Related papers: Plumbing Analog of Molecular Computation
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
We propose a sampling algorithm relying on a collective variable (CV) of mid-size dimension modelled by a normalizing flow and using non-equilibrium dynamics to propose full configurational moves from the proposition of a refreshed value of…
Cells make use of semi-flexible biopolymers such as actin or intermediate filaments to control their local viscoelastic response by dynamically adjusting the concentration and type of cross-linker molecules. The microstructure of the…
Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…
The predictions of the geometric collective model (GCM) for different sets of Hamiltonian parameter values are related by analytic scaling relations. For the quartic truncated form of the GCM -- which describes harmonic oscillator, rotor,…
Molecular Communications (MC) is a bio-inspired paradigm for transmitting information using chemical signals, which can enable novel applications at the junction of biotechnology, nanotechnology, and information and communication…
Granular fluids consist of collections of activated mesoscopic or macroscopic particles (e.g., powders or grains) whose flows often appear similar to those of normal fluids. To explore the qualitative and quantitative description of these…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
In this work we introduce some preliminary analyses on the role of a semi-permeable membrane in the dynamics of a stochastic model of catalytic reaction sets (CRSs) of molecules. The results of the simulations performed on ensembles of…
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown,…
Engineering simple, artificial models of living cells allows synthetic biologists to study cellular functions under well-controlled conditions. Reconstituting multicellular behaviors with synthetic cell-mimics is still a challenge because…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
Molecular communication (MC) is a communication paradigm in which information is conveyed through the controlled release, propagation, and reception of molecules. Many envisioned healthcare applications of MC are expected to operate inside…
A key challenge in systems biology is the elucidation of the underlying principles, or fundamental laws, which determine the cellular phenotype. Understanding how these fundamental principles are altered in diseases like cancer is important…
We develop, analyse and numerically simulate a model of a prototype, glucose-driven, rhythmic drug delivery device, aimed at hormone therapies, and based on chemomechanical interaction in a polyelectrolyte gel membrane. The pH-driven…
Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making…
This paper presents a Markov-based system model for microfluidic molecular communication (MC) channels. By discretizing the advection-diffusion dynamics, the proposed model establishes a physically consistent state-space formulation. The…
Motivated by the perspective of advanced time-series prediction and exploitation of Quantum Reservoir Computing (QRC), we explored the design and implementation of a Hybrid Photonic-Quantum Reservoir Computing (HPQRC) paradigm. It brings…
Unconventional computing explores multi-scale platforms connecting molecular-scale devices into networks for the development of scalable neuromorphic architectures, often based on new materials and components with new functionalities. We…
Understanding the dynamics of phase boundaries in fluids requires quantitative knowledge about the microscale processes at the interface. We consider the sharp-interface motion of compressible two-component flow, and propose a heterogeneous…