Sun, 06 Jul 2008 02:06:19 BST CiteULike: sas's library [505 articles] http://www.citeulike.org/user/sas CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/sas/article/2902674 <i>EPL (Europhysics Letters), Vol. 27, No. 7. (1994), pp. 549-554.</i><br /><br />Computer simulations of lattice systems have not been performed under constant pressure conditions since a volume change move involving the addition or removal of a whole lattice layer has a low acceptance probability. We propose a new method to improve the efficiency of the volume change move and thus allow for the simulation of lattice systems in the isothermal-isobaric ensemble. The method is shown to predict properties for lattice polymer systems in two and three dimensions in excellent agreement with thermodynamic integration results. Constant-Pressure Monte Carlo Simulations for Lattice Models AD Mackie AZ Panagiotopoulos D Frenkel SK Kumar doi:10.1209/0295-5075/27/7/010 EPL (Europhysics Letters), Vol. 27, No. 7. (1994), pp. 549-554. 2008-06-17T15:07:09-00:00 1994 EPL (Europhysics Letters) 27 7 549 554 constant isobaric lattice mc polymer pressure http://www.citeulike.org/user/sas/article/2877067 <i>Progress of Theoretical Physics (2000), pp. 330-335.</i> Electrophoresis of a Polyelectrolyte in a Space with Immobile Obstacles R Azuma H Takayama Progress of Theoretical Physics (2000), pp. 330-335. 2008-06-09T14:43:19-00:00 2000 Progress of Theoretical Physics 330 335 bfm electrophoresis http://www.citeulike.org/user/sas/article/2876945 <i>Physical Review E, Vol. 59, No. 1. (1 January 1999), 650.</i> Bond fluctuation method for a polymer undergoing gel electrophoresis Ryuzo Azuma Hajime Takayama doi:10.1103/PhysRevE.59.650 Physical Review E, Vol. 59, No. 1. (1 January 1999), 650. 2008-06-09T13:33:51-00:00 1999 Physical Review E 59 1 650 American Physical Society bfm electrophoresis http://www.citeulike.org/user/sas/article/2861300 <i>The Journal of Chemical Physics, Vol. 96, No. 3. (1992), pp. 1776-1783.</i> New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles AP Lyubartsev AA Martsinovski SV Shevkunov Vorontsov Velyaminov The Journal of Chemical Physics, Vol. 96, No. 3. (1992), pp. 1776-1783. 2008-06-04T14:42:54-00:00 1992 The Journal of Chemical Physics 96 3 1776 1783 AIP energy ensemble extended free mc http://www.citeulike.org/user/sas/article/1153438 <i>Physical Review Letters, Vol. 97, No. 24. (2006)</i><br /><br />By studying the relaxation of small amounts of short entangled “probe” chains in a high molecular weight matrix, we show that the deviations from reptation scaling of the longest relaxation time are not as much dominated by single-chain effects (usually referred to as contour length fluctuations or CLF) as assumed by current mesoscopic models but also originate to a very significant extent from mutual chain relaxation effects. This result is in fact consistent with literature data on tracer and self-diffusion. Moreover, tube theories also overpredict the influence of CLF on the plateau modulus. Improved theories, simulations, and careful experiments are urgently needed to resolve this important question. Do Deviations from Reptation Scaling of Entangled Polymer Melts Result from Single- or Many-Chain Effects? Chen Liu Roland Keunings Christian Bailly doi:10.1103/PhysRevLett.97.246001 Physical Review Letters, Vol. 97, No. 24. (2006) 2007-03-11T07:47:24-00:00 2006 Physical Review Letters 97 24 APS blend constraint linear probe release reptation http://www.citeulike.org/user/sas/article/2847306 <i>Progress in Polymer Science, Vol. 28, No. 1. (January 2003), pp. 115-172.</i><br /><br />Polymers are good glass formers and allow for the study of melts near the glass transition in (meta-)stable equilibrium. Theories of the glass transition imply such an equilibrium and can, hence, be tested by the study of polymer melts. After a brief summary of the basic experimental facts about the glass transition in polymers, the main theoretical concepts are reviewed: mode coupling theory (MCT), entropy theory, free-volume theory, the idea of a growing length describing the size of cooperative regions, etc. Then, two basic coarse-grained models of polymers are described, which have been developed aiming at a test of these concepts. The first model is the bond-fluctuation model on the simple cubic lattice; the second is a bead-spring model in the continuum. While the first model is studied by kinetic Monte Carlo methods, the second is studied by molecular dynamics simulation: the issue is addressed which aspects of the results are model-dependent and which aspects are generic and should universally apply, including real materials. Attempts to include chemical detail in order to describe real materials are discussed, too. It is shown that idealized MCT is a good description for the onset of slow relaxation ([`]cage effect') in the discussed model polymer melts, but the singularities at the critical temperature of MCT are rounded, and the correct description of the dynamics close to the calorimetric glass transition remains controversial. While the configurational entropy of the polymer melt does decrease strongly when the glass transition is approached, evidence is presented that the [`]entropy catastrophe' of the theory of Gibbs and Di Marzio is an artifact of inaccurate approximations. Simulations of polymer melts confined in a thin film geometry are also reviewed, emphasizing the question to which extent they shed light on the issue of a growing glass correlation length. Finally, we discuss the implications of the glass transition on the motion of polymers at larger length scales. It is shown that for short (non-entangled) chains the Rouse model stays essentially valid, the friction coefficient reflecting the slowing down as described by the [alpha]-relaxation, while for small-scale motions (e.g. [beta]-relaxation regime of MCT) the connectivity of the polymer is not very relevant. We conclude that the theories describe some aspects of vitrification phenomena correctly, but a unified description that puts all these phenomena into one coherent framework, does not yet exist. Glass transition of polymer melts: test of theoretical concepts by computer simulation Kurt Binder Jörg Baschnagel Wolfgang Paul doi:10.1016/S0079-6700(02)00030-8 Progress in Polymer Science, Vol. 28, No. 1. (January 2003), pp. 115-172. 2008-05-30T13:15:48-00:00 2003 Progress in Polymer Science 28 1 115 172 glass review simulation transition http://www.citeulike.org/user/sas/article/824802 <i>Physical Review Letters, Vol. 53, No. 22. (26 November 1984), 2145.</i><br /><br />Tracer diffusion coefficients D * of deuterated polystyrene of molecular weight M diffusing into polystyrene of molecular weight P are measured by means of an ion-beam analysis method. While for P > 200 000; these D * values are independent of P ; consistent with a reptation mechanism ( D * = D R ) for the diffusion of M chains; D * increases rapidly as P is decreased; in quantitative agreement with D * = D R + D CR ; where D CR is the diffusion coefficient of the M chain by constraint release. Limits of Reptation in Polymer Melts Peter Green Peter Mills Christopher Palmstrã¸m James Mayer Edward Kramer doi:10.1103/PhysRevLett.53.2145 Physical Review Letters, Vol. 53, No. 22. (26 November 1984), 2145. 2006-09-01T07:57:54-00:00 1984 Physical Review Letters 53 22 2145 American Physical Society binary blends constraint linear release reptation http://www.citeulike.org/user/sas/article/2830900 <i>Macromolecules, Vol. 19, No. 4. (1986), pp. 1108-1114.</i> Matrix effects on the diffusion of long polymer chains Peter Green Edward Kramer Macromolecules, Vol. 19, No. 4. (1986), pp. 1108-1114. 2008-05-25T15:53:40-00:00 1986 Macromolecules 19 4 1108 1114 blend chains constraint diffusion release http://www.citeulike.org/user/sas/article/2827979 <i>Macromolecules, Vol. 19, No. 6., pp. 1754-1760.</i> Effects of polydispersity on the linear viscoelastic properties of entangled polymers. 2. Comparison of viscosity and recoverable compliance with tube model predictions William Graessley Mark Struglinski Macromolecules, Vol. 19, No. 6., pp. 1754-1760. 2008-05-24T16:37:28-00:00 Macromolecules 19 6 1754 1760 constraint linear polydisperse release viscoelasticity http://www.citeulike.org/user/sas/article/2817180 <i>Current Opinion in Colloid & Interface Science, Vol. 6, No. 5-6. (November 2001), pp. 430-437.</i><br /><br />Recent developments in the fundamental understanding of the rheology and dynamics of particles in viscoelastic media are reviewed. Suspensions of particles dispersed in a complex fluid matrix are central to applications in the area of coatings, pharmaceuticals, filled polymer melts, nanocomposites and biomaterials. Recent studies have established the range of validity of the generalized Stokes-Einstein equation to describe the relationship between the linear rheological behavior of the viscoelastic medium and the displacement of dispersed particles due to applied oscillatory or fluctuating forces. The extension of such microrheological methods to account for interactions between particle pairs is discussed. The scope for practical implementation of microrheology to characterize viscoelasticity in particle/complex fluid mixtures used in the aforementioned applications is assessed. Rheology and dynamics of particles in viscoelastic media Michael Solomon Qiang Lu doi:10.1016/S1359-0294(01)00111-X Current Opinion in Colloid & Interface Science, Vol. 6, No. 5-6. (November 2001), pp. 430-437. 2008-05-20T16:42:45-00:00 2001 Current Opinion in Colloid & Interface Science 6 5-6 430 437 filled microrheology nanocomposites rheology viscoelastic http://www.citeulike.org/user/sas/article/2802688 <i>Polymer, Vol. 45, No. 26. (December 2004), pp. 8863-8870.</i><br /><br />A series of composites of polycarbonate (PC) with 23 different contents of multiwalled carbon nanotubes (MWNT) was produced by melt mixing using the masterbatch dilution method. In dielectric measurements, AC conductivity and complex permittivity data obtained in the frequency range between 10-3 and 107 Hz at room temperature indicated the electrical percolation threshold at about 1.0 wt%. The dynamic mode melt rheological measurements for the same samples at eight temperatures between 170 and 280 °C showed a visible change in the frequency dependence of dynamic moduli and the absolute value of the complex viscosity [eta]* particularly at low frequencies. In literature these changes are sometimes related to so called [`]percolation threshold concentration'. Applying this picture to our experimental data we have to assume that the percolation threshold is strongly dependent on the measurement temperature. It changes from about 5 to 0.5 wt% MWNT by increasing the measurement temperature from 170 to 280 °C, respectively. This temperature dependence cannot be explained by a classical liquid-solid transition but may be related to the existence of a combined nanotube-polymer network. Rheological and dielectrical characterization of melt mixed polycarbonate-multiwalled carbon nanotube composites Petra Pötschke Mahmoud Abdel-Goad Ingo Alig Sergej Dudkin Dirk Lellinger doi:10.1016/j.polymer.2004.10.040 Polymer, Vol. 45, No. 26. (December 2004), pp. 8863-8870. 2008-05-15T21:01:59-00:00 2004 Polymer 45 26 8863 8870 cnt mwnt nanocomposite rheology http://www.citeulike.org/user/sas/article/2802683 <i>Current Opinion in Colloid & Interface Science, Vol. 6, No. 5-6. (November 2001), pp. 464-470.</i><br /><br />Layered silicate based polymer nanocomposites have gained significant technological interest because of the recent commercialization of nylon 6 and polypropylene based materials. Aside from the natural interests in understanding and improving the processing of these hybrids, viscoelastic measurements have also proven to be a sensitive tool to probe the mesoscale structure and the strength of polymer-nanoparticle interactions. Rheology of polymer layered silicate nanocomposites Ramanan Krishnamoorti Koray Yurekli doi:10.1016/S1359-0294(01)00121-2 Current Opinion in Colloid & Interface Science, Vol. 6, No. 5-6. (November 2001), pp. 464-470. 2008-05-15T21:00:59-00:00 2001 Current Opinion in Colloid & Interface Science 6 5-6 464 470 nanocomposite rheology silicate http://www.citeulike.org/user/sas/article/2802680 <i>Macromolecules, Vol. 35, No. 23. (5 November 2002), pp. 8825-8830.</i><br /><br />Abstract: Polystyrene nanocomposites with functionalized single-walled carbon nanotubes (SWNTs), prepared by the in-situ generation and reaction of organic diazonium compounds, were characterized using melt-state linear dynamic viscoelastic measurements. These were contrasted to the properties of polystyrene composites prepared with unfunctionalized SWNTs at similar loadings. The functionalized nanocomposites demonstrated a percolated SWNT network structure at concentrations of 1 vol % SWNT, while the unfunctionalized SWNT-based composites at twice the loading of SWNT exhibited viscoelastic behavior comparable to that of the unfilled polymer. This formation of the SWNT network structure for the functionalized SWNT-based composites is because of the improved compatibility between the SWNTs and the polymer matrix and the resulting better dispersion of the SWNT. Dispersion of Functionalized Carbon Nanotubes in Polystyrene CA Mitchell JL Bahr S Arepalli JM Tour R Krishnamoorti doi:10.1021/ma020890y Macromolecules, Vol. 35, No. 23. (5 November 2002), pp. 8825-8830. 2008-05-15T20:59:53-00:00 2002 Macromolecules 35 23 8825 8830 cnt dispersion nanocomposite polystyrene swnt http://www.citeulike.org/user/sas/article/2802679 <i>Macromolecules, Vol. 30, No. 14. (14 July 1997), pp. 4097-4102.</i><br /><br />Abstract: The rheology of end-tethered polymer layered silicate nanocomposites is investigated using linear viscoelastic measurements in oscillatory shear with small strain amplitudes. Two systems consisting of poly(-caprolactone) and nylon-6 with varying amounts of layered silicate (montmorillonite) are examined. The storage (G') and loss (G”) moduli increase at all frequencies with increasing silicate loading, consistent with previous findings with conventionally filled polymer systems. However, the power-law dependence of G' and G” in the terminal zone is different from that observed in homopolymers and decreases with increasing silicate loading. At low frequencies the rheological response becomes almost invariant with frequency, suggestive of a solid-like response. Comparisons are drawn with rheology of other intrinsically anisotropic materials, and an attempt is made to explain phenomenologically their rich-rheological behavior. Rheology of End-Tethered Polymer Layered Silicate Nanocomposites R Krishnamoorti EP Giannelis doi:10.1021/ma960550a Macromolecules, Vol. 30, No. 14. (14 July 1997), pp. 4097-4102. 2008-05-15T20:59:07-00:00 1997 Macromolecules 30 14 4097 4102 end nanocomposite rheology silicate tethered http://www.citeulike.org/user/sas/article/2802678 <i>Macromolecules, Vol. 37, No. 24. (30 November 2004), pp. 9048-9055.</i><br /><br />Abstract: Single-walled carbon nanotube (SWNT)/poly(methyl methacrylate) (PMMA) nanocomposites were prepared via our coagulation method providing uniform dispersion of the nanotubes in the polymer matrix. Optical microscopy, Raman imaging, and SEM were employed to determine the dispersion of nanotube at different length scales. The linear viscoelastic behavior and electrical conductivity of these nanocomposites were investigated. At low frequencies, G' becomes almost independent of the frequency as nanotube loading increases, suggesting an onset of solidlike behavior in these nanocomposites. By plotting G' vs nanotube loading and fitting with a power law function, the rheological threshold of these nanocomposites is ~0.12 wt %. This rheological threshold is smaller than the percolation threshold of electrical conductivity, ~0.39 wt %. This difference in the percolation threshold is understood in terms of the smaller nanotube-nanotube distance required for electrical conductivity as compared to that required to impede polymer mobility. Furthermore, decreased SWNT alignment, improved SWNT dispersion, and/or longer polymer chains increase the elastic response of the nanocomposite, as is consistent with our description of the nanotube network. Nanotube Networks in Polymer Nanocomposites: Rheology and Electrical Conductivity F Du RC Scogna W Zhou S Brand JE Fischer KI Winey doi:10.1021/ma049164g Macromolecules, Vol. 37, No. 24. (30 November 2004), pp. 9048-9055. 2008-05-15T20:58:09-00:00 2004 Macromolecules 37 24 9048 9055 nanocomposite nanotube polymer rheology http://www.citeulike.org/user/sas/article/2802105 <i>Macromolecules, Vol. 39, No. 16. (8 August 2006), pp. 5194-5205.</i><br /><br />Abstract: We review the present state of polymer nanocomposites research in which the fillers are single-wall or multiwall carbon nanotubes. By way of background we provide a brief synopsis about carbon nanotube materials and their suspensions. We summarize and critique various nanotube/polymer composite fabrication methods including solution mixing, melt mixing, and in situ polymerization with a particular emphasis on evaluating the dispersion state of the nanotubes. We discuss mechanical, electrical, rheological, thermal, and flammability properties separately and how these physical properties depend on the size, aspect ratio, loading, dispersion state, and alignment of nanotubes within polymer nanocomposites. Finally, we summarize the current challenges to and opportunities for efficiently translating the extraordinary properties of carbon nanotubes to polymer matrices in hopes of facilitating progress in this emerging area. Polymer Nanocomposites Containing Carbon Nanotubes M Moniruzzaman KI Winey doi:10.1021/ma060733p Macromolecules, Vol. 39, No. 16. (8 August 2006), pp. 5194-5205. 2008-05-15T16:30:25-00:00 2006 Macromolecules 39 16 5194 5205 cnt nanocomposite swnt http://www.citeulike.org/user/sas/article/2795411 <i>Physical Review E, Vol. 64, No. 2. (27 July 2001), 021802.</i> Effects of a nanoscopic filler on the structure and dynamics of a simulated polymer melt and the relationship to ultrathin films Francis Starr Thomas Schrøder Sharon Glotzer doi:10.1103/PhysRevE.64.021802 Physical Review E, Vol. 64, No. 2. (27 July 2001), 021802. 2008-05-13T15:25:10-00:00 2001 Physical Review E 64 2 021802 American Physical Society dynamics nanocomposite http://www.citeulike.org/user/sas/article/2795379 <i>Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 75, No. 3. (2007)</i><br /><br />A study is presented on the effects of smooth nanoparticles on the structure and elastic moduli of a polymer matrix. Structural changes between the unfilled polymer matrix and the nanocomposite give rise to the formation of a glassy layer that surrounds the nanoparticles. Results for the effects of particle size and concentration on the local and overall mechanical properties of the polymer are consistent with experimental macroscopic observations. At the molecular level, it is found that dispersed, attractive nanoparticles alter the nonaffine displacement fields that arise in the polymer glass upon deformation, thereby rendering the nanocomposite glass less fragile. Calculation of local mechanical properties of filled polymers George Papakonstantopoulos Manolis Doxastakis Paul Nealey Jean Barrat Juan de Pablo doi:10.1103/PhysRevE.75.031803 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 75, No. 3. (2007) 2008-05-13T15:18:03-00:00 2007 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 75 3 APS filled mechanical nanocomposite polymer http://www.citeulike.org/user/sas/article/2795384 <i>Journal of Rheology, Vol. 50, No. 5. (2006), pp. 655-683.</i><br /><br />We use coarse-grained computer simulations to delineate the mechanisms governing the steady-shear rheology of polymer-nanoparticle composites. Our studies specifically focus on the regimes where the particle sizes and the interparticle distances become comparable to the polymer sizes and where the interactions between polymer and particles become relevant in influencing the dynamical characteristics. Our results suggest the shear rheology of the composite is very similar to that of colloidal suspensions in a simple fluid when polymer rheology, the particle-induced changes in the polymer rheology and the polymer slip effects are accounted. At dilute and semidilute nanoparticle concentrations, the composite shear rheology is shown to be dominated by the shear thinning of the polymer chains which in turn is modified by the presence of the particles. For higher particle loads, the polymeric contribution to the rheology becomes much less important and the shear rheology is dominated by the particles stresses. Using our results we suggest how a simple empirical model can be constructed for the shear rheology of the composite over the entire range of volume fractions. Our results and mechanistic explanations are in very good agreement with associated experimental observations. ©2006 The Society of Rheology Mechanisms of steady-shear rheology in polymer-nanoparticle composites Victor Pryamitsyn Venkat Ganesan doi:10.1122/1.2234483 Journal of Rheology, Vol. 50, No. 5. (2006), pp. 655-683. 2008-05-13T15:19:38-00:00 2006 Journal of Rheology 50 5 655 683 SOR dynamics nanocomposite rheology shear http://www.citeulike.org/user/sas/article/2795374 <i>The Journal of Chemical Physics, Vol. 126, No. 14. (2007)</i><br /><br />View this record in Web of Science Dynamics of free chains in polymer nanocomposites RC Picu A Rakshit The Journal of Chemical Physics, Vol. 126, No. 14. (2007) 2008-05-13T15:16:25-00:00 2007 The Journal of Chemical Physics 126 14 AIP dynamics nanocomposite reptation http://www.citeulike.org/user/sas/article/2795350 <i>The Journal of Chemical Physics, Vol. 117, No. 20. (2002), pp. 9478-9489.</i><br /><br />View This Record in Scopus A molecular dynamics simulation study of the viscoelastic properties of polymer nanocomposites Grant Smith Dmitry Bedrov Liwei Li Oleksiy Byutner The Journal of Chemical Physics, Vol. 117, No. 20. (2002), pp. 9478-9489. 2008-05-13T15:13:36-00:00 2002 The Journal of Chemical Physics 117 20 9478 9489 AIP md nanocomposite viscoelastic http://www.citeulike.org/user/sas/article/2753333 <i>Nature, Vol. 272, No. 5650. (16 March 1978), pp. 226-229.</i> Molecular morphology in semicrystalline polymers Paul Flory Do Yoon doi:10.1038/272226a0 Nature, Vol. 272, No. 5650. (16 March 1978), pp. 226-229. 2008-05-04T13:42:15-00:00 1978 Nature 272 5650 226 229 crystallization entanglement http://www.citeulike.org/user/sas/article/2753329 <i>Macromolecules, Vol. 33, No. 3. (8 February 2000), pp. 916-932.</i><br /><br />Abstract: A method of obtaining polymer with markedly decreased entanglements concentration in melt, via high-pressure crystallization of high-density polyethylene (HDPE), is elaborated. It is shown, by calculations and experiments, that melting of chain-extended crystals obtained in this process provides a chain-disentangled melt for a period of 20-30 min. The disentanglement is tested by means of spherulite growth rate measurements in a regime II melt crystallization. Spherulites grow faster from partially disentangled melt than from melt with normal concentration of entanglements: the growth rate is increased by 25-45%, and the conversion rate is also markedly higher. The difference is augmenting with decreasing undercooling-consistently with conclusions made from nucleation theory including reptation-and decaying with increasing time of melt annealing at 160 C before crystallization, which is a result of entanglements reconstitution. The crystallization behavior in initially chain disentangled samples subjected to 25-30 min melt annealing is typical of entangled polyethylene, which indicates a complete entanglement restoration. The activation energy for reptation, determined from these data, is approximately 25 kJ/mol. Differences in overall isothermal crystallization kinetics of chain entangled and chain disentangled samples are considerable at moderate undercooling. The nucleation density during crystallization from disentangled melt is reduced in consequence of desorption of chains from heterogeneities surfaces during prior high-pressure crystallization of the samples. Melt annealing causes readsorption and restoration of normal nucleation density. The morphology of samples crystallized from a chain-disentangled melt is significantly different than those crystallized from a chain-entangled melt while the crystal thicknesses are similar. Crystallization of Polyethylene from Melt with Lowered Chain Entanglements M Psarski E Piorkowska A Galeski doi:10.1021/ma990298h Macromolecules, Vol. 33, No. 3. (8 February 2000), pp. 916-932. 2008-05-04T13:40:05-00:00 2000 Macromolecules 33 3 916 932 crystallization disentangled melt pe http://www.citeulike.org/user/sas/article/2708000 <i>Journal of Computational Physics (March 1995), pp. 1-19.</i><br /><br />Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.Copyright 1995, 1999 Academic Press Fast Parallel Algorithms for Short-Range Molecular Dynamics S Plimpton Journal of Computational Physics (March 1995), pp. 1-19. 2008-04-23T15:45:34-00:00 1995 Journal of Computational Physics 0021-9991 1 19 Academic Press lammps reference http://www.citeulike.org/user/sas/article/2702736 <i>Reviews of Modern Physics, Vol. 72, No. 3. (1 July 2000), 813.</i> Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms Jean-Louis Viovy doi:10.1103/RevModPhys.72.813 Reviews of Modern Physics, Vol. 72, No. 3. (1 July 2000), 813. 2008-04-22T18:52:35-00:00 2000 Reviews of Modern Physics 72 3 813 American Physical Society dna electrophoresis review http://www.citeulike.org/user/sas/article/2698277 <i>ELECTROPHORESIS, Vol. 23, No. 16. (2002), pp. 2562-2568.</i><br /><br />This article presents an overview of lattice polymer models used to study DNA electrophoresis. Three commonly used models - the bond fluctuation model, the cage model, and the repton model - are discussed, as well their extension to include electric fields, and simulation results obtained. Physical properties that are shared amongst these models are identified, and differences between the models are discussed. Lattice models of DNA electrophoresis Alexander van Heukelum Gerard Barkema doi:10.1002/1522-2683(200208)23:16<2562::AID-ELPS2562>3.0.CO;2-R ELECTROPHORESIS, Vol. 23, No. 16. (2002), pp. 2562-2568. 2008-04-21T21:49:44-00:00 2002 ELECTROPHORESIS 23 16 2562 2568 dna electrophoresis lattice review http://www.citeulike.org/user/sas/article/2698251 <i>ELECTROPHORESIS, Vol. 28, No. 16. (2007), pp. 2783-2800.</i><br /><br />We use a coarse-grained model proposed by Graham and Larson based on the temporary network model by Schieber et al.. [1] to simulate the electrophoretic motion of ssDNA and corresponding band broadening due to dispersion. With dimensionless numbers reflecting the experimental physical properties, we are able to simulate ssDNA behavior under weak to moderate electric field strengths for chains with 8-50 entanglements per chain ( Modeling ssDNA electrophoretic migration with band broadening in an entangled or cross-linked network Zheng Chen Richard Graham Mark Burns Ronald Larson doi:10.1002/elps.200600684 ELECTROPHORESIS, Vol. 28, No. 16. (2007), pp. 2783-2800. 2008-04-21T21:31:58-00:00 2007 ELECTROPHORESIS 28 16 2783 2800 bd dna electrophoresis slip-link http://www.citeulike.org/user/sas/article/2698250 <i>Macromolecules, Vol. 40, No. 2. (23 January 2007), pp. 366-378.</i><br /><br />Abstract: We derive a course-grained Brownian dynamics simulation algorithm for the motion of DNA chains under an external electric field. We generalize a model for bulk rheological response of entangled polymers by Schieber et al. [J. Rheol. 2003, 47, 213], allowing both rheology and electrophoresis to be modeled under the same theoretical framework. The effect of the external electric field is included by modifying the strand free energy, which then influences both the monomer sliding dynamics between entanglements and the renewal of entanglements at the chain ends. We also modify the free energy to include the finite extensibility of the chain segments and account for changes in local chain mobility with chain configuration. The resulting model gives a detailed account of the chain dynamics on length scales above the tube diameter and is suitable to model a wide range of field conditions. Simulation results for a constant-field mobility are presented, which fully characterize the model under these conditions. We ensure that the model captures known scaling regimes from analytic theory and compare the predictions to a set of experimental data for constant-field mobility of double-stranded DNA in agarose gels at a range of gel concentrations. This data comparison provides a method to characterize DNA-matrix systems, providing possibilities for modeling of more general field conditions. Coarse-Grained Brownian Dynamics Simulations of Electrophoresis of DNA Molecules from Generalized Reptation Models RS Graham RG Larson doi:10.1021/ma061912+ Macromolecules, Vol. 40, No. 2. (23 January 2007), pp. 366-378. 2008-04-21T21:31:27-00:00 2007 Macromolecules 40 2 366 378 bd dna electrophoresis slip-link http://www.citeulike.org/user/sas/article/2698195 <i>Biophys. J., Vol. 69, No. 4. (1 October 1995), pp. 1596-1605.</i><br /><br />Sister chromatids are topologically intertwined at the onset of anaphase: their segregation during anaphase is known to require strand-passing activity by type II DNA topoisomerase. We propose that the removal of the intertwinings involves at the same time the traction of the mitotic spindle and the activity of topoisomerases. This implies that the velocity of the chromatids is compatible with the kinetic constraints imposed by the enzymatic reaction. We show that the greatest observed velocities (about 0.1 microns s-1) are close to the theoretical upper bound compatible with both the diffusion rate (calculated here within a probabilistic model) and the measured reaction rate of the enzyme. Anaphase chromatid motion: involvement of type II DNA topoisomerases. B Duplantier G Jannink JL Sikorav Biophys. J., Vol. 69, No. 4. (1 October 1995), pp. 1596-1605. 2008-04-21T21:08:07-00:00 1995 Biophys. J. 69 4 1596 1605 catenane cyclic dna enzyme knots ring http://www.citeulike.org/user/sas/article/2698190 <i>J. Biol. Chem., Vol. 260, No. 8. (25 April 1985), pp. 4975-4983.</i> Duplex DNA knots produced by Escherichia coli topoisomerase I. Structure and requirements for formation FB Dean A Stasiak T Koller NR Cozzarelli J. Biol. Chem., Vol. 260, No. 8. (25 April 1985), pp. 4975-4983. 2008-04-21T21:06:00-00:00 1985 J. Biol. Chem. 260 8 4975 4983 catenane cyclic dna enzyme knots ring http://www.citeulike.org/user/sas/article/2698189 <i>Cell, Vol. 42, No. 1. (August 1985), pp. 325-334.</i><br /><br />Summary We studied the mechanism of recombination by determining the structure of the products of the phage [lambda] Int system. Electron microscopy of RecA-coated products revealed only knots and catenanes containing a regular right-handed spiral structure. The structure and distribution of products establish that the recombination sites pair by essentially random collision, rather than by tracking. However, the distribution also indicates that the binding of the enzyme must introduce nonrandom components into the reaction and stabilize at least two additional supercoils that become links In the product. Moreover, the regularity of the structures indicates that the strand exchange is accomplished in a very simple way, introducing only a single link into the product. All other links result from the direct conversion of substrate supercoils into knot and catenane links. These supercoils must be in a right-handed, braided form, rather than solenoidally wound as in nucleosomes. The stereostructure of knots and catenanes produced by phage [lambda] integrative recombination: implications for mechanism and DNA structure Sylvia Spengler Andrzej Stasiak Nicholas Cozzarelli doi:10.1016/S0092-8674(85)80128-8 Cell, Vol. 42, No. 1. (August 1985), pp. 325-334. 2008-04-21T21:05:59-00:00 1985 Cell 42 1 325 334 catenane cyclic dna enzyme knots ring http://www.citeulike.org/user/sas/article/504191 <i>Proc Natl Acad Sci U S A, Vol. 99, No. 18. (3 September 2002), pp. 11593-11598.</i><br /><br />The nuclease hypersensitivity element III(1) upstream of the P1 promoter of c-MYC controls 85-90% of the transcriptional activation of this gene. We have demonstrated that the purine-rich strand of the DNA in this region can form two different intramolecular G-quadruplex structures, only one of which seems to be biologically relevant. This biologically relevant structure is the kinetically favored chair-form G-quadruplex, which is destabilized when mutated with a single G --> A transition, resulting in a 3-fold increase in basal transcriptional activity of the c-MYC promoter. The cationic porphyrin TMPyP4, which has been shown to stabilize this G-quadruplex structure, is able to suppress further c-MYC transcriptional activation. These results provide compelling evidence that a specific G-quadruplex structure formed in the c-MYC promoter region functions as a transcriptional repressor element. Furthermore, we establish the principle that c-MYC transcription can be controlled by ligand-mediated G-quadruplex stabilization. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. A Siddiqui-Jain CL Grand DJ Bearss LH Hurley doi:10.1073/pnas.182256799 Proc Natl Acad Sci U S A, Vol. 99, No. 18. (3 September 2002), pp. 11593-11598. 2006-02-13T18:33:44-00:00 2002 Proc Natl Acad Sci U S A 0027-8424 99 18 11593 11598 cyclic dna knot quadruplex http://www.citeulike.org/user/sas/article/2689262 <i>Journal of Molecular Biology, Vol. 278, No. 1. (24 April 1998), pp. 1-3.</i><br /><br />Various site-specific recombination enzymes produce different types of knots or catenanes while acting on circular DNA in vitro and in vivo. By analysing the types of knots or links produced, it is possible to reconstruct the order of events during the reaction and to deduce the molecular "architecture" of the complexes that different enzymes form with DNA. Until recently it was necessary to use laborious electron microscopy methods to identify the types of knots or catenanes that migrate in different bands on the agarose gels used to analyse the products of the reaction. We reported recently that electrophoretic migration of different knots and catenanes formed on the same size DNA molecules is simply related to the average crossing number of the ideal representations of the corresponding knots and catenanes. Here we explain this relation by demonstrating that the expected sedimentation coefficient of randomly fluctuating knotted or catenated DNA molecules in solution shows approximately linear correlation with the average crossing number of ideal configurations of the corresponding knots or catenanes. Sedimentation and electrophoretic migration of DNA knots and catenanes Alexander Vologodskii Nancy Crisona Ben Laurie Piotr Pieranski Vsevolod Katritch Jacques Dubochet Andrzej Stasiak doi:10.1006/jmbi.1998.1696 Journal of Molecular Biology, Vol. 278, No. 1. (24 April 1998), pp. 1-3. 2008-04-18T19:01:25-00:00 1998 Journal of Molecular Biology 278 1 1 3 catenenes dna electrophoresis knots http://www.citeulike.org/user/sas/article/2674390 <i>Journal of Rheology, Vol. 35, No. 2. (1991), pp. 213-219.</i><br /><br />We present the results of a dynamic Monte Carlo simulation of macromolecules in a dilute solution subjected to plane Poiseuille flow in a channel between impenetrable walls, in two dimensions. The polymer dimensions parallel and perpendicular to the flow direction and the polymer distribution in the flow channel are calculated as a function of the distance from the walls and the difference with previous work on self-avoiding chains in simple-shear flow is discussed. In agreement with our previous analysis of the simple-shear flow case we find that Poiseuille flows also produce narrowing of wall-depletion layers. Polymers in plane Poiseuille flow: Dynamic Monte Carlo simulation Edgardo Duering Yitzhak Rabin doi:10.1122/1.550252 Journal of Rheology, Vol. 35, No. 2. (1991), pp. 213-219. 2008-04-15T17:32:16-00:00 1991 Journal of Rheology 35 2 213 219 SOR flow mc shear http://www.citeulike.org/user/sas/article/2674381 <i>Macromolecules, Vol. 29, No. 6. (11 March 1996), pp. 2289-2297.</i><br /><br />Abstract: We have studied the conformation of a polymer brush in equilibrium with a solvent that is subject to a shear flow. The interplay between the polymer brush and the hydrodynamic flow of the solvent has been modeled, with simple but largely justifiable approximations. The main technique used in our study is a Monte-Carlo simulation algorithm that is distinct from many standard numerical methods used in studies of polymer brushes in that it combines an off-lattice description of polymer brushes-the Edwards Hamiltonian-with a modification of the standard Metropolis Monte-Carlo transition probability to take into account the effective force acting upon the polymer molecules by the moving solvent. The conformation of the polymer brush, the configurations of each individual chain in particular, is investigated in detail. It is found that the significant response of the brush to the solvent shear flow manifests principally in the form of the chain tilting toward and stretching along the direction of the flow, whereas the overall conformational properties, such as the averaged local monomer density, and the linear span of the brush in the direction normal to that of the flow remain essentially unaffected by the flow. Such response can be understood both qualitatively and semiquantitatively in terms of a notion of the mechanical balance of the different physical forces involved, which was used in the theory of Rabin and Alexander (Rabin, Y.; Alexander, S. Europhys. Lett. 1990, 13, 49). The relevance of our study to some recent experiments is briefly discussed. Conformation of Polymer Brushes under Shear: Chain Tilting and Stretching L Miao H Guo MJ Zuckermann doi:10.1021/ma951071z Macromolecules, Vol. 29, No. 6. (11 March 1996), pp. 2289-2297. 2008-04-15T17:30:54-00:00 1996 Macromolecules 29 6 2289 2297 brush flow mc shear http://www.citeulike.org/user/sas/article/2674378 <i>Journal of Polymer Science Part B: Polymer Physics, Vol. 38, No. 18. (2000), pp. 2422-2428.</i><br /><br />We present a novel Monte-Carlo lattice model for the study of the coil-stretch transition for polymer chains in deformation flows. Our results indicate that elongational flows are much more effective than shear flows in stretching polymer chains, in full agreement with experimental observation. Our model data also show that the &epsiv;·c Coil-stretch transition in deformation flows Yves Termonia doi:10.1002/1099-0488(20000915)38:18<2422::AID-POLB90>3.0.CO;2-Y Journal of Polymer Science Part B: Polymer Physics, Vol. 38, No. 18. (2000), pp. 2422-2428. 2008-04-15T17:29:40-00:00 2000 Journal of Polymer Science Part B: Polymer Physics 38 18 2422 2428 flow lattice mc shear http://www.citeulike.org/user/sas/article/2674371 <i>Physical Review E, Vol. 54, No. 6. (1 December 1996), 6958.</i> Polymer brush under strong shear Pik-Yin Lai Chee-Yuen Lai doi:10.1103/PhysRevE.54.6958 Physical Review E, Vol. 54, No. 6. (1 December 1996), 6958. 2008-04-15T17:26:58-00:00 1996 Physical Review E 54 6 6958 American Physical Society brush flow mc nonequilibrium shear http://www.citeulike.org/user/sas/article/2674042 <i>Physical Review E, Vol. 70, No. 3. (2004), 031501.</i> Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films Gaurav Arya Athanassios Panagiotopoulos doi:10.1103/PhysRevE.70.031501 Physical Review E, Vol. 70, No. 3. (2004), 031501. 2008-04-15T16:44:55-00:00 2004 Physical Review E 70 3 031501 American Physical Society flow mc nemc non-equilibrium shear http://www.citeulike.org/user/sas/article/2670155 <i>J. Chem. Phys., Vol. 106, No. 18. (1997), pp. 7792-7801.</i><br /><br />A new approach for the equilibrium deformation of three-dimensional chains, that are bigrafted to parallel planes is presented. The underlying lattice Monte Carlo algorithm is the bond fluctuation model. In addition to the excluded-volume interaction of this a priori athermal algorithm, we incorporated external potentials in order to enable direct detection of forces. The whole deformation process is split up into a series of separate steps. Each step consists of a generation process and subsequent relaxation procedures. Stress and strain are simultaneously calculated as time-averaged quantities of sufficiently equilibrated systems. Stress–strain relations ranging from compression to the highly stretched regime were simulated by variation of both chain length, N, and grafting density, sigma. In the high-density limit the simulation data agree perfectly with a simple one-dimensional theory. The N and sigma dependency of the distance, h0(N,sigma), of grafting planes at vanishing force is in qualitative agreement with theoretical predictions for an intermediate regime of sigma. The simulated force–length relations are in satisfactory agreement with current scaling predictions. Uniaxial deformation of bridging polymer systems: A Monte Carlo study Th Hölzl M Wittkop S Kreitmeier D Göritz doi:10.1063/1.473779 J. Chem. Phys., Vol. 106, No. 18. (1997), pp. 7792-7801. 2008-04-14T17:51:55-00:00 1997 J. Chem. Phys. 106 18 7792 7801 elongational extensional flow mc http://www.citeulike.org/user/sas/article/2670152 <i>Macromolecules, Vol. 34, No. 20. (25 September 2001), pp. 7113-7120.</i><br /><br />Abstract: We examine the roles of several types of intramolecular interactions in the behavior of the steady elongational flow properties of infinitely dilute polymer solutions. In particular, bond stretching, bond bending, bond torsion, and nonbonded intramolecular interactions are included. Geometric and rheological properties are calculated using Monte Carlo integration. We observe that bond bending and nonbonded interactions result in significant changes over the traditional bond stretching predictions, but bond torsion plays only a minor role. Bond bending results in more abrupt chain expansion with increasing elongation rate, and the corresponding increase in the elongational viscosity is also more steep. Nonbonded interactions cause the chain to be more spheroidal at lower elongation rates, and they result in a minimum in the elongational viscosity at an intermediate elongation rate-presumably as a result of excluded-volume effects causing the chain to be slightly more expanded. Steady Uniaxial Elongational Flows: Roles of Intramolecular Potentials AS Bhandar JM Wiest doi:10.1021/ma001357q Macromolecules, Vol. 34, No. 20. (25 September 2001), pp. 7113-7120. 2008-04-14T17:46:33-00:00 2001 Macromolecules 34 20 7113 7120 elongational mc steadt http://www.citeulike.org/user/sas/article/2670150 <i>Macromolecular Theory and Simulations, Vol. 7, No. 1. (1998), pp. 19-26.</i><br /><br />Configuration Biased Monte Carlo (CBMC) and Non-Equilibrium Brownian Dynamics (NEBD) simulations are used to understand the dynamics of semi-flexible macromolecules undergoing extensional flow. The mathematical model utilizes a discretized version of the Kratky-Porod wormlike (or persistent) chain as the building block, and using kinetic theory, generalized to include flow. In steady, potential flows, the solution of the Fokker-Planck equation exists and is used in the generation of trial and acceptance moves in the CBMC scheme. For the NEBD, the Fokker-Planck equation is converted to a Stochastic Differential Equation (SDE) from which the simulation algorithm is obtained. Various conformational quantities are monitored, under both steady-state and transient conditions, with the primary independent variable being the flexibility parameter Configuration biased Monte Carlo and Brownian dynamics simulations of semiflexible polymers in extensional flows Naveen Andrews Anthony Mchugh Jay Schieber doi:10.1002/(SICI)1521-3919(19980101)7:1<19::AID-MATS19>3.0.CO;2-B Macromolecular Theory and Simulations, Vol. 7, No. 1. (1998), pp. 19-26. 2008-04-14T17:45:46-00:00 1998 Macromolecular Theory and Simulations 7 1 19 26 extensional flow mc semiflexible http://www.citeulike.org/user/sas/article/2669988 <i>Journal of Statistical Physics, Vol. 34, No. 3. (21 February 1984), pp. 497-537.</i><br /><br />We investigate theoretically and via computer simulation the stationary nonequilibrium states of a stochastic lattice gas under the influence of a uniform external fieldE. The effect of the field is to bias jumps in the field direction and thus produce a current carrying steady state. Simulations on a periodic 30 × 30 square lattice with attractive nearest-neighbor interactions suggest a nonequilibrium phase transition from a disordered phase to an ordered one, similar to the para-to-ferromagnetic transition in equilibriumE=0. At low temperatures and largeE the system segregates into two phases with an interface oriented parallel to the field. The critical temperature is larger than the equilibrium Onsager value atE=0 and increases with the field. For repulsive interactions the usual equilibrium phase transition (ordering on sublattices) is suppressed. We report on conductivity, bulk diffusivity, structure function, etc. in the steady state over a wide range of temperature and electric field. We also present rigorous proofs of the Kubo formula for bulk diffusivity and electrical conductivity and show the positivity of the entropy production for a general class of stochastic lattice gases in a uniform electric field. Nonequilibrium steady states of stochastic lattice gas models of fast ionic conductors Sheldon Katz Joel Lebowitz Herbert Spohn doi:10.1007/BF01018556 Journal of Statistical Physics, Vol. 34, No. 3. (21 February 1984), pp. 497-537. 2008-04-14T17:33:40-00:00 1984 Journal of Statistical Physics 34 3 497 537 mc nonequilibrium http://www.citeulike.org/user/sas/article/2669981 <i>Macromolecular Theory and Simulations, Vol. 5, No. 3. (1996), pp. 417-448.</i><br /><br />As a coarse-grained model for dense amorphous polymer systems interacting with solid walls (i.e., the fiber surface in a composite), the bond fluctuation model of flexible polymer chains confined between two repulsive surfaces is studied by extensive Monte Carlo simulations. Choosing a potential for the length of an effective bond that favors rather long bonds, the full temperature region from ordinary polymer melts down to the glass transition is accessible. It is shown that in the supercooled state near the glass transition an Monte Carlo simulation studies of the interfaces between polymeric and other solids as models for fiber-matrix interactions in advanced composite materials Jörg Baschnagel Kurt Binder doi:10.1002/mats.1996.040050304 Macromolecular Theory and Simulations, Vol. 5, No. 3. (1996), pp. 417-448. 2008-04-14T17:31:49-00:00 1996 Macromolecular Theory and Simulations 5 3 417 448 composite flow mc http://www.citeulike.org/user/sas/article/2669751 <i>Progress in Polymer Science, Vol. 33, No. 2. (February 2008), pp. 191-269.</i><br /><br />Polymer nanocomposites offer a wide range of promising applications because of their much enhanced properties arising from the reinforcement of nanoparticles. However, further development of such nanomaterials depends on the fundamental understanding of their hierarchical structures and behaviors which requires multiscale modeling and simulation strategies to provide seamless coupling among various length and time scales. In this review, we first introduce some computational methods that have been applied to polymer nanocomposites, covering from molecular scale (e.g., molecular dynamics, Monte Carlo), microscale (e.g., Brownian dynamics, dissipative particle dynamics, lattice Boltzmann, time-dependent Ginzburg-Landau method, dynamic density functional theory method) to mesoscale and macroscale (e.g., micromechanics, equivalent-continuum and self-similar approaches, finite element method). Then, we discuss in some detail their applications to various aspects of polymer nanocomposites, including the thermodynamics and kinetics of formation, molecular structure and dynamics, morphology, processing behaviors, and mechanical properties. Finally, we address the importance of multiscale simulation strategies in the understanding and predictive capabilities of polymer nanocomposites in which few studies have been reported. The present review aims to summarize the recent advances in the fundamental understanding of polymer nanocomposites reinforced by nanofillers (e.g., spherical nanoparticles, nanotubes, clay platelets) and stimulate further research in this area. Multiscale modeling and simulation of polymer nanocomposites QH Zeng AB Yu GQ Lu doi:10.1016/j.progpolymsci.2007.09.002 Progress in Polymer Science, Vol. 33, No. 2. (February 2008), pp. 191-269. 2008-04-14T16:53:25-00:00 2008 Progress in Polymer Science 33 2 191 269 nanocomposite review http://www.citeulike.org/user/sas/article/2669728 <i>The Journal of Chemical Physics, Vol. 112, No. 13. (2000), pp. 6073-6083.</i><br /><br />View this record in Web of Science Monte Carlo simulation of homopolymer melts in plane Poiseuille flow Seth Gleiman John Dorgan The Journal of Chemical Physics, Vol. 112, No. 13. (2000), pp. 6073-6083. 2008-04-14T16:37:28-00:00 2000 The Journal of Chemical Physics 112 13 6073 6083 AIP flow mc melt shear http://www.citeulike.org/user/sas/article/2669707 <i>Computer Physics Communications, Vol. 169, No. 1-3. (1 July 2005), pp. 262-266.</i><br /><br />This paper presents results from Monte Carlo (MC) and molecular dynamics (MD) simulations on the shear-induced long-ranged alignment of cylindrical micelles in thin films. The surfactant is represented on a lattice and the shear flow is simulated via incorporation of a shear-induced potential energy term within the acceptance criteria in the MC simulations. The MD simulations are conducted on a coarse-grained, off-lattice surfactant while the shear flow is imposed in thin films by sliding confining walls in opposite directions. It is shown that the two methods lead to different steady state orientations of micelles. We also discuss several problematic issues concerned with incorporating shear or dynamics within MC schemes. Molecular modeling of shear-induced alignment of cylindrical micelles Gaurav Arya Athanassios Panagiotopoulos doi:10.1016/j.cpc.2005.03.060 Computer Physics Communications, Vol. 169, No. 1-3. (1 July 2005), pp. 262-266. 2008-04-14T16:26:15-00:00 2005 Computer Physics Communications 169 1-3 262 266 flow mc md shear http://www.citeulike.org/user/sas/article/2661010 <i>Polymer, Vol. 41, No. 9. (2000), pp. 3289-3295.</i><br /><br />This paper has extended a lattice Monte Carlo (MC) method to simulate the simple shear flow of multiple self-avoiding chains in three dimensions following our research work in two dimensions. Comparisons of simulation outputs with experimental observations, theoretical predictions and other simulation results are made. The steady-state scaling analysis to scattering functions of deformed chains confirms the existence of anisotropic scaling laws at fixed reduced shear rates found in molecular dynamics (MD) simulation. The exponent of chain deformation shown in the MC simulation falls into a normal regime measured from neutron scattering and light scattering experiments. The relation between orientation angles and shear rates is consistent with some scattering experiments. Both Newtonian and non-Newtonian regimes are reproduced in our lattice MC simulation. Non-zero first and second normal stress differences and their dependence of the shear rate are found, as well as the shear thinning effect. The stress growth at inception and stress decay after cessation of shear flow is also examined. The validity of our novel simulation approach is thus confirmed. Since both chain conformations and rheological properties under shear flow can be studied, our MC approach can be used to reveal non-linear viscoelasticity of polymer fluids and polymer-flow interaction. Monte Carlo simulation of self-avoiding lattice chains subject to simple shear flow Part II. Three-dimensional results and comparison with experiments Guoqiang Xu Jiandong Ding Yuliang Yang doi:10.1016/S0032-3861(99)00492-9 Polymer, Vol. 41, No. 9. (2000), pp. 3289-3295. 2008-04-12T17:18:34-00:00 2000 Polymer 41 9 3289 3295 bfm flow mc potential shear http://www.citeulike.org/user/sas/article/2660676 <i>Journal of Molecular Biology, Vol. 332, No. 1., pp. 257-264.</i><br /><br />Circular versions of a large number of proteins have been designed by connecting the N and C termini via peptide linkers. A motivation for these designs is the assumed enhancement in folding stability, because backbone cyclization reduces the chain entropy of the unfolded state. Here, it is recognized that backbone cyclization also reduces the chain entropy of a flexible peptide linker in the folded state. Specifically, the end-to-end distance of the linker is restricted to fluctuations around the average displacement between the N and C termini of the folded protein. The balance of the chain-entropy reductions in the folded and unfolded states is used to predict the change in the unfolding free energy, ΔΔGcycl, by backbone cyclization. Predicted values of ΔΔGcycl are in quantitative agreement with results of a careful study on cyclizing the 34 residue PIN1 WW domain by linkers with two to seen residues. The experimental results of an optimal linker length l=4 and a maximum stabilization of 1.7 kcal/mol are reproduced. Calculations of ΔΔGcycl for a broad selection of circular proteins suggest that the stabilizing effect of backbone cyclization is modest, reflecting entropy reductions in both the unfolded and the folded states. Effect of Backbone Cyclization on Protein Folding Stability: Chain Entropies of both the Unfolded and the Folded States are Restricted Huan-Xiang Zhou doi:doi:10.1016/S0022-2836(03)00886-6 Journal of Molecular Biology, Vol. 332, No. 1., pp. 257-264. 2008-04-12T14:57:00-00:00 Journal of Molecular Biology 332 1 257 264 cyclic entropy proteins ring http://www.citeulike.org/user/sas/article/1727433 <i>Journal of Molecular Recognition, Vol. 17, No. 5. (2004), pp. 368-375.</i><br /><br />Simple theoretical models are presented to illustrate the effects of spatial confinement and macromolecular crowding on the equilibria and rates of protein folding and binding. Confinement is expected to significantly stabilize the folded state, but for crowding only a marginal effect on protein stability is expected. In confinement the unfolded chain is restricted to a cage but in crowding the unfolded chain may explore different interstitial voids. Because confinement and crowding eliminate the more expanded conformations of the unfolded state, folding from the compact unfolded state is expected to speed up. Crowding will shift the binding equilibrium of proteins toward the bound state. The significant slowing down in protein diffusion by crowding, perhaps beneficial for chaperonin action, could result in a decrease in protein binding rates. Copyright © 2004 John Wiley & Sons, Ltd. Protein folding and binding in confined spaces and in crowded solutions Huan-Xiang Zhou doi:10.1002/jmr.711 Journal of Molecular Recognition, Vol. 17, No. 5. (2004), pp. 368-375. 2007-10-04T13:33:02-00:00 2004 Journal of Molecular Recognition 17 5 368 375 zhou04 http://www.citeulike.org/user/sas/article/2660637 <i>J. Am. Chem. Soc., Vol. 125, No. 31. (6 August 2003), pp. 9280-9281.</i><br /><br />Abstract: Building on previous studies of the effects of covalent linking and backbone cyclization on protein folding stability, a theory is developed for the stabilization effect of catenating a dimeric protein. Relative to covalent linking, catenation is up to 1000-fold more powerful in stabilizing the folded structure. This dramatic stabilization derives from the dual effects of backbone cyclization and constrained relative motion between the subunits afforded by the catenane topology. Effect of Catenation on Protein Folding Stability HX Zhou doi:10.1021/ja0355978 J. Am. Chem. Soc., Vol. 125, No. 31. (6 August 2003), pp. 9280-9281. 2008-04-12T14:35:00-00:00 2003 J. Am. Chem. Soc. 125 31 9280 9281 catenation cyclic folding protein ring