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Diffusion models are a class of generative models that learn to synthesize samples by inverting a diffusion process that gradually maps data into noise. While these models have enjoyed great success recently, a full theoretical…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot…
In this paper, we present an analytical model for a diffusive molecular communication (MC) system with a reversible adsorption receiver in a fluid environment. The time-varying spatial distribution of the information molecules under the…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
Morphogens are secreted signaling molecules that mediate tissue patterning and growth of embryonic tissues. They are secreted in a localized region and spread through the tissue to form a graded concentration profile. We present a…
Molecular communication (MC) can enable the transfer of information between nanomachines using molecules as the information carrier. In MC systems, multiple receiver nanomachines often co-exist in the same communication channel to serve…
The response of cells during spreading and motility is dictated by several multi-physics events, which are triggered by extracellular cues and occur at different time-scales. For this sake, it is not completely appropriate to provide a cell…
One of the important applications of molecular communication is the targeted drug delivery process in which the drug molecules are released toward the target (receiver) in a way that the side effects are minimized in the human body. As the…
Molecular Communication via Diffusion (MCvD) is a prominent small-scale technology, which roots from the nature. With solid analytical foundations on channel response and advanced modulation techniques, molecular single-input-single-output…
Diffusive molecular communication (DMC) is envisioned as a promising approach to help realize healthcare applications within bounded biological environments. In this paper, a DMC system within a biological spherical environment is…
Tumour spheroids have been the focus of a variety of mathematical models, ranging from Greenspan's classical study of the 1970s through to contemporary agent-based models. Of the many factors that regulate spheroid growth, mechanical…
Aggregation and fragmentation of single molecules in the cell environment lead to a spectrum of diffusivities and to statistical laws of movement very different from typical Brownian motion. Current models of intracellular transport do not…
Molecular communication is an expanding body of research. Recent advances in biology have encouraged using genetically engineered bacteria as the main component in the molecular communication. This has stimulated a new line of research that…
We develop a mesoscopic modeling framework for diffusion in a crowded environment, particularly targeting applications in the modeling of living cells. Through homogenization techniques we effectively coarse-grain a detailed microscopic…
Growing experimental evidence highlights the relevant role of mechanics in the physiology of solid tumours, even in their early stages. While most of the mathematical models describe tumour growth as a volumetric increase of mass in the…
In the simplest scenario, disk galaxies form predominantly in halos with high angular momentum and quiet recent assembly history, whereas spheroids are the slowly-rotating remnants of repeated merging events. We explore these assumptions…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
We present an efficient point-particle approach to simulate reaction-diffusion processes of spherical absorbing particles in the diffusion-limited regime, as simple models of cellular uptake. The exact solution for a single absorber is used…
The speed and the versatility of today's computers open up new opportunities to simulate complex biological systems. Here we review a computational approach recently proposed by us to model large tumor cell populations and spheroids, and we…