flotation, poses a significant…
To date, testing interactions in high dimensions has been a challenging task. Existing methods often have issues with sensitivity to modeling assumptions and heavily asymptotic nominal p-values. To help alleviate these issues, we propose a…
When physical testbeds are out of reach for evaluating a networked system, we frequently turn to simulation. In today's datacenter networks, bottlenecks are rarely at the network protocol level, but instead in end-host software or hardware…
Workflows are critical for scientific discovery. However, the sophistication, heterogeneity, and scale of workflows make building, testing, and optimizing them increasingly challenging. Furthermore, their complexity and heterogeneity make…
Lightweight Vision-Language Models (VLMs) are indispensable for resource-constrained applications. The prevailing approach to aligning vision and language models involves freezing both the vision encoder and the language model while…
The high-performance computing (HPC) landscape is undergoing rapid transformation, with an increasing emphasis on energy-efficient and heterogeneous computing environments. This comprehensive study extends our previous research on SYCL's…
Modern software systems are typically configurable, a fundamental prerequisite for wide applicability and reusability. This flexibility poses an extraordinary challenge for quality assurance, as the enormous number of possible…