相关论文: Modelling an Ammonium Transporter with SCLS
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems.…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
We present a stochastic simulation method designed to study at an atomic resolution the growth kinetics of compounds characterized by the sp3-type bonding symmetry. Formalization and implementation details are discussed for the particular…
We present a novel probabilistic deep learning approach, the 'Stochastic Latent Transformer' (SLT), designed for the efficient reduced-order modelling of stochastic partial differential equations. Stochastically driven flow models are…
We present AutoTraces, an autoregressive vision-language-trajectory model for robot trajectory forecasting in humam-populated environments, which harnesses the inherent reasoning capabilities of large language models (LLMs) to model complex…
Increasing availability and quality of actual, as opposed to scheduled, open transport data offers new possibilities for capturing the spatiotemporal dynamics of the railway and other networks of social infrastructure. One way to describe…
Water flow in plant tissues takes place in two different physical domains separated by semipermeable membranes: cell insides and cell walls. The assembly of all cell insides and cell walls are termed symplast and apoplast, respectively.…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Efficient stochastic simulation algorithms are of paramount importance to the study of spreading phenomena on complex networks. Using insights and analytical results from network science, we discuss how the structure of contacts affects the…
We establish results for the first sensitivity analysis of the stochastic fluid models (SFMs). We derive expressions for the sensitivity analysis of the key stationary and transient (time-dependent) quantities of this class of models. We…
Style transfer algorithms strive to render the content of one image using the style of another. We propose Style Transfer by Relaxed Optimal Transport and Self-Similarity (STROTSS), a new optimization-based style transfer algorithm. We…
A new approach to computing the equilibria and steady-states of biomolecular systems modelled by bond graphs is presented. The approach is illustrated using a model of a biomolecular cycle representing a membrane transporter and a model of…
The emerging demand for advanced structural and biological materials calls for novel modeling tools that can rapidly yield high-fidelity estimation on materials properties in design cycles. Lattice spring model (LSM), a coarse-grained…
Background: The growing demand for efficient and deployable language models has led to increased interest in Small Language Models (SLMs). However, existing research remains fragmented, lacking a unified lifecycle perspective. Objective:…
In this paper, two flux-only least-squares finite element methods (LSFEM) for the linear hyperbolic transport problem are developed. The transport equation often has discontinuous solutions and discontinuous inflow boundary conditions, but…
Recent State Space Models (SSMs) such as S4, S5, and Mamba have shown remarkable computational benefits in long-range temporal dependency modeling. However, in many sequence modeling problems, the underlying process is inherently modular…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
The objective of the paper is to evaluate the ability of reactive transport models and their numerical implementations (such as MIN3P) to simulate simple microbial transformations in conditions of chemostat or gradostat models, that are…
In this paper we study the dynamics of stochastic microorganism flocculation models. Given the strong influence of environmental and seasonal fluctuations that are present in these models, we propose a stochastic model that includes…
Stochastic simulators are an indispensable tool in many branches of science. Often based on first principles, they deliver a series of samples whose distribution implicitly defines a probability measure to describe the phenomena of…