相关论文: Representing catalytic mechanisms with rule compos…

We study the predictability of emergent phenomena in complex systems. Using nearest neighbor, one-dimensional Cellular Automata (CA) as an example, we show how to construct local coarse-grained descriptions of CA in all classes of Wolfram's…

Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…

Phosphorylation, the enzyme-mediated addition of a phosphate group to a molecule, is a ubiquitous chemical mechanism in biology. Multisite phosphorylation, the addition of phosphate groups to multiple sites of a single molecule, may be…

Hypergraphs provide a natural way to represent polyadic relationships in network data. For large hypergraphs, it is often difficult to visually detect structures within the data. Recently, a scalable polygon-based visualization approach was…

-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…

Graphs are a fundamental abstraction in computer science and discrete mathematics, where information is encoded in their combinatorial structure. Graph-reduction techniques aim at simplifying graphs while preserving selected structural…

The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…

The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…

We present a method to simplify expressions in the context of an equational theory. The basic ideas and concepts of the method have been presented previously elsewhere but here we tackle the difficult task of making it efficient in…

Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on…

Generalized Reactivity(1) (GR(1)) synthesis is a reactive synthesis approach in which the specification is split into two parts: a symbolic game graph, describing the safe transitions of a system, a liveness specification in a subset of…

Tackling molecular optimization problems using conventional computational methods is challenging, because the determination of the optimized configuration is known to be an NP-hard problem. Recently, there has been increasing interest in…

Recent works in multimodal recommendations, which leverage diverse modal information to address data sparsity and enhance recommendation accuracy, have garnered considerable interest. Two key processes in multimodal recommendations are…

A flexible treatment for gas- and aerosol-phase chemical processes has been developed for models of diverse scale, from box models up to global models. At the core of this novel framework is an "abstracted aerosol representation" that…

Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…

Cloth manipulation is very relevant for domestic robotic tasks, but it presents many challenges due to the complexity of representing, recognizing and predicting the behaviour of cloth under manipulation. In this work, we propose a generic,…

A formalism for the study of highly interacting electronic systems is presented. The proposed scheme is based on two key concepts: composite operators and algebra constraints. Composite field operators, that naturally appear as a…

We develop a new thermodynamic approach to stochastic graph-rewriting. The ingredients are a finite set of reversible graph-rewriting rules called generating rules, a finite set of connected graphs P called energy patterns and an energy…

Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…

Existing research on action recognition treats activities as monolithic events occurring in videos. Recently, the benefits of formulating actions as a combination of atomic-actions have shown promise in improving action understanding with…