Molecular dynamics simulation of the collapse of a single polymer chain

Computer simulation of electrospinning. Part I. Effect of solvent in electrospinning

“…K l is the bond-stretching constant; K q is the bond-bending constant; 3 segment is Lennard-Jone parameters between molecule segments; 3 v is Lennard-Jone parameters between chain segment and solvent; 3 hydro is Lennard-Jone parameters between chain segment and water molecule [27][28][29].…”

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

“…If the only interaction is self-avoidance, a single chain is in a coil phase whose large-scale behavior is in the same class as a self-avoiding walk. Upon adding an attractive interaction between pairs of non-adjacent monomers, the chain undergoes compaction into a highly degenerate compact phase at low temperatures [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 ]. While the notion of phases and phase transitions for a polymeric chain strictly refers to a chain with an infinite number of monomers, proteins are modest length chains, which yet exhibit several common characteristics.…”

Coil–globule transition in two-dimensional polymer chains in an explicit solvent

“…Theoretical studies were performed by means of mean field, scaling considerations and real space renormalization. 20–27 Numerous computer simulations were also carried out employing Monte Carlo, 24,28–41 Molecular Dynamics, 34,42–46 Brownian Dynamics 47,48 and Dissipative Particle Dynamics 49,50 methods. Studies of the homopolymer chain collapse process showed the mechanism of this process and the existence of an intermediate disordered structure called the molten globule having a dense core and molten shell.…”

“…3,[5][6][7][8][9][10][11][12][13][14][15][16][17][18][19] Theoretical studies were performed by means of mean field, scaling considerations and real space renormalization. [20][21][22][23][24][25][26][27] Numerous computer simulations were also carried out employing Monte Carlo, 24,[28][29][30][31][32][33][34][35][36][37][38][39][40][41] Molecular Dynamics, 34,[42][43][44][45][46] Brownian Dynamics 47,48 and Dissipative Particle Dynamics 49,50 methods. Studies of the homopolymer chain collapse process showed the mechanism of this process and the existence of an inte...…”