Related papers: A Spatial Calculus of Wrapped Compartments
The fabric of porous and fractured media contains solid regions (grains) and voids. The space conducting fluids is a system of connected voids with variable geometries. Relative to the grain sizes, the voids can be voluminous with three…
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…
We introduce a Geometry of Interaction model for higher-order quantum computation, and prove its adequacy for a full quantum programming language in which entanglement, duplication, and recursion are all available. Our model comes with a…
Modeling of high-dimensional data is very important to categorize different classes. We develop a new mixture model called Multinomial cluster-weighted model (MCWM). We derive the identifiability of a general class of MCWM. We estimate the…
We present multiscale models of cancer tumor invasion with components at the molecular, cellular, and tissue levels. We provide biological justifications for the model components, present computational results from the model, and discuss…
Spatial processes with nonstationary and anisotropic covariance structure are often used when modelling, analysing and predicting complex environmental phenomena. Such processes may often be expressed as ones that have stationary and…
Cell complexes (CCs) are a higher-order network model deeply rooted in algebraic topology that has gained interest in signal processing and network science recently. However, while the processing of signals supported on CCs can be described…
This survey concerns probabilistic models motivated by cooperative sequential adsorption (CSA) models. CSA models are widely used in physics and chemistry for modelling adsorption processes in which adsorption rates depend on the spatial…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Uncovering the structure of socioeconomic systems and timely estimation of socioeconomic status are significant for economic development. The understanding of socioeconomic processes provides foundations to quantify global economic…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and…
Coordination is essential for dynamic distributed systems whose components exhibit interactive and autonomous behaviors. Spatially distributed, locally interacting, propagating computational fields are particularly appealing for allowing…
Multivariate spatial-statistical models are often used when modeling environmental and socio-demographic processes. The most commonly used models for multivariate spatial covariances assume both stationarity and symmetry for the…
Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g., populations or communities). The analysis of such data often leads to a two-step approach where groups containing similar…
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to…
Spatial concurrent constraint programming (SCCP) is an algebraic model of spatial modalities in constrained-based process calculi; it can be used to reason about spatial information distributed among the agents of a system. This work…
Making sense of the world and acting in it relies on building simplified mental representations that abstract away aspects of reality. This principle of cognitive mapping is universal to agents with limited resources. Living organisms,…
Space and movement through space play an important role in many collective adaptive systems (CAS). CAS consist of multiple components interacting to achieve some goal in a system or environment that can change over time. When these…
This article proposes a new way to construct computationally efficient `wrappers' around fine scale, microscopic, detailed descriptions of dynamical systems, such as molecular dynamics, to make predictions at the macroscale `continuum'…