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The simulation of diffusion-based molecular communication systems with absorbing receivers often requires a high computational complexity to produce accurate results. In this work, a new a priori Monte Carlo (APMC) algorithm is proposed to…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…
Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be able to treat ever larger molecules or…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic…
Despite the recent progress in quantum computational algorithms for chemistry, there is a dearth of quantum computational simulations focused on material science applications, especially for the energy sector, where next generation sorbing…
Advancing temporal resolution in computation, signal modulation, and measurement is crucial for pushing the frontiers of modern science and technology. Optical resonators have recently demonstrated computational operations at frequencies…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Gaussian Boson Samplers are photonic quantum devices with the potential to perform tasks that are intractable for classical systems. As with other near-term quantum technologies, an outstanding challenge is to identify specific problems of…
This proposal presents a graph computing framework intending to support both online and offline computing on large dynamic graphs efficiently. The framework proposes a new data model to support rich evolving vertex and edge data types. It…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
A mathematical model of the process of carbon capture in a packed column by adsorption is developed and analysed. First a detailed study is made of the governing equations. Due to the complexity of the internal geometry it is standard…
This paper introduces a novel, fast atomic-snapshot protocol for asynchronous message-passing systems. In the process of defining what ``fast'' means exactly, we spot a few interesting issues that arise when conventional time metrics are…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…