JCP: Polymers, Biopolymers, and Complex Systems http://scitation.aip.org/ JCP: Polymers, Biopolymers, and Complex Systems Determination of rotary diffusivity of poly(n-propyl isocyanate) by molecular dynamics http://link.aip.org/link/?JCP/125/244901/1&agg=rss M. Laso, N. Jimeno, L. M. Muneta, and M. Muller<br/> The rotational dynamics of a nondilute solution of the rodlike polymer poly(n-propyl isocyanate) (PPIC) has been studied on an atomistic model by means of a large-scale classical molecular dynamics investigation. The rotary diffusivity of PPIC in toluene solution has been determined from the Einstei ... [J. Chem. Phys. 125, 244901 (2006)] published Tue Dec 26, 2006. Unified model of association-induced lower critical solution temperature phase separation and its application to solutions of telechelic poly(ethylene oxide) and of telechelic poly(N-isopropylacrylamide) in water http://link.aip.org/link/?JCP/125/244902/1&agg=rss Yukinori Okada, Fumihiko Tanaka, Piotr Kujawa, and Francoise M. Winnik<br/> The authors present a model describing the coexistence of hydrophobic association and phase separation with lower critical solution temperature (LCST) in aqueous solutions of polymers carrying short hydrophobic chains at both chain ends (telechelic associating polymers). The LCST of these solutions ... [J. Chem. Phys. 125, 244902 (2006)] published Tue Dec 26, 2006. Simulations of the dynamics of thermal undulations in lipid bilayers in the tensionless state and under stress http://link.aip.org/link/?JCP/125/234905/1&agg=rss S. A. Shkulipa, W. K. den Otter, and W. J. Briels<br/> The relaxation processes of height undulations and density fluctuations in a membrane have been studied by molecular dynamics simulations of a coarse grained amphiphilic bilayer model. We observe a double exponential decay in their time correlations, with relaxation rates in good quantitative agreem ... [J. Chem. Phys. 125, 234905 (2006)] published Thu Dec 21, 2006. Anomalous small angle x-ray scattering determination of ion distribution around a polyelectrolyte biopolymer in salt solution http://link.aip.org/link/?JCP/125/234904/1&agg=rss Ferenc Horkay, Anne Marie Hecht, Cyrille Rochas, Peter J. Basser, and Erik Geissler<br/> The distribution of counterions in solutions of high molecular mass hyaluronic acid, in near-physiological conditions where mono- and divalent ions are simultaneously present, is studied by small angle neutron scattering and anomalous small angle x-ray scattering. The solutions contain either sodium ... [J. Chem. Phys. 125, 234904 (2006)] published Wed Dec 20, 2006. Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation http://link.aip.org/link/?JCP/125/234903/1&agg=rss Subrata Pal, Prabal K. Maiti, and Biman Bagchi<br/> Dynamics of water molecules in the grooves of DNA are of great interest both for practical (functionality of DNA) and fundamental (as examples of confined systems) interest. Here the authors employ atomistic molecular dynamics simulations to understand varying water dynamics at the minor and the maj ... [J. Chem. Phys. 125, 234903 (2006)] published Wed Dec 20, 2006. Heterogeneous dynamics, ageing, and rejuvenating in van der Waals liquids http://link.aip.org/link/?JCP/125/234901/1&agg=rss Samy Merabia and Didier Long<br/> It has been shown over the past ten years that the dynamics close to the glass transition is strongly heterogeneous: fast domains coexist with domains three or four decades slower, the size of these regions being about 3 nm at T. The authors extend here a model that has been proposed recently for t ... [J. Chem. Phys. 125, 234901 (2006)] published Fri Dec 15, 2006. Analytical coarse-grained description for polymer melts http://link.aip.org/link/?JCP/125/234902/1&agg=rss E. J. Sambriski, G. Yatsenko, M. A. Nemirovskaya, and M. G. Guenza<br/> Starting from the Ornstein-Zernike equation the authors derive an analytical theory, at the level of pair correlation functions, which coarse grains polymer melts into liquids of interacting soft colloidal particles. Since it is analytical, the presented coarse-graining approach will be useful in de ... [J. Chem. Phys. 125, 234902 (2006)] published Fri Dec 15, 2006. Analytical model for studying how environmental factors influence protein conformational stability in solution http://link.aip.org/link/?JCP/125/224903/1&agg=rss Jason K. Cheung, Prajakta S. Raverkar, and Thomas M. Truskett<br/> We introduce an analytical modeling strategy for probing the conformational stability of globular proteins in aqueous solution. In this approach, the intrinsic (i.e., infinite dilution) thermodynamic stability and coarse structural properties of the proteins, as well as the effective protein-protein ... [J. Chem. Phys. 125, 224903 (2006)] published Tue Dec 12, 2006. Association-dissociation equilibrium of loop structures in single-chain folding into a toroidal condensate http://link.aip.org/link/?JCP/125/224901/1&agg=rss Takafumi Iwaki<br/> Recently, it has been revealed that a semiflexible polyelectrolyte chain can form a partially folded conformation stably as a result of an electrostatic interaction. Interestingly, there are cases where the appearance of this structure requires a high-salt condition of a solution. In order to solve ... [J. Chem. Phys. 125, 224901 (2006)] published Fri Dec 8, 2006. Self-trapping of the NH vibrational mode in alpha-helical polypeptides http://link.aip.org/link/?JCP/125/224902/1&agg=rss Dmitry V. Tsivlin and Volkhard May<br/> Recent calculations on the formation of self-trapped amide group vibrational states in alpha-helical polypeptides [J. Chem. Phys. 124, 134907 (2006)] are extended to the amide NH normal mode vibrations. First, the adiabatic NH vibrational single- and two-exciton states are examined by treating the l ... [J. Chem. Phys. 125, 224902 (2006)] published Fri Dec 8, 2006. Thermal diffusion of dilute polymer solutions: The role of solvent viscosity http://link.aip.org/link/?JCP/125/214904/1&agg=rss M. Hartung, J. Rauch, and W. Kohler<br/> We have performed measurements of the thermal diffusion coefficient D in the dilute limit on polystyrene in cyclo-octane, cyclohexane, benzene, toluene, tetrahydrofuran, ethyl acetate, and methyl ethyl ketone and of poly(dimethyl-siloxane) in toluene. These data have been combined with literature da ... [J. Chem. Phys. 125, 214904 (2006)] published Thu Dec 7, 2006. Simulation studies of the fidelity of biomolecular structure ensemble recreation http://link.aip.org/link/?JCP/125/214905/1&agg=rss Joachim Latzer, Michael P. Eastwood, and Peter G. Wolynes<br/> We examine the ability of Bayesian methods to recreate structural ensembles for partially folded molecules from averaged data. Specifically we test the ability of various algorithms to recreate different transition state ensembles for folding proteins using a multiple replica simulation algorithm us ... [J. Chem. Phys. 125, 214905 (2006)] published Thu Dec 7, 2006. Theoretical aspects and computer simulations of flexible charged oligomers in salt-free solutions http://link.aip.org/link/?JCP/125/214907/1&agg=rss A. Bizjak, J. Rescic, Yu. V. Kalyuzhnyi, and V. Vlachy<br/> The structural and thermodynamic properties of a model solution containing flexible charged oligomers and an equivalent number of counterions were studied by means of the canonical Monte Carlo simulation and integral equation theory. The oligomers were represented as freely jointed chains of charged ... [J. Chem. Phys. 125, 214907 (2006)] published Thu Dec 7, 2006. Computation of the nonhomogeneous equilibrium states of a rigid-rod solution http://link.aip.org/link/?JCP/125/214906/1&agg=rss Micah J. Green, Robert C. Armstrong, and Robert A. Brown<br/> The nonhomogeneous equilibrium phase behavior of a solution of rigid rods is analyzed for a periodic one-dimensional system. Stable and unstable equilibrium solutions for the distribution function are computed as extrema of the free energy of the system expressed by the nonhomogeneous generalization ... [J. Chem. Phys. 125, 214906 (2006)] published Thu Dec 7, 2006. Nonequilibrium molecular dynamics simulation study on the orientation transition in the amphiphilic lamellar phase under shear flow http://link.aip.org/link/?JCP/125/214902/1&agg=rss Hongxia Guo<br/> By the extensive large-scale nonequilibrium molecular dynamics simulation on an effective generic model-A2B2 tetramer for amphiphiles, we investigate the shear-induced parallel to perpendicular orientation transition in the lamellar phase as a function of segregation degree and shear rate. Under low ... [J. Chem. Phys. 125, 214902 (2006)] published Tue Dec 5, 2006. Molecular dynamics simulation of the polymer electrolyte poly(ethylene oxide)/LiClO. II. Dynamical properties http://link.aip.org/link/?JCP/125/214903/1&agg=rss Leonardo J. A. Siqueira and Mauro C. C. Ribeiro<br/> The dynamical properties of the polymer electrolyte poly(ethylene oxide) (PEO)/LiClO have been investigated by molecular dynamics simulations. The effect of changing salt concentration and temperature was evaluated on several time correlation functions. Ionic displacements projected on different dir ... [J. Chem. Phys. 125, 214903 (2006)] published Tue Dec 5, 2006. Viral structural transitions: An all-atom multiscale theory http://link.aip.org/link/?JCP/125/214901/1&agg=rss Yinglong Miao and Peter J. Ortoleva<br/> An all-atom theory of viral structural transitions (STs) is developed based on a multiscale analysis of the N-atom Liouville equation. The approach yields an understanding of viral STs from first principles and a calibrated interatomic force field. To carry out the multiscale analysis, we introduce ... [J. Chem. Phys. 125, 214901 (2006)] published Fri Dec 1, 2006. Thermal diffusion behavior of hard-sphere suspensions http://link.aip.org/link/?JCP/125/204911/1&agg=rss Hui Ning, Johan Buitenhuis, Jan K. G. Dhont, and Simone Wiegand<br/> We studied the thermal diffusion behavior of octadecyl coated silica particles (R=27 nm) in toluene between 15.0 and 50.0 degrees C in a volume fraction range of 1%30% by means of thermal diffusion forced Rayleigh scattering. The colloidal particles behave like hard spheres at high temperatures a ... [J. Chem. Phys. 125, 204911 (2006)] published Thu Nov 30, 2006. Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality http://link.aip.org/link/?JCP/125/204910/1&agg=rss Daniel K. West, Peter D. Olmsted, and Emanuele Paci<br/> The equilibrium free energy difference between two long-lived molecular species or conformational states of a protein (or any other molecule) can in principle be estimated by measuring the work needed to shuttle the system between them, independent of the irreversibility of the process. This is the ... [J. Chem. Phys. 125, 204910 (2006)] published Wed Nov 29, 2006. Helix formation in linear achiral dendronized polymers: A computer simulation study http://link.aip.org/link/?JCP/125/204907/1&agg=rss D. K. Christopoulos, A. F. Terzis, A. G. Vanakaras, and D. J. Photinos<br/> We present a molecular simulation study of the structure of linear dendronized polymers. We use excluded volume interactions in the context of a generic coarse grained molecular model whose geometrical parameters are tuned to represent a poly(paraphenylene) backbone with benzyl ether, Frechet-type d ... [J. Chem. Phys. 125, 204907 (2006)] published Tue Nov 28, 2006. Starlike dendrimers in solutions: Structural properties and internal dynamics http://link.aip.org/link/?JCP/125/204908/1&agg=rss Silke Rathgeber, Michael Monkenbusch, James L. Hedrick, Mikael Trollsas, and Alice P. Gast<br/> We measured the shape and the internal dynamics of starlike dendrimers under good solvent conditions with small-angle neutron scattering and neutron spin-echo (NSE) spectroscopy, respectively. Architectural parameters such as the spacer length and generation were varied in a systematic manner. Struc ... [J. Chem. Phys. 125, 204908 (2006)] published Tue Nov 28, 2006.