Fig. 2: Behavior of a motor away from equilibrium. | Nature Communications

Fig. 2: Behavior of a motor away from equilibrium.

From: Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics

Fig. 2

Motor II was simulated with \({\mu }_{{{{{{{{\rm{FTC}}}}}}}}}^{\prime}=0.5\), \({\mu }_{{{{{{{{\rm{ETC}}}}}}}}}^{\prime}=-10\), and \({\mu }_{{{{{{{{\rm{C}}}}}}}}}^{\prime}=-10\) corresponding to an average of about 8.5 FTC molecules, 0.1 ETC molecules, and 0.9 C particles in the simulation box. a The distribution for the shuttling ring position, measured as the index of large ring particle nearest to the shuttling ring center of mass, for NESS and equilibrium (Eq.) conditions in the absence of FTC, ETC, and C. An unfolded schematic of the large ring is superimposed over the particle indices to visualize the particle types at each location around the large ring. Orange particles are binding sites, white particles are catalytic sites, and black particles are inert. b In the NESS conditions, the shuttling ring executes more clockwise (CW, orange) than counterclockwise (CCW, blue) cycles around the large ring when measured in the frame of the large ring. c Decomposition reactions FTC → ETC + C include those catalyzed by the motor (green) and spontaneous reactions in the bulk, which combine to give the total (pink). Decompositions occurring within 2 distance units of a white catalytic particle are classified as having been catalyzed by the motor. Means and standard deviations are generated from 50 independent simulations for each motor.

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