Search results for "Molecular model"
showing 10 items of 274 documents
Monte Carlo Simulations of Alloy Phase Transformations
1994
The use of Monte Carlo simulation methods for study of order-disorder phase transitions in lattice models of alloys is reviewed, with an emphasis on interfacial phenomena and the kinetics of ordering and/or phase separation. Topics discussed include the attempt to predict the phase diagram of Fe-Al alloys from recent measurements of effective interaction parameters, competition between magnetic and crystallographic ordering in such alloys, and the structure of their antiphase domain boundaries. Both an interfacial roughening transition of this domain wall and interfacial enrichment phenomena are predicted. Then simulations of alloy-vacuum surfaces are discussed, and it is shown that both ca…
Simulation of Transport in Partially Miscible Binary Fluids: Combination of Semigrandcanonical Monte Carlo and Molecular Dynamics Methods
2004
Binary Fluids that exhibit a miscibility gap are ubiquitous in nature (glass melts, polymer solutions and blends, mixtures of molten metals, etc.) and exhibit a delicate interplay between static and dynamic properties. This is exemplified for a simple model system, the symmetrical AB Lennard-Jones mixture. It is shown how semigrandcanonical Monte Carlo methods, that include A→B (B→A) identity switches as Monte Carlo moves, can yield the phase diagram, the interfacial tension between coexisting phases, and various pair correlation functions and structure factors. In addition to the build-up of long-ranged concentration correlations near the critical point, unmixing is also accompanied by the…
Monte Carlo Simulations of Polymer Systems
1988
The impact of Monte Carlo “computer experiments” in polymer physics is described, emphasizing three examples taken from the author’s research group. The first example is a test of the classical Flory—Huggins theory for polymer mixtures, including a discussion of cricital phenomena. Also “technical aspects” of such simulations (“grand-canonical” ensemble, finite—size scaling, etc.) are explained briefly. The second example refers to configurational statistics and dynamics of chains confined to cylindrical tubes; the third example deals with the adsorption of polymers at walls. These simulations check scaling concepts developed along the lines of de Gennes.
Monte Carlo Simulations in Polymer Science
2012
Monte Carlo methods are useful for computing the statistical properties of both single macromolecules of various chemical architectures and systems containing many polymers (solutions, melts, blends, etc.). Starting with simple models (lattice models such as the self-avoiding walk or the bond fluctuation model, as well as coarse-grained or chemically realistic models in the continuum) various algorithms exist to generate conformations typical for thermal equilibrium, but dynamic Monte Carlo methods can also model diffusion and relaxation processes (as described by the Rouse and the reptation models for polymer melt dynamics). Limitations of the method are explained, and also the measures to…
Monte Carlo Simulations of Growth Kinetics and Phase Transitions at Interfaces: Some Recent Results
1991
ABSTRACTIn the first part Monte Carlo studies of the kinetics of multilayer adsorption (without screening) are described. The approach to the jamming coverage in each layer is asymptotically exponential. The jamming coverages approach the infinite-layer limit value according to a power law. In the second part, studies of phase transitions in two dimensional fluids are reviewed. With a combination of Monte Carlo and finite size scaling block analysis techniques, accurate values are obtained for the critical temperatures, coexistence densities and the compressibilities of an adsorbed fluid layer in an NVT ensemble.
Isotropic–isotropic phase separation in mixtures of rods and spheres: Some aspects of Monte Carlo simulation in the grand canonical ensemble
2008
Abstract In this article we consider mixtures of non-adsorbing polymers and rod-like colloids in the isotropic phase, which upon the addition of polymers show an effective attraction via depletion forces. Above a certain concentration, the depletant causes phase separation of the mixture. We performed Monte Carlo simulations to estimate the phase boundaries of isotropic–isotropic coexistence. To determine the phase boundaries we simulated in the grand canonical ensemble using successive umbrella sampling [J. Chem. Phys. 120 (2004) 10925]. The location of the critical point was estimated by a finite size scaling analysis. In order to equilibrate the system efficiently, we used a cluster move…
Novel lithocholaphanes: Syntheses, NMR, MS, and molecular modeling studies
2007
Abstract Novel head-to-head lithocholaphanes 6 and 11 have been synthesized via precursors 1 – 5 and 7 – 10 with overall good yields, and characterized by 1 H, 13 C, and 15 N NMR spectroscopy, ESI-TOF mass spectrometry, thermal analysis, and molecular modeling. In addition, the binding abilities of 6 and 11 towards alkali metal cations have been investigated via competitive complexation studies using equimolar mixtures of Li + , Na + , K + , and Rb + -cations, and cholaphanes 6 and 11 . The formation of cation–cholaphane adducts was detected by ESI-TOF mass spectrometry. The trends in these comparative binding studies are nicely reproduced theoretically with PM3 energetically optimized stru…
Complete1H,13C{1H}, and31P NMR spectral parameters of some pyrophosphates
2017
The 1 H, 13 C{1 H}, and 31 P NMR spectral parameters of some pyrophosphates were determined in CDCl3 . The most complicated 1 H spectrum can be solved fully only as (A3 MN)R6 XX'R6 '(MNA3 )', where R6 (= -N(CH3 )2 ) is coupled only to phosphorus (X). Second-order coupling between phosphorus was found and solved with iterative analysis. A signal shape of one of the carbon resonance cannot be explained only with couplings. Explanation for exceptional shape was searched from molecular modeling results. Copyright © 2017 John Wiley & Sons, Ltd.
Quaternary structure and molecular model of a 4x6mer arthropod hemocyanin in oxygenated and deoxygenated states by 3D cryo-electron microscopy
2007
Extended abstract of a paper presented at MC 2007, 33rd DGE Conference in Saarbrücken, Germany, September 2 – September 7, 2007
The solid-state architecture of a metallosupramolecular polyelectrolyte
2006
Self-assembly of Fe(II) and the ditopic ligand 1,4-bis(2,2′:6′,2″-terpyridine-4′-yl)benzene results in equilibrium structures in solutions, so-called metallosupramolecular coordination polyelectrolytes (MEPEs). It is exceedingly difficult to characterize such macromolecular assemblies, because of the dynamic nature. Therefore, hardly any structural information is available for this type of material. Here, we show that from dilute solutions, where small aggregates predominate, it is possible to grow nanoscopic crystals at an interface. A near atomic resolution structure of MEPE is obtained by investigating the nanoscopic crystals with electron diffraction in combination with molecular model…