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Retrosynthesis poses a key challenge in biopharmaceuticals, aiding chemists in finding appropriate reactant molecules for given product molecules. With reactants and products represented as 2D graphs, retrosynthesis constitutes a…
We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations…
MuSim is a new user-friendly program designed to interface to many different particle simulation codes, regardless of their data formats or geometry descriptions. It presents the user with a compelling graphical user interface that includes…
Computational chemistry has become an indispensable tool for generating data and insights, pervading all branches of experimental chemistry. Its most central concept is the potential energy hypersurface, key to all chemistry and materials…
A variety of simulation methodologies have been used for modeling reaction-diffusion dynamics -- including approaches based on Differential Equations (DE), the Stochastic Simulation Algorithm (SSA), Brownian Dynamics (BD), Green's Function…
Realistic simulation is critical for applications ranging from robotics to animation. Traditional analytic simulators sometimes struggle to capture sufficiently realistic simulation which can lead to problems including the well known…
In this paper we present computational techniques to investigate the solutions of two-component, nonlinear reaction-diffusion (RD) systems on arbitrary surfaces. We build on standard techniques for linear and nonlinear analysis of RD…
This paper introduces AcCoRD (Actor-based Communication via Reaction-Diffusion) version 1.0. AcCoRD is a sandbox reaction-diffusion solver designed for the study of molecular communication systems. It uses a hybrid of microscopic and…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Understanding the evolution of electrified solid-liquid interfaces during electrochemical reactions is crucial. However, capturing the dynamic behavior of the interfaces with high temporal resolution and accuracy over long timescales…
We discuss important aspects of HCI research regarding Research Data Management (RDM) to achieve better publication processes and higher reuse of HCI research results. Various context elements of RDM for HCI are discussed, including…
Low-dose CT (LDCT) denoising remains an important yet challenging problem in medical imaging. Although recent learning-based methods have shown promising performance, those optimized using classical pixel-level objectives often produce…
Cross-reactions and other systematic issues generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key…
Mastering computational architectures is essential for developing fast and power-efficient programs. Our advanced simulator empowers both IT students and professionals to grasp the fundamentals of superscalar RISC-V processors, HW/SW…
Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
RRAM technology has experienced explosive growth in the last decade, with multiple device structures being developed for a wide range of applications. However, transitioning the technology from the lab into the marketplace requires the…
The reaction-diffusion master equation (RDME) is a lattice-based stochastic model for spatially resolved cellular processes. It is often interpreted as an approximation to spatially continuous reaction-diffusion models, which, in the limit…
One of the current challenges in physically-based simulations, and, more specifically, fluid simulations, is to produce visually appealing results at interactive rates, capable of being used in multiple forms of media. In recent times, a…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…