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Subclinical leaflet thrombosis (SLT) is a potentially serious complication of aortic valve replacement with a bioprosthetic valve in which blood clots form on the replacement valve. SLT is associated with increased risk of transient…
Many foraging microorganisms rely upon cellular transport networks to deliver nutrients, fluid and organelles between different parts of the organism. Networked organisms ranging from filamentous fungi to slime molds demonstrate a…
Networked control systems (NCS) are spatially distributed systems where communication among plants, sensors, actuators and controllers occurs in a shared communication network. NCS have been studied for the last ten years and important…
Recent advances in metagenomics have revealed macroecological patterns or "laws" describing robust statistical regularities across microbial communities. Stochastic logistic models (SLMs), which treat species as independent -- akin to ideal…
Quantum many-fermion systems give rise to diverse states of matter that often reveal themselves in distinctive transport properties. While some of these states can be captured by microscopic models accessible to numerical exact quantum…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
Supply chains (SCs), complex networks spanning from raw material acquisition to product delivery, with enterprises as interconnected nodes, play a pivotal role in organizational success. However, optimizing SCs remains challenging,…
We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics…
The Chord Length Sampling (CLS) algorithm is a powerful Monte Carlo method that models the effects of stochastic media on particle transport by generating on-the-fly the material interfaces seen by the random walkers during their…
Recent advances in large language models (LLMs) have demonstrated transformative potential across diverse fields. While LLMs have been applied to molecular simplified molecular input line entry system (SMILES) in computer-aided synthesis…
A numerical scheme is proposed for the simulation of reactive settling in sequencing batch reactors (SBRs) in wastewater treatment plants. Reactive settling is the process of sedimentation of flocculated particles (biomass; activated…
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…
We propose a new field-level emulator that bridges two simulators using unpaired simulation datasets. Our method leverages a flow-based approach to learn the likelihood transport from one simulator to the other. Since multiple transport…
Sequential sampling models (SSMs) are a widely used framework describing decision-making as a stochastic, dynamic process of evidence accumulation. SSMs popularity across cognitive science has driven the development of various software…
Modeling and simulation are transforming all fields of biology. Tools like AlphaFold have revolutionized structural biology, while molecular dynamics simulations provide invaluable insights into the behavior of macromolecules in solution or…
We identify putative load-bearing structures (bridges) in experimental colloidal systems studied by confocal microscopy. Bridges are co-operative structures that have been used to explain stability and inhomogeneous force transmission in…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
Simulations of scanning tunneling microscopy measurements for molecules on surfaces are traditionally based on a perturbative approach, most typically employing the Tersoff-Hamann method. This assumes that the STM tip is far from the sample…
Molecular crystals compose the current state of the art when it comes to organic-based optoelectronic applications. Charge transport is a crucial aspect of their performance. The ability to predict accurate electron mobility is needed in…
We formalize the derivation of a generalized coarse-graining $n$-resolved master equation by introducing a virtual detector counting the number of transferred charges in single-electron transport. Our approach enables the convenient…