Related papers: Chemical mass-action systems as analog computers: …
Chemical transport models (CTMs), which simulate air pollution transport, transformation, and removal, are computationally expensive, largely because of the computational intensity of the chemical mechanisms: systems of coupled differential…
This paper presents an analysis of the fundamental limits on energy efficiency in both digital and analog in-memory computing architectures, and compares their performance to single instruction, single data (scalar) machines specifically in…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
Traditional heterogeneous parallel algorithms, designed for heterogeneous clusters of workstations, are based on the assumption that the absolute speed of the processors does not depend on the size of the computational task. This assumption…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
Embedding efficient calculation instructions into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reaction modules that act as units of computation and make…
The recent development in analog computation is reviewed in this paper. Analog computation was used in many applications where power and energy efficiency is of paramount importance. It is shown that by using innovative architecture and…
Dynamic mechanical metamaterials (MMs) are artificial media composed of periodic micro-structures, designed to manipulate wave propagation. Modeling and designing these materials can be computationally demanding due to the broad design…
Chemical reaction prediction, involving forward synthesis and retrosynthesis prediction, is a fundamental problem in organic synthesis. A popular computational paradigm formulates synthesis prediction as a sequence-to-sequence translation…
We have presented some practical consequences on the molecular-dynamics simulations arising from the numerical algorithm published recently in paper Int. J. Mod. Phys. C 16, 413 (2005). The algorithm is not a finite-difference method and…
This paper provides a description of a new method for information processing based on holistic approach wherein analysis is a direct product of synthesis. The core of the method is iterative averaging of all the elements of a system…
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
Neural networks have been applied to tackle many-body electron correlations for small molecules and physical models in recent years. Here we propose a new architecture that extends molecular neural networks with the inclusion of periodic…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
We present shared-memory parallel methods for Maximal Clique Enumeration (MCE) from a graph. MCE is a fundamental and well-studied graph analytics task, and is a widely used primitive for identifying dense structures in a graph. Due to its…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
In present day technology, storing and processing of information occur on physically distinct regions of space. Not only does this result in space limitations; it also translates into unwanted delays in retrieving and processing of relevant…
Computing long-timescale kinetics of biomolecular processes remains a major challenge for atomistic simulations. A way out is to exploit local kinetic information to construct the global stationary flux across the reaction space. The…
Traditional algorithm analysis treats all basic operations as equally costly, which hides significant differences in time, energy consumption, and cost between different types of computations on modern processors. We propose a…