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21 May 2012

Volume 136, Issue 19 (partial)

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J. Chem. Phys. 136, 191101 (2012); http://dx.doi.org/10.1063/1.4718380 (4 pages)

Gerald R. Kneller, Konrad Hinsen, and Paolo Calligari
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Communication: A minimal model for the diffusion-relaxation backbone dynamics of proteins

Gerald R. Kneller, Konrad Hinsen, and Paolo Calligari

J. Chem. Phys. 136, 191101 (2012); http://dx.doi.org/10.1063/1.4718380 (4 pages)

Online Publication Date: 15 May 2012

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We present a model for the local diffusion-relaxation dynamics of the Cα-atoms in proteins describing both the diffusive short-time dynamics and the asymptotic long-time relaxation of the position autocorrelation functions. The relaxation rate spectra of the latter are represented by shifted gamma distributions, where the standard gamma distribution describes anomalous slow relaxation in macromolecular systems of infinite size and the shift accounts for a smallest local relaxation rate in macromolecules of finite size. The resulting autocorrelation functions are analytic for any time t ⩾ 0. Using results from a molecular dynamics simulation of lysozyme, we demonstrate that the model fits the position autocorrelation functions of the Cα-atoms exceptionally well and reveals moreover a strong correlation between the residue's solvent-accessible surface and the fitted model parameters.
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87.15.ap Molecular dynamics simulation
87.15.Vv Diffusion
87.15.R- Reactions and kinetics
87.15.H- Dynamics of biomolecules
87.14.ej Enzymes
87.15.M- Spectra of biomolecules
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back to top Theoretical Methods and Algorithms

Replica exchange with nonequilibrium switches: Enhancing equilibrium sampling by increasing replica overlap

Andrew J. Ballard and Christopher Jarzynski

J. Chem. Phys. 136, 194101 (2012); http://dx.doi.org/10.1063/1.4712028 (11 pages)

Online Publication Date: 15 May 2012

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We describe a replica exchange strategy where trial swap configurations are generated by nonequilibrium switching simulations. By devoting simulation time to the switching simulations, one can systematically increase an effective overlap between replicas, which leads to an increased exchange acceptance rate and less correlated equilibrium samples. In this paper, we derive our method for a general class of stochastic dynamics, and discuss various strategies for enhancing replica overlap through novel dynamical schemes and prudent choices of switching protocols. We then demonstrate our method on a model system of alanine dipeptide in implicit solvent, characterizing decreases in data correlations and gains in sampling efficiency.
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87.14.ef Peptides
02.50.Ey Stochastic processes
87.15.H- Dynamics of biomolecules

A new multiscale modeling method for simulating the loss processes in polymer solar cell nanodevices

Anton Pershin, Sergii Donets, and Stephan A. Baeurle

J. Chem. Phys. 136, 194102 (2012); http://dx.doi.org/10.1063/1.4712622 (11 pages)

Online Publication Date: 15 May 2012

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The photoelectric power conversion efficiency of polymer solar cells is till now, compared to conventional inorganic solar cells, still relatively low with maximum values ranging from 7% to 8%. This essentially relates to the existence of exciton and charge carrier loss phenomena, reducing the performance of polymer solar cells significantly. In this paper we introduce a new computer simulation technique, which permits to explore the causes of the occurrence of such phenomena at the nanoscale and to design new photovoltaic materials with optimized opto-electronic properties. Our approach consists in coupling a mesoscopic field-theoretic method with a suitable dynamic Monte Carlo algorithm, to model the elementary photovoltaic processes. Using this algorithm, we investigate the influence of structural characteristics and different device conditions on the exciton generation and charge transport efficiencies in case of a novel nanostructured polymer blend. More specifically, we find that the disjunction of continuous percolation paths leads to the creation of dead ends, resulting in charge carrier losses through charge recombination. Moreover, we observe that defects are characterized by a low exciton dissociation efficiency due to a high charge accumulation, counteracting the charge generation process. From these observations, we conclude that both the charge carrier loss and the exciton loss phenomena lead to a dramatic decrease in the internal quantum efficiency. Finally, by analyzing the photovoltaic behavior of the nanostructures under different circuit conditions, we demonstrate that charge injection significantly determines the impact of the defects on the solar cell performance.
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88.40.hj Efficiency and performance of solar cells
88.40.jr Organic photovoltaics

Equation of state of charged colloidal suspensions and its dependence on the thermodynamic route

Thiago E. Colla, Alexandre P. dos Santos, and Yan Levin

J. Chem. Phys. 136, 194103 (2012); http://dx.doi.org/10.1063/1.4718367 (7 pages)

Online Publication Date: 16 May 2012

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The thermodynamic properties of highly charged colloidal suspensions in contact with a salt reservoir are investigated in the framework of the renormalized Jellium model (RJM). It is found that the equation of state is very sensitive to the particular thermodynamic route used to obtain it. Specifically, the osmotic pressure calculated within the RJM using the contact value theorem can be very different from the pressure calculated using the Kirkwood-Buff fluctuation relations. On the other hand, Monte Carlo simulations show that both the effective pair potentials and the correlation functions are accurately predicted by the RJM. It is suggested that the lack of self-consistency in the thermodynamics of the RJM is a result of neglected electrostatic correlations between the counterions and coions.
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82.70.Dd Colloids
61.20.Ja Computer simulation of liquid structure
82.70.Kj Emulsions and suspensions
64.30.-t Equations of state of specific substances

Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model

Alisa Solovyeva, Michele Pavanello, and Johannes Neugebauer

J. Chem. Phys. 136, 194104 (2012); http://dx.doi.org/10.1063/1.4709771 (14 pages)

Online Publication Date: 16 May 2012

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Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn–Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a π-stacked guanine–thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn–Sham DFT calculations. In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn–Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.
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31.15.ej Spin-density functionals
31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)
87.15.ag Quantum calculations
87.15.M- Spectra of biomolecules
82.50.Hp Processes caused by visible and UV light
87.16.-b Subcellular structure and processes

Hybrid coupled cluster methods: Combining active space coupled cluster methods with coupled cluster singles, doubles, and perturbative triples

Zhuangfei Kou, Jun Shen, Enhua Xu, and Shuhua Li

J. Chem. Phys. 136, 194105 (2012); http://dx.doi.org/10.1063/1.4716185 (8 pages)

Online Publication Date: 16 May 2012

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Based on the coupled-cluster singles, doubles, and a hybrid treatment of triples (CCSD(T)-h) method developed by us [J. Shen, E. Xu, Z. Kou, and S. Li, J. Chem. Phys. 132, 114115 (2010)10.1063/1.3359851; J. Shen, E. Xu, Z. Kou, and S. Li, J. Chem. Phys. 133, 234106 (2010)10.1063/1.3518100; J. Shen, E. Xu, Z. Kou, and S. Li, J. Chem. Phys. 134, 044134 (2011)10.1063/1.3541250], we developed and implemented a new hybrid coupled cluster (CC) method, named CCSD(T)q-h, by combining CC singles and doubles, and active triples and quadruples (CCSDtq) with CCSD(T) to deal with the electronic structures of molecules with significant multireference character. These two hybrid CC methods can be solved with non-canonical and canonical MOs. With canonical MOs, the CCSD(T)-like equations in these two methods can be solved directly without iteration so that the storage of all triple excitation amplitudes can be avoided. A practical procedure to divide canonical MOs into active and inactive subsets is proposed. Numerical calculations demonstrated that CCSD(T)-h with canonical MOs can well reproduce the corresponding results obtained with non-canonical MOs. For three atom exchange reactions, we found that CCSD(T)-h can offer a significant improvement over the popular CCSD(T) method in describing the reaction barriers. For the bond-breaking processes in F2 and H2O, our calculations demonstrated that CCSD(T)q-h is a good approximation to CCSDTQ over the entire bond dissociation processes.
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31.15.bw Coupled-cluster theory
33.15.-e Properties of molecules
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Full-dimensional quantum dynamics study of exchange processes for the D + H2O and D + HOD reactions

Bina Fu and Dong H. Zhang

J. Chem. Phys. 136, 194301 (2012); http://dx.doi.org/10.1063/1.4718386 (7 pages)

Online Publication Date: 16 May 2012

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The exchange processes of D + H2O and D + HOD reactions are studied using initial state-selected time-dependent wave packet approach in full dimension. The total reaction probabilities for different partial waves, together with the integral cross sections, are obtained both by the centrifugal sudden (CS) approximation and exact coupled-channel (CC) calculations, for the H2O(HOD) reactant initially in the ground rovibrational state. In the CC calculations, small resonance peaks in the reaction probabilities and quick diminishing of the resonance peaks with the increase of total angular momenta J do not lead to clear step-like features just above the threshold in the cross sections for the title reactions, which are different in other isotopically substituted reactions where the hydrogen atom was included as the reactant instead of the deuterium atom [B. Fu, Y. Zhou, and D. H. Zhang, Chem. Sci. 3, 270 (2012)10.1039/c1sc00684c; B. Fu and D. H. Zhang, J. Phys. Chem. A 116, 820 (2012)10.1021/jp211096q]. It is interesting that the shape resonance-induced features resulting from the reaction tunneling are significantly diminished accordingly in the reactions of the deuterium atom and H2O or HOD, owing to the weaker tunneling capability of the reagent deuterium atom in the title reactions than the reagent hydrogen atom in other reactions. In the CS calculations, the resonance peaks persist in many partial waves but cannot survive the partial-wave summations. The cross sections for the D′ + H2O → D′OH + H and D′ + HOD → D′OD + H reactions are substantially larger than those for the D′ + HOD → HOD′ + D reaction, indicating that the D′/H exchange reactions are much more favored than the D′/D exchange.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.20.-w Chemical kinetics and dynamics
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Resonant inelastic x-ray scattering of CeB6 at the Ce L1- and L3-edges

Lijia Liu, Tsun-Kong Sham, Hisashi Hayashi, Noriko Kanai, Yuki Takehara, Naomi Kawamura, Masaichiro Mizumaki, and Robert A. Gordon

J. Chem. Phys. 136, 194501 (2012); http://dx.doi.org/10.1063/1.4716180 (8 pages)

Online Publication Date: 15 May 2012

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We report a resonant inelastic x-ray scattering (RIXS) study of crystalline CeB6. Ce Lα1,2 RIXS was measured with excitation energies resonant with the Ce L3-edge. A lifetime-broadening suppressed x-ray absorption near-edge structure (LBS-XANES), which successfully reproduced the Lα1,2 RIXS spectra over wide ranges of excitation and emission energies, was simulated using the SIM-RIXS program. A pre-edge structure in the LBS-XANES can be resolved, and many-body effects were suggested in the Lα1,2 RIXS around the Ce L3-edge energy. No convincing signs of Ce (II) or Ce (IV) states were observed in the LBS-XANES. Ce Lγ4 RIXS was measured at 302 K and 28 K with excitation energies across the Ce L1-edge. The interactions of p-valence electrons between Ce and B6 were found to be considerably small, regardless of temperature. Thus, the electronic state of CeB6 was concluded to be suitably described as a nominally Ce(4f 1)3+(e−)(B6)2− system with some hybridization among all valence orbitals of Ce and B.
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78.70.Ck X-ray scattering
78.70.Dm X-ray absorption spectra
71.20.Ps Other inorganic compounds

Theory and simulation of anisotropic pair correlations in ferrofluids in magnetic fields

Ekaterina A. Elfimova, Alexey O. Ivanov, and Philip J. Camp

J. Chem. Phys. 136, 194502 (2012); http://dx.doi.org/10.1063/1.4717718 (12 pages)

Online Publication Date: 16 May 2012

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Anisotropic pair correlations in ferrofluids exposed to magnetic fields are studied using a combination of statistical-mechanical theory and computer simulations. A simple dipolar hard-sphere model of the magnetic colloidal particles is studied in detail. A virial-expansion theory is constructed for the pair distribution function (PDF) which depends not only on the length of the pair separation vector, but also on its orientation with respect to the field. A detailed comparison is made between the theoretical predictions and accurate simulation data, and it is found that the theory works well for realistic values of the dipolar coupling constant (λ = 1), volume fraction (φ ⩽ 0.1), and magnetic field strength. The structure factor is computed for wavevectors either parallel or perpendicular to the field. The comparison between theory and simulation is generally very good with realistic ferrofluid parameters. For both the PDF and the structure factor, there are some deviations between theory and simulation at uncommonly high dipolar coupling constants, and with very strong magnetic fields. In particular, the theory is less successful at predicting the behavior of the structure factors at very low wavevectors, and perpendicular Gaussian density fluctuations arising from strongly correlated pairs of magnetic particles. Overall, though, the theory provides reliable predictions for the nature and degree of pair correlations in ferrofluids in magnetic fields, and hence should be of use in the design of functional magnetic materials.
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61.20.Ja Computer simulation of liquid structure
75.50.Mm Magnetic liquids
75.50.Tt Fine-particle systems; nanocrystalline materials
61.20.Gy Theory and models of liquid structure
back to top Surfaces, Interfaces, and Materials

Relaxation and jump dynamics of water at the mica interface

Ateeque Malani and K. G. Ayappa

J. Chem. Phys. 136, 194701 (2012); http://dx.doi.org/10.1063/1.4717710 (11 pages)

Online Publication Date: 15 May 2012

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The orientational relaxation dynamics of water confined between mica surfaces is investigated using molecular dynamics simulations. The study illustrates the wide heterogeneity that exists in the dynamics of water adjacent to a strongly hydrophilic surface such as mica. Analysis of the survival probabilities in different layers is carried out by normalizing the corresponding relaxation times with bulk water layers of similar thickness. A 10-fold increase in the survival times is observed for water directly in contact with the mica surface and a non-monotonic variation in the survival times is observed moving away from the mica surface to the bulk-like interior. The orientational relaxation time is highest for water in the contact layer, decreasing monotonically away from the surface. In all cases the ratio of the relaxation times of the 1st and 2nd rank Legendre polynomials of the HH bond vector is found to lie between 1.5 and 1.9 indicating that the reorientational relaxation in the different water layers is governed by jump dynamics. The orientational dynamics of water in the contact layer is particularly novel and is found to undergo distinct two-dimensional hydrogen bond jump reorientational dynamics with an average waiting time of 4.97 ps. The waiting time distribution is found to possess a long tail extending beyond 15 ps. Unlike previously observed jump dynamics in bulk water and other surfaces, jump events in the mica contact layer occur between hydrogen bonds formed by the water molecule and acceptor oxygens on the mica surface. Despite slowing down of the water orientational relaxation near the surface, life-times of water in the hydration shell of the K+ ion are comparable to that observed in bulk salt solutions.
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68.08.Bc Wetting
61.20.Ja Computer simulation of liquid structure
61.50.Lt Crystal binding; cohesive energy

Molecular modification of coumarin dyes for more efficient dye sensitized solar cells

Rocío Sánchez-de-Armas, Miguel A. San-Miguel, Jaime Oviedo, and Javier Fdez. Sanz

J. Chem. Phys. 136, 194702 (2012); http://dx.doi.org/10.1063/1.4711049 (7 pages)

Online Publication Date: 16 May 2012

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In this work, new coumarin based dyes for dye sensitized solar cells (DSSC) have been designed by introducing several substituent groups in different positions of the NKX-2311 structure. Two types of substitutions have been considered: the introduction of three electron-donating groups (–OH, –NH2, and –OCH3) and two different substituents with steric effect: –CH2–CH2–CH2– and –CH2–HC=CH–. The electronic absorption spectra (position and width of the first band and absorption threshold) and the position of the LUMO level related to the conduction band have been used as theoretical criteria to evaluate the efficiency of the new dyes. The introduction of a –NH2 group produces a redshift of the absorption maximum position and the absorption threshold, which could improve the cell efficiency. In contrast, the introduction of –CH2–CH2–CH2– does not modify significantly the electronic structure of NKX-2311, but it might prevent aggregation. Finally, –CH2–HC=CH– produces important changes both in the electronic spectrum and in the electronic structure of the dye, and it would be expected as an improvement of cell efficiency for these dyes.
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33.20.Kf Visible spectra
82.50.Hp Processes caused by visible and UV light
31.15.ee Time-dependent density functional theory
88.40.J- Types of solar cells
33.15.Bh General molecular conformation and symmetry; stereochemistry
back to top Polymers and Complex Systems

Semiflexible polymers grafted to a solid planar substrate: Changing the structure from polymer brush to “polymer bristle”

A. Milchev and Kurt Binder

J. Chem. Phys. 136, 194901 (2012); http://dx.doi.org/10.1063/1.4712138 (8 pages)

Online Publication Date: 15 May 2012

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Monte Carlo simulations are presented for a coarse-grained model of polymer brushes with polymers having a varying degree of stiffness. Both linear chains and ring polymers grafted to a flat structureless non-adsorbing substrate surface are considered. Applying good solvent conditions, it is shown that with growing polymer stiffness the brush height increases significantly. The monomer density profiles for the case of ring polymers (chain length NR = 64) are very similar to the case of corresponding linear chains (NL = 32, grafting density larger by a factor of two) in the case of flexible polymers, while slight differences appear with increasing stiffness. Evidence is obtained that the chain dynamics in brushes is slowed down dramatically with increasing stiffness. Very short stiff rings (NR ⩽ 16) behave like disks, grafted to the substrate such that the vector, perpendicular to the disk plane, is oriented parallel to the substrate surface. It is suggested that such systems can undergo phase transitions to states with liquid crystalline order.
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61.41.+e Polymers, elastomers, and plastics
81.40.Jj Elasticity and anelasticity, stress-strain relations
62.20.dq Other elastic constants
64.70.D- Solid-liquid transitions

Lattice cluster theory of associating telechelic polymers. III. Order parameter and average degree of self-assembly, transition temperature, and specific heat

Jacek Dudowicz, Karl F. Freed, and Jack F. Douglas

J. Chem. Phys. 136, 194902 (2012); http://dx.doi.org/10.1063/1.4714562 (7 pages)

Online Publication Date: 15 May 2012

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The lattice cluster theory of strongly interacting, structured polymer fluids is applied to determine the thermodynamic properties of solutions of telechelic polymers that may associate through bifunctional end groups. Hence, this model represents a significant albeit natural extension of a diverse array of prior popular equilibrium polymerization models in which structureless “bead” monomers associate into chain-like clusters under equilibrium conditions. In particular, the thermodynamic description of the self-assembly of linear telechelic chains in small molecule solvents (initiated in Paper II) is systematically extended through calculations of the order parameter Φ and average degree ⟨N⟩ of self-assembly, the self-assembly transition temperature Tp, and the specific heat CV of solutions of telechelic molecules. Special focus is placed on examining how molecular and thermodynamic parameters, such as the solution composition ϕ, temperature T, microscopic interaction energies (εs and ε), and length M of individual telechelic chains, influence the computed thermodynamic quantities that are commonly used to characterize self-assembling systems.
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65.20.Jk Studies of thermodynamic properties of specific liquids
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
82.30.Nr Association, addition, insertion, cluster formation
82.35.-x Polymers: properties; reactions; polymerization

Lattice cluster theory of associating polymers. IV. Phase behavior of telechelic polymer solutions

Jacek Dudowicz, Karl F. Freed, and Jack F. Douglas

J. Chem. Phys. 136, 194903 (2012); http://dx.doi.org/10.1063/1.4714563 (8 pages)

Online Publication Date: 15 May 2012

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The newly developed lattice cluster theory (in Paper I) for the thermodynamics of solutions of telechelic polymers is used to examine the phase behavior of these complex fluids when effective polymer-solvent interactions are unfavorable. The telechelics are modeled as linear, fully flexible, polymer chains with mono-functional stickers at the two chain ends, and these chains are assumed to self-assemble upon cooling. Phase separation is generated through the interplay of self-assembly and polymer/solvent interactions that leads to an upper critical solution temperature phase separation. The variations of the boundaries for phase stability and the critical temperature and composition are analyzed in detail as functions of the number M of united atom groups in a telechelic chain and the microscopic nearest neighbor interaction energy εs driving the self-assembly. The coupling between self-assembly and unfavorable polymer/solvent interactions produces a wide variety of nontrivial patterns of phase behavior, including an enhancement of miscibility accompanying the increase of the molar mass of the telechelics under certain circumstances. Special attention is devoted to understanding this unusual trend in miscibility.
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64.75.Bc Solubility
64.75.Va Phase separation and segregation in polymer blends/polymeric solutions
65.20.Jk Studies of thermodynamic properties of specific liquids
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
47.57.Ng Polymers and polymer solutions
61.25.he Polymer solutions
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