Related papers: Plumbing Analog of Molecular Computation
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
We cast the metabolism of interacting cells within a statistical mechanics framework considering both, the actual phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
Studying geological fluids mixing systems allows to understand interaction among water sources. The Hug model is an interaction point process model that can be used to estimate the number and the chemical composition of the water sources…
Chemical thermodynamic models of solvent and solute activities predict the equilibrium behaviour of aqueous solutions. How-ever, these models are semi-empirical. They represent micro-scale ion and solvent behaviours that control the…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving…
Artificial intelligence (AI) is reshaping computational and network biology by enabling new approaches to decode cellular communication networks. We introduce Hierarchical Molecular Language Models (HMLMs), a novel framework that models…
There is increasing evidence that mammalian cells not only crawl on substrates but can also swim in fluids. To elucidate the mechanisms of the onset of motility of cells in suspension, a model which couples actin and myosin kinetics to…
This report is concerned with the relevance of the microscopic rules, that implement individual neuronal activation, in determining the collective dynamics, under variations of the network topology. To fix ideas we study the dynamics of two…
The control of complex systems is of critical importance in many branches of science, engineering, and industry. Controlling an unsteady fluid flow is particularly important, as flow control is a key enabler for technologies in energy…
Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For…
The fluidic behavior of water at the micro/nano scale is studied by using of single DNA molecules as a model system. Stable curved DNA patterns with spans about one micron were generated by using of water flows, and observed by Atomic Force…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate…
In groundwater hydrology, geophysical imaging holds considerable promise for improving parameter estimation, due to the generally high resolution and spatial coverage of geophysical data. However, inversion of geophysical data alone cannot…
Molecular modeling, a central topic in quantum mechanics, aims to accurately calculate the properties and simulate the behaviors of molecular systems. The molecular model is governed by physical laws, which impose geometric constraints such…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…