Related papers: A Process Calculus for Molecular Interaction Maps
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…
Metal-organic frameworks (MOFs) offer a vast design space, and as such, computational simulations play a critical role in predicting their structural and physicochemical properties. However, MOF simulations remain difficult to access…
Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…
Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
An unified language for the communicative acts between agents is essential for the design of multi-agents architectures. Whatever the type of interaction (linguistic, multimodal, including particular aspects such as force feedback),…
Molecular communication is a biologically-inspired method of communication with attractive properties for microscale and nanoscale devices. In molecular communication, messages are transmitted by releasing a pattern of molecules at a…
The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small…
We have applied the graph theory to estimation of interactions between electronic excitations in molecular crystals. Intramolecular and intermolecular excitations have been considered. The intermolecular interactions contain molecular…
Mean-field molecular dynamics based on path integrals is used to approximate canonical quantum observables for particle systems consisting of nuclei and electrons. A computational bottleneck is the sampling from the Gibbs density of the…
Many interesting and useful symbolic computation algorithms manipulate mathematical expressions in mathematically meaningful ways. Although these algorithms are commonplace in computer algebra systems, they can be surprisingly difficult to…
We demonstrate that the algorithmic information content of a system is deeply connected to its potential dynamics, thus affording an avenue for moving systems in the information-theoretic space and controlling them in the phase space. To…
Optical chemical structure recognition (OCSR) systems aim to extract the molecular structure information, usually in the form of molecular graph or SMILES, from images of chemical molecules. While many tools have been developed for this…
Recently, action recognition has been dominated by transformer-based methods, thanks to their spatiotemporal contextual aggregation capacities. However, despite the significant progress achieved on scene-related datasets, they do not…
One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…
Processing in Memory (PIM) and similar terms such as Compute In Memory (CIM), Logic in Memory (LIM), In Memory Computing (IMC), and Near Memory Computing (NMC) have gained attention recently as a potentially ``revolutionary new'' technique.…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
Motivated by the fact that living cells use molecular circuits (i.e. a set of chemical reactions) for information processing, this paper investigates the problem of designing molecular circuits for demodulation. In our earlier work, we use…
We propose a hybrid probabilistic process calculus for modelling and reasoning on cyber-physical systems (CPSs). The dynamics of the calculus is expressed in terms of a probabilistic labelled transition system in the SOS style of Plotkin.…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…