The explicit bonding reaction ensemble Monte Carlo method
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F24%3A10485760" target="_blank" >RIV/00216208:11310/24:10485760 - isvavai.cz</a>
Result on the web
<a href="https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=Yu9s~yj_Be" target="_blank" >https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=Yu9s~yj_Be</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1063/5.0226122" target="_blank" >10.1063/5.0226122</a>
Alternative languages
Result language
angličtina
Original language name
The explicit bonding reaction ensemble Monte Carlo method
Original language description
We present the explicit bonding Reaction ensemble Monte Carlo (eb-RxMC) method, designed to sample reversible bonding reactions in macromolecular systems in thermodynamic equilibrium. Our eb-RxMC method is based on the reaction ensemble method; however, its implementation differs from the latter by the representation of the reaction. In the eb-RxMC implementation, we are adding or deleting bonds between existing particles, instead of inserting or deleting particles with different chemical identities. This new implementation makes the eb-RxMC method suitable for simulating the formation of reversible linkages between macromolecules, which would not be feasible with the original implementation. To enable coupling of our eb-RxMC algorithm with molecular dynamics algorithm for the sampling of the configuration space, we biased the sampling of reactions only within a certain inclusion radius. We validated our algorithm using a set of ideally behaving systems undergoing dimerization and polycondensation reactions, for which analytical results are available. For dimerization reactions with various equilibrium constants and initial compositions, the degree of conversion measured in our simulations perfectly matched the reference values given by the analytical equations. We also showed that this agreement is not affected by the arbitrary choice of the inclusion radius or the stiffness of the harmonic bond potential. Next, we showed that our simulations can correctly match the analytical results for the distribution of the degree of polymerization and end-to-end distance of ideal chains in polycondensation reactions. Altogether, we demonstrated that our eb-RxMC simulations correctly sample both reaction and configuration spaces of these reference systems, opening the door to future simulations of more complex interacting macromolecular systems.
Czech name
—
Czech description
—
Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
<a href="/en/project/GC21-31978J" target="_blank" >GC21-31978J: Simulations of reaction equilibria in polymer systems - method development and applications</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Physics
ISSN
0021-9606
e-ISSN
1089-7690
Volume of the periodical
161
Issue of the periodical within the volume
9
Country of publishing house
US - UNITED STATES
Number of pages
12
Pages from-to
094906
UT code for WoS article
001304263600011
EID of the result in the Scopus database
2-s2.0-85203104268