TY - JOUR
T1 - Perspective on Integrative Simulations of Bioenergetic Domains
AU - Pirnia, Adam
AU - Maqdisi, Ranel
AU - Mittal, Sumit
AU - Sener, Melih
AU - Singharoy, Abhishek
N1 - Publisher Copyright:
© 2024 American Chemical Society.
PY - 2024/4/11
Y1 - 2024/4/11
N2 - Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.
AB - Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.
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U2 - 10.1021/acs.jpcb.3c07335
DO - 10.1021/acs.jpcb.3c07335
M3 - Review article
C2 - 38562105
AN - SCOPUS:85189535231
SN - 1520-6106
VL - 128
SP - 3302
EP - 3319
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
IS - 14
ER -