Giovanni Bellesia | Searcharxiv

arXiv2015

Brownian dynamics simulations of an idealized chemical reaction network under spatial confinement and crowding conditions

We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of inert crowders has a non-nontrivial effect on the dynamics of the network and, consequently, that effective modeling efforts aiming at a general understanding of the behavior of biochemical networks in vivo should be stochastic in nature and based on an explicit representation of both spatial confinement and macromolecular crowding.

physics.bio-ph↗

arXiv2013

Sodium Chloride interaction with solvated and crystalline cellulose : sodium ion affects the tetramer and fibril in aqueous solution

Inorganic salts are a natural component of biomass which have a significant effect on the product yields from a variety of biomass conversion processes. Understanding their effect on biomass at the microscopic level can help discover their mechanistic role. We present a study of the effect of aqueous sodium chloride (NaCl) on the largest component of biomass, cellulose, focused on the thermodynamic and structural effect of a sodium ion on the cellulose tetramer, and fibril. Replica exchange molecular dynamics simulations of a cellulose tetramer reveal a number of preferred cellulose-Na contacts and bridging positions. Large scale MD simulations on a model cellulose fibril find that Na+ perturbs the hydroxymethyl rotational state population and consequently disrupts the "native" hydrogen bonding network.

physics.chem-ph↗