@article {Rey1992, title = {Effect of double bonds on the dynamics of hydrocarbon chains}, journal = {Journal of Chemical Physics}, volume = {97}, year = {1992}, pages = {1240{\textendash}1249}, abstract = {Brownian dynamics simulations of isolated 18-carbon chains have been performed, both for saturated and unsaturated hydrocarbons. The effect of one or several (nonconjugated) double bonds on the properties of the chains is discussed in terms of both equilibrium and dynamic properties. The introduction of a cis double bond increases the relaxation rates of the unsaturated chain with respect to the saturated alkane. On the other hand, coupling effects in the torsional transitions around a trans double bond make the dynamics of this unsaturated chain very similar to the saturated one. Based on these results, the parameters and moves of a dynamic Monte Carlo algorithm are tuned to reproduce the observed behavior, providing an efficient method for the study of more complicated systems.}, keywords = {Algorithms, Brownian Movement, Chains, Coupling, Double Bonds, dynamics, equilibrium, Hydrocarbons, Monte Carlo Method, Relaxation, Saturation, simulation, Torsion}, doi = {10.1063/1.463250}, url = {http://smartech.gatech.edu/handle/1853/26936}, author = {Antonio Rey and Andrzej Koli{\'n}ski and Jeffrey Skolnick and Yehudi K. Levine} } @article {Levine1991, title = {Monte Carlo dynamics study of motions in cis-unsaturated hydrocarbon chains}, journal = {The Journal of Chemical Physics}, volume = {95}, year = {1991}, pages = {3826{\textendash}3834}, abstract = {A Monte Carlo dynamics study of the motions of hydrocarbon chains containing cis double bonds is presented. The simulations utilize the high-coordination {2 1 0} lattice for the simultaneous representation of the tetrahedrally bonded carbon atoms and the planar unsaturated segment. Results on single chains undergoing free motion in space and tethered to an impenetrable planar interface are reported. The introduction of a cis double bond into a hydrocarbon chain induces a slowdown in the dynamics. The simulations show this to be a universal result independent of the representation of the chain on the lattice. In contrast, polyunsaturated chains are found to be more mobile than saturated ones.}, keywords = {Bilayers, Chains, Chemical Bonds, Hydrocarbons, Hydrogen Bonds, Lipids, Molecular Motion, Monte Carlo Method, Temperature Effects}, doi = {10.1063/1.460782}, url = {http://smartech.gatech.edu/handle/1853/26899}, author = {Yehudi K. Levine and Jeffrey Skolnick and Andrzej Koli{\'n}ski} } @article {Kolinski1991, title = {Static and dynamic properties of a new lattice model of polypeptide chains}, journal = {The Journal of Chemical Physics}, volume = {94}, number = {5}, year = {1991}, pages = {3978}, abstract = {The equilibrium and dynamic properties of a new lattice model of proteins are explored in the athermal limit. In this model, consecutive α-carbons of the model polypeptide are connected by vectors of the type ({\textpm}2,{\textpm}1,0). In all cases, the chains have a finite backbone thickness which is close to that present in real proteins. Three different polypeptides are examined: polyglycine, polyalanine, and polyleucine. In the latter two cases, the side chains (whose conformations are extracted from known protein crystal structures) are included. For the equilibrium chain dimensions, with increasing side chain bulkiness, the effective chain length is smaller. The calculations suggest that these model polypeptides are in the same universality class as other polymer models. One surprising result is that although polyalanine and polyleucine have chiral sidechains, they do not induce a corresponding handedness of the main chain. For both polyleucine and polyalanine, the scaling of the self-diffusion constant and the terminal relaxation time are consistent with Rouse dynamics of excluded volume chains. Polyglycine exhibits a slightly stronger chain length dependence for these properties. This results from a finite length effect due to moderately long lived, local self-entanglements arising from the thin effective cross section of the chain backbone.}, keywords = {Alanines, Chains, Glycine, Lattice Dynamics, Polypeptides, Proteins, Relaxation Time, Self-Diffusion}, issn = {00219606}, doi = {10.1063/1.460675}, url = {http://link.aip.org/link/JCPSA6/v94/i5/p3978/s1\&Agg=doi}, author = {Andrzej Koli{\'n}ski and Mariusz Milik and Jeffrey Skolnick} } @article {Milik1990, title = {Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model}, journal = {The Journal of Chemical Physics}, volume = {93}, number = {6}, year = {1990}, pages = {4440{\textendash}4446}, abstract = {The static and dynamic properties of a dense system of flexible lattice chain molecules, one of whose ends is constrained to lie near an impenetrable interface, have been studied by means of the dynamic Monte Carlo method. It is found that increasing the surface density of the chains in the layer increases the orientational order. The value of the order parameter of the chain segments decreases with increasing distance from the interace. The short time dynamics of the model chains are similar to those observed in polymer melts. Then, there is a time regime of strongly hindered collective motion at intermediate distance scales. Finally, for distances greater than the chain dimensions, free lateral diffusion of the chains is recovered. It is shown that the model exhibits many features of the real systems such as detergents on a surface and lipid bilayers.}, keywords = {Bilayers, Chains, Constraints, Density, Interface Phenomena, Lipids, Liquid Structure, Membranes, Monte Carlo Method, Order Parameters, Orientation}, url = {http://link.aip.org/link/JCPSA6/v93/i6/p4440/s1}, author = {Mariusz Milik and Andrzej Koli{\'n}ski and Jeffrey Skolnick} } @article {Kolinski1987b, title = {Does reptation describe the dynamics of entangled, finite length polymer systems? A model simulation}, journal = {The Journal of Chemical Physics}, volume = {86}, year = {1987}, pages = {1567{\textendash}1585}, abstract = {In order to examine the validity of the reptation model of motion in a dense collection of polymers, dynamic Monte Carlo (MC) simulations of polymer chains composed of n beads confined to a diamond lattice were undertaken as a function of polymer concentration ϕ and degree of polymerization n. We demonstrate that over a wide density range these systems exhibit the experimentally required molecular weight dependence of the center-of-mass self-diffusion coefficient D\~{}n-2.1 and the terminal relaxation time of the end-to-end vector τR\~{}n3.4. Thus, these systems should represent a highly entangled collection of polymers appropriate to look for the existence of reptation. The time dependence of the average single bead mean-square displacement, as well as the dependence of the single bead displacement on position in the chain were examined, along with the time dependence of the center-of-mass displacement. Furthermore, to determine where in fact a well-defined tube exists, the mean-square displacements of a polymer chain down and perpendicular to its primitive path defined at zero time were calculated, and snapshots of the primitive path as a function of time are presented. For an environment where all the chains move, no evidence of a tube, whose existence is central to the validity of the reptation model, was found. However, if a single chain is allowed to move in a partially frozen matrix of chains (where all chains but one are pinned every ne beads, and where between pin points the other chains are free to move), reptation with tube leakage is recovered for the single mobile chain. The dynamics of these chains possesses aspects of Rouse-like motion; however, unlike a Rouse chain, these chains undergo highly cooperative motion that appears to involve a backflow between chains to conserve constant average density. While these simulations cannot preclude the onset of reptation at higher molecular weight, they strongly argue at a minimum for the existence with increasing n of a crossover regime from simple Rouse dynamics in which reptation plays a minor role at best.}, keywords = {Chains, Computerized Simulation, dynamics, Monte Carlo Method, Polymers}, doi = {10.1063/1.452196}, url = {http://link.aip.org/link/JCPSA6/v86/i3/p1567/s1}, author = {Andrzej Koli{\'n}ski and Jeffrey Skolnick and Robert Yaris} } @article {Kolinski1987a, title = {Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric melt}, journal = {The Journal of Chemical Physics}, volume = {86}, year = {1987}, pages = {7164{\textendash}7174}, abstract = {Dynamic Monte Carlo simulations of long chains confined to a cubic lattice system at a polymer volume fraction of ϕ=0.5 were employed to investigate the dynamics of polymer melts. It is shown that in the range of chain lengths n, from n=64 to n=800 there is a crossover from a weaker dependence of the diffusion coefficient on chain length to a much stronger one, consistent with D\~{}n-2. Since the n-2 scaling relation signals the onset of highly constrained dynamics, an analysis of the character of the chain contour motion was performed. We found no evidence for the well-defined tube required by the reptation model of polymer melt dynamics. The lateral motions of the chain contour are still large even in the case when n=800, and the motion of the chain is essentially isotropic in the local coordinates. Hence, the crossover to the D\~{}n-2 regime with increasing chain length of this monodisperse model melt is not accompanied by the onset of reptation dynamics.}, keywords = {Chains, Computerized Simulation, dynamics, Liquid Structure, Melts, Monte Carlo Method, Polymers}, url = {http://link.aip.org/link/JCPSA6/v86/i12/p7164/s1}, author = {Andrzej Koli{\'n}ski and Jeffrey Skolnick and Robert Yaris} } @article {Kolinski1987c, title = {Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. II. Probe polymer in a matrix of different degrees of polymerization}, journal = {The Journal of Chemical Physics}, volume = {86}, year = {1987}, pages = {7174{\textendash}7180}, abstract = {The dynamics of a probe chain consisting of nP =100 segments in a matrix of chains of length of nM=50 up to nM=800 at a total volume fraction of polymer ϕ=0.5 have been simulated by means of cubic lattice Monte Carlo dynamics. The diffusion coefficient of the probe chain over the range of nM under consideration decreases by about 30\%, a behavior rather similar to that seen in real melts of very long chains. Furthermore, the analysis of the probe chain motion shows that the mechanism of motion is not reptation-like and that the cage effect of the matrix is negligible. That is, the local fluctuations of the topological constraints imposed by the long matrix chains (even for nM=800) are sufficiently large to provide for essentially isotropic, but somewhat slowed down, motion of the probe, nP =100, chains relative to the homopolymer melt. The results of these MC experiments are discussed in the context of theoretical predictions and experimental findings for related systems.}, keywords = {Chains, Computerized Simulation, dynamics, Liquid Structure, Matrix Isolation, Melts, Monte Carlo Method, Polymerization, Polymers}, doi = {10.1063/1.452367}, url = {http://link.aip.org/link/JCPSA6/v86/i12/p7174/s1}, author = {Andrzej Koli{\'n}ski and Jeffrey Skolnick and Robert Yaris} } @article {Kolinski1986b, title = {The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model system}, journal = {The Journal of Chemical Physics}, volume = {85}, year = {1986}, pages = {3585{\textendash}3597}, abstract = {Monte Carlo simulations have been performed on a diamond lattice model of semiflexible polymers for a range of flexibilities and a range of chain lengths from 50 to 800 segments. The model includes both repulsive (excluded volume) and attractive segment{\textendash}segment interactions. It is shown that the polymers group into two classes, {\textquoteleft}{\textquoteleft}flexible{\textquoteright}{\textquoteright} and {\textquoteleft}{\textquoteleft}stiff.{\textquoteright}{\textquoteright} The flexible polymers exhibit decreasing chain dimensions as the temperature decreases with a gradual collapse from a loose random coil, high temperature state to a dense random coil, low temperature state. The stiffer polymers, on the other hand, exhibit increasing chain dimensions with decreasing temperature until at a critical temperature there is a sudden collapse to an ordered high density, low temperature state. This difference is due to the relative strength of the segment{\textendash}segment attractive interactions compared to the energetic preference for a trans conformational state over a gauche state. When the attractive interaction is relatively strong (flexible case) the polymer starts to collapse before rotational degrees of freedom freeze out, leading to a disordered dense state. When the attractive interaction is relatively weak (stiff case) the polymer starts to freeze out rotational degrees of freedom before it finally collapses to a highly ordered dense state.}, keywords = {Chains, Computerized Simulation, Conformational Changes, Diamond Lattices, Flexibility, Mathematical Models, Molecular Structure, Monte Carlo Method, Polymers}, doi = {10.1063/1.450930}, url = {http://link.aip.org/link/JCPSA6/v85/i6/p3585/s1}, author = {Andrzej Koli{\'n}ski and Jeffrey Skolnick and Robert Yaris} } @article {277, title = {Monte Carlo study of dynamics of the multichain polymer system on the tetrahedral lattice}, journal = {The Journal of Chemical Physics}, volume = {79}, year = {1983}, pages = {1523-1526}, publisher = {AIP}, abstract = {Diffusion of the chain molecules in the concentrated solutions was studied by means of the computer simulation method. The computations were made for various chain lengths and polymer concentrations. It was observed that the rate of diffusion of the polymer chains strongly depends on the chain length according to the relation D∝n-b. It was found that the value of exponent b increases with the polymer concentration.}, keywords = {Chains, Computerized Simulation, Diffusion, dynamics, Monte Carlo Method, Polymers, solutions}, doi = {10.1063/1.445944}, url = {http://link.aip.org/link/?JCP/79/1523/1}, author = {Andrzej Koli{\'n}ski and Piotr Romiszowski} }