Modeling of Nanomachine/Micromachine Crowds: Interplay between the Internal State and Surroundings

Abstract

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 enzymes. The working cycles of these machines are often coupled with their internal motion (conformational changes). In the crowded environment of a cell, motion interference between neighboring molecules is not negligible, and this interference can affect the reaction dynamics through machine operation. To simulate such a situation, we propose a reaction-diffusion model consisting of particles whose shape depends on an internal state variable, for crowds of nano-to micro-machines. The interference between nearby particles is naturally introduced through excluded volume repulsion. In the simulations, we observed segregation and flow-like patterns enhanced by crowding out of relevant molecules, as well as molecular synchronization waves and phase transitions. The presented model is simple and extensible for diverse molecular machinery, and may serve as a framework to study the interplay between the mechanical stress/strain network and the chemical reaction network in the cell. Applications to more macroscopic systems, e.g., crowds of cells, are also discussed.

Diverse behaviors in non-uniform chiral and non-chiral swarmalators

“…If , then , meaning that its inherent circular orbit is clockwise (CW). The nature of our model is similar to recent work by Togashi 45 , which maps an agent’s internal state/phase to its shape (radius), which affects how it interacts with its neighbors and thus the emergent collective behaviors.…”

Virtual Issue on Protein Crowding and Stability

“…35 In yet another twist, crowding in solution was found to modulate peptide-induced membrane pore formation 36 and a few studies examine crowding effects at larger scales, such as the stability of viral particles 37 and in a more abstract context of molecular machines operating cooperatively under crowded conditions. 38 Apart from structure and interactions, crowding also affects molecular diffusion. Building on the general notion that crowding slows diffusion, a few studies examine specific aspects of how crowder properties such as size and chemistry modulate translational and rotational diffusion 39,40 viscosity depends on protein association at high concentration.…”

“…In the case of lactate dehydrogenase, crowding affected the enzyme active site conformation as well as product release, whereas dihydropteroate synthase activity was either reduced or increased depending on ligand–osmolyte interactions . In yet another twist, crowding in solution was found to modulate peptide-induced membrane pore formation and a few studies examine crowding effects at larger scales, such as the stability of viral particles and in a more abstract context of molecular machines operating cooperatively under crowded conditions …”

Glassy dynamics of a model of bacterial cytoplasm with metabolic activities

“…(1) by commonly used MD simulation techniques with discretization of the time step ∆t [41]. The effect of conformational change in constituent particles with ATP consumption is treated as an effective volume change in particles [42]. We assume that each particle can take two states with different diameters: for the ith particle, the diameter is (1 + a)σ 0 i in one state and (1 − a)σ 0 i in the other, where σ 0 i is the reference diameter of the ith particle and a represents the amplitude of the active diameter change.…”