Related papers: Calculating Voronoi diagrams using simple chemical…
Molecule- and particle-based simulations provide the tools to test, in microscopic detail, the validity of classical nucleation theory. In this endeavour, determining nucleation mechanisms and rates for phase separation requires an…
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…
Automated and high-throughput quantum chemical investigations into chemical processes have become feasible in great detail and broad scope. This results in an increase in complexity of the tasks and in the amount of generated data. An…
Symbolic Mathematical tasks such as integration often require multiple well-defined steps and understanding of sub-tasks to reach a solution. To understand Transformers' abilities in such tasks in a fine-grained manner, we deviate from…
When a voltage is applied across a thin layer of cholesteric liquid crystal, fingers of cholesteric alignment can form and propagate in the layer. In computer simulation, based on experimental laboratory results, we demonstrate that these…
We present a new open source code for massive parallel computation of Voronoi tessellations(VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several…
The precise control of complex reactions is critical for biological processes yet our inability to design for specific outcomes limits the development of synthetic analogues. Here, we leverage differentiable simulators to design nontrivial…
Chemical reactions can be understood as transformations of multigraphs (molecules) that preserve vertex labels (atoms) and degrees (sums of bonding and non-bonding electrons), thereby implying the atom-atom map of a reaction. The…
In distributed mobile sensing applications, networks of agents that are heterogeneous respecting both actuation as well as body and sensory footprint are often modelled by recourse to power diagrams --- generalized Voronoi diagrams with…
Computing the Voronoi diagram of mixed geometric objects in $R^3$ is challenging due to the high cost of exact geometric predicates via Cylindrical Algebraic Decomposition (CAD). We propose an efficient exact verification framework that…
In the Hausdorff Voronoi diagram of a family of \emph{clusters of points} in the plane, the distance between a point $t$ and a cluster $P$ is measured as the maximum distance between $t$ and any point in $P$, and the diagram is defined in a…
We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by…
Angular Voronoi diagram was introduced by Asano et al. as fundamental research for a mesh generation. In an angular Voronoi diagram, the edges are curves of degree three. From view of computational robustness we need to treat the curves…
We consider the Voronoi diagram generated by $n$ i.i.d. $\mathbb{R}^{d}$-valued random variables with an arbitrary underlying probability density function $f$ on $\mathbb{R}^{d}$, and analyse the asymptotic behaviours of certain geometric…
The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing…
The transition from ordered to disordered structures in Voronoi tessellation is obtained by perturbing the seeds that were originally identified with two types of lattice in 2D and one type in 3D. The area in 2D and the volume in 3D are…
Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…