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| <title>New content is available for The Journal of Chemical Physics</title> | |
| <link>http://scitation.aip.org</link> | |
| <description>New content is now available online. Please follow the links to view the content.</description> | |
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| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863558"> | |
| <title>Enhanced ordering of water at hydrophobic surfaces</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863558</link> | |
| <description><p>We study the properties of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">water</span> molecules adjacent to a <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">hydrophobic</span> molecular layer with vibrational sum-frequency generation spectroscopy. We find that the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">water</span> molecules at D<span class="jp-sub">2</span>O/hexane, D<span class="jp-sub">2</span>O/heptane, and D<span class="jp-sub">2</span>O/polydimethylsiloxane <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">interfaces</span> show an enhanced ordering and stronger hydrogen-bond <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">interactions</span> than the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">water</span> molecules at a D<span class="jp-sub">2</span>O/air <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">interface.</span> With increasing temperature (up to 80 °C) the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">water</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">structure</span> becomes significantly less ordered and the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">hydrogen bonds</span> become weaker.</p></description> | |
| <dc:date>2014-02-07T14:50:42Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863862"> | |
| <title>Dynamical steering in an electron transfer surface reaction: Oriented NO(v = 3, 0.08 < Ei < 0.89 eV) relaxation in collisions with a Au(111) surface</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863862</link> | |
| <description><p>We report measurements of the incidence translational energy dependence of steric effects in collisions of NO(<span class="jp-italic">v</span> = 3) molecules with a Au(111) <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">surface</span> using a recently developed technique to orient <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">beams</span> of vibrationally excited NO molecules at incidence energies of translation between 0.08 and 0.89 eV. Incidence orientation dependent vibrational state distributions of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">scattered</span> molecules are detected by means of resonance enhanced multiphoton ionization spectroscopy. Molecules oriented with the N-end towards the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">surface</span> exhibit a higher vibrational relaxation probability than those oriented with the O-end towards the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">surface.</span> This strong orientation dependence arises from the orientation dependence of the underlying <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">electron transfer</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">reaction</span> responsible for the vibrational relaxation. At reduced incidence translational energy, we observe a reduced steric effect. This reflects dynamical steering and re-orientation of the NO molecule upon its approach to the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">surface.</span> </p></description> | |
| <dc:date>2014-02-07T14:50:28Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864118"> | |
| <title>Anomalous composition-dependent dynamics of nanoconfined water in the interlayer of disordered calcium-silicates</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864118</link> | |
| <description><p>With shear interest in nanoporous materials, the ultraconfining interlayer spacing of calcium–silicate–hydrate (C–S–H) provides an excellent medium to study reactivity, <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">structure,</span> and dynamic properties of water. In this paper, we present how substrate composition affects chemo-physical properties of water in ultraconfined <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">hydrophilic</span> media. This is achieved by performing <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">molecular dynamics simulation</span> on a set of 150 realistic models with different compositions of calcium and silicon contents. It is demonstrated that the substrate chemistry directly affects the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">structural</span> properties of water molecules. The motion of confined water shows a multi-stage dynamics which is characteristic of supercooled liquids and glassy phases. Inhomogeneity in that dynamics is used to differentiate between mobile and immobile water molecules. Furthermore, it is shown that the mobility of water molecules is composition-dependent. Similar to the pressure-driven self-diffusivity anomaly observed in bulk water, we report the first study on composition-driven <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion</span> anomaly, the self diffusivity increases with increasing confined water density in C–S–H. Such anomalous behavior is explained by the decrease in the typical activation energy required for a water molecule to escape its dynamical cage.</p></description> | |
| <dc:date>2014-02-07T14:41:34Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863502"> | |
| <title>Kohn-Sham band gaps and potentials of solids from the optimised effective potential method within the random phase approximation</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863502</link> | |
| <description><p>We present an implementation of the optimised effective potential (OEP) scheme for the exact-exchange (EXX) and random phase approximation (RPA) energy functionals and apply these methods to a range of bulk materials. We calculate the Kohn-Sham (KS) potentials and the corresponding <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">band gaps</span> and compare them to the potentials obtained by standard local density approximation <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">(LDA)</span> calculations. The KS <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">gaps</span> increase upon going from the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">LDA</span> to the OEP in the RPA and finally to the OEP for EXX. This can be explained by the different depth of the potentials in the bonding and interstitial regions. To obtain the true quasi-particle <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">gaps</span> the derivative discontinuities or <span class="jp-italic">G</span> <span class="jp-sub">0</span> <span class="jp-italic">W</span> <span class="jp-sub">0</span> corrections need to be added to the RPA-OEP KS <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">gaps.</span> The predicted <span class="jp-italic">G</span> <span class="jp-sub">0</span> <span class="jp-italic">W</span> <span class="jp-sub">0</span>@RPA-OEP quasi-particle <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">gaps</span> are about 5% too large compared to the experimental values. However, compared to <span class="jp-italic">G</span> <span class="jp-sub">0</span> <span class="jp-italic">W</span> <span class="jp-sub">0</span> calculations based on local or semi-local functionals, where the errors vary between different materials, we obtain a rather consistent description among all the materials.</p></description> | |
| <dc:date>2014-02-07T14:41:13Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864109"> | |
| <title>K6 carbon: A metallic carbon allotrope in sp3 bonding networks</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864109</link> | |
| <description><p>We identify by <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">first-principles calculations</span> a new cubic <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">carbon</span> phase in <span class="jp-italic">I</span>4<span class="jp-sub">1</span>32 (<span class="jp-italic">O</span> <sup xmlns="http://pub2web.metastore.ingenta.com/ns/">8</sup>) symmetry, named <span class="jp-italic">K</span> <span class="jp-sub">6</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">carbon,</span> which has a six atom primitive cell comprising <span class="jp-italic">sp</span> <sup xmlns="http://pub2web.metastore.ingenta.com/ns/">3</sup> hybridized C<span class="jp-sub">3</span> triangle rings. The structural stability is verified by <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">phonon</span> mode analysis. The calculated <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">elastic</span> constants show that the <span class="jp-italic">K</span> <span class="jp-sub">6</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">carbon</span> is a high <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">ductile</span> material with a density even lower than <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">graphite.</span> Electronic band and <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">density of states</span> calculations reveal that it is a metallic <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">carbon</span> allotrope with a high electronic <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">density of states</span> of ∼0.10 states/eV per atom at the Fermi level. These results broaden our understanding of the structural and electronic properties of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">carbon</span> allotropes.</p></description> | |
| <dc:date>2014-02-07T14:41:06Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863443"> | |
| <title>Optical and electronic properties of mixed Ag-Au tetramer cations</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863443</link> | |
| <description><p>We present experimental and <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">theoretical</span> studies of the optical response of mixed <span class="capture-id"> <script xmlns="http://pub2web.metastore.ingenta.com/ns/" type="math/mml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi> Ag </mml:mi> <mml:mi>n</mml:mi> </mml:msub> <mml:msubsup> <mml:mi> Au </mml:mi> <mml:mrow> <mml:mn>4</mml:mn> <mml:mo>−</mml:mo> <mml:mi>n</mml:mi> </mml:mrow> <mml:mo>+</mml:mo> </mml:msubsup> </mml:mrow> </mml:math> </script> </span> (<span class="jp-italic">n</span>=1–3) clusters in the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">photon</span> energy range ℏω = 1.9–3.5 eV. <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Absorption spectra</span> are recorded by a newly built longitudinal molecular <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">beam</span> depletion spectroscopy apparatus providing lower limits to absolute photodissociation cross sections. The experimental data are compared to optical response calculations in the framework of long-range corrected time-dependent density functional theory with initial cluster geometries obtained by the unbiased Birmingham Cluster Genetic Algorithm coupled with <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">density functional theory.</span> Experiments and excited state calculations shed light on the structural and electronic <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">properties</span> of the mixed Ag-Au tetramer cations.</p></description> | |
| <dc:date>2014-02-07T14:30:16Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864038"> | |
| <title>Electronic responses of long chains to electrostatic fields: Hartree-Fock vs. density-functional theory: A model study</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864038</link> | |
| <description><p>The response to an <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">electrostatic</span> field is determined through simple <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">model</span> calculations, within both the restricted Hartree-Fock and <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">density functional theory</span> methods, for long, finite as well as infinite, periodic chains. The permanent <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">dipole moment,</span> μ<span class="jp-sub">0</span>, the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">polarizability,</span> α, and the hyperpolarizabilities β and γ, calculated using a finite-field approach, are extensively analyzed. Our simple <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">model</span> allows for treatment of large systems and for separation of the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">properties</span> into atomic and unit-cell contributions. That part of the response <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">properties</span> attributable to the terminations of the finite system change into delocalized current contributions in the corresponding infinite periodic system. Special emphasis is placed on analyzing the reasons behind the dramatic overestimation of the response <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">properties</span> found with <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">density functional theory</span> methods presently in common use.</p></description> | |
| <dc:date>2014-02-07T14:21:43Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863991"> | |
| <title>Generalized event-chain Monte Carlo: Constructing rejection-free global-balance algorithms from infinitesimal steps</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863991</link> | |
| <description><p>In this article, we present an event-driven algorithm that generalizes the recent hard-sphere event-chain <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Monte Carlo method</span> without introducing discretizations in time or in space. A factorization of the Metropolis filter and the concept of infinitesimal <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Monte Carlo</span> moves are used to design a rejection-free <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Markov-chain</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Monte Carlo algorithm</span> for particle systems with arbitrary pairwise interactions. The algorithm breaks detailed balance, but satisfies maximal global balance and performs better than the classic, local Metropolis algorithm in large systems. The new algorithm generates a continuum of samples of the stationary <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">probability density.</span> This allows us to compute the pressure and stress <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">tensor</span> as a byproduct of the simulation without any additional computations.</p></description> | |
| <dc:date>2014-02-07T14:21:33Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864360"> | |
| <title>Communication: Rigidity of the molecular ion H5+</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864360</link> | |
| <description><p>The fourth-age quantum chemical code GENIUSH is used for the variational determination of rotational-vibrational <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">energy</span> levels corresponding to reduced- and full-dimensional models of <span class="capture-id"> <script xmlns="http://pub2web.metastore.ingenta.com/ns/" type="math/mml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mi>H</mml:mi> <mml:mn>5</mml:mn> <mml:mo>+</mml:mo> </mml:msubsup> </mml:math> </script> </span>, a molecular ion exhibiting several strongly coupled large-amplitude motions. The computations are supplemented with one- and two-dimensional analytic results which help to understand the peculiar rovibrational energy-level structure computed correctly for the first time. An unusual aspect of the results is that the canonical Eckart-embedding of molecule-fixed axes, a cornerstone of the computational <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">spectroscopy</span> of semirigid molecules, is found to be inadequate. Furthermore, it is shown that while the 1D “active torsion” model provides proper results when compared to the full, 9D treatment, models excluding the torsion have limited physical significance. The structure of the rovibrational <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">energy</span> levels of <span class="capture-id"> <script xmlns="http://pub2web.metastore.ingenta.com/ns/" type="math/mml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mi>H</mml:mi> <mml:mn>5</mml:mn> <mml:mo>+</mml:mo> </mml:msubsup> </mml:math> </script> </span> proves that this is a prototypical astructural molecule: the rotational and vibrational level spacings are of the same order of magnitude and the level structure drastically deviates from that computed via perturbed rigid-rotor and harmonic-oscillator models.</p></description> | |
| <dc:date>2014-02-07T14:10:44Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863990"> | |
| <title>Validity conditions for stochastic chemical kinetics in diffusion-limited systems</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863990</link> | |
| <description><p>The chemical master <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">equation</span> (CME) and the mathematically equivalent stochastic simulation algorithm (SSA) assume that the reactant molecules in a chemically reacting system are “dilute” and “well-mixed” throughout the containing volume. Here we clarify what those two conditions mean, and we show why their satisfaction is necessary in order for bimolecular <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">reactions</span> to physically occur in the manner assumed by the CME and the SSA. We prove that these conditions are closely connected, in that a system will stay well-mixed if and only if it is dilute. We explore the implications of these validity conditions for the reaction-diffusion (or spatially inhomogeneous) extensions of the CME and the SSA to systems whose containing volumes are not necessarily well-mixed, but can be partitioned into cubical subvolumes (voxels) that are. We show that the validity conditions, together with an additional condition that is needed to ensure the physical validity of the diffusion-induced jump probability rates of molecules between voxels, require the voxel edge length to have a strictly positive lower bound. We prove that if the voxel edge length is steadily decreased in a way that respects that lower bound, the average rate at which bimolecular <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">reactions</span> occur in the reaction-diffusion CME and SSA will remain constant, while the average rate of diffusive <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">transfer reactions</span> will increase as the inverse square of the voxel edge length. We conclude that even though the reaction-diffusion CME and SSA are inherently approximate, and cannot be made exact by shrinking the voxel size to zero, they should nevertheless be useful in many practical situations.</p></description> | |
| <dc:date>2014-02-06T19:49:08Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863559"> | |
| <title>Omni-conducting and omni-insulating molecules</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863559</link> | |
| <description><p>The source and sink potential model is used to predict the existence of omni-conductors (and omni-insulators): molecular conjugated π systems that respectively support ballistic conduction or show insulation at the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Fermi level,</span> irrespective of the centres chosen as connections. <span class="jp-italic">Distinct</span>, <span class="jp-italic">ipso,</span> and <span class="jp-italic">strong</span>omni-conductors/omni-insulators show Fermi-level conduction/insulation for all <span class="jp-italic">distinct</span> pairs of connections, for all connections via a <span class="jp-italic">single</span> centre, and for <span class="jp-italic">both</span>, respectively. The class of conduction behaviour depends critically on the number of non-bonding orbitals (NBO) of the molecular system (corresponding to the nullity of the graph). Distinct omni-conductors have at most one NBO; distinct omni-insulators have at least two NBO; strong omni-insulators do not exist for any number of NBO. Distinct omni-conductors with a single NBO are all also strong and correspond exactly to the class of graphs known as <span class="jp-italic">nut</span> graphs. Families of conjugated hydrocarbons corresponding to <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">chemical</span> graphs with predicted omni-conducting/insulating behaviour are identified. For example, most <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">fullerenes</span> are predicted to be strong omni-conductors.</p></description> | |
| <dc:date>2014-02-06T18:47:13Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863329"> | |
| <title>Adaptive resolution simulation of an atomistic protein in MARTINI water</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863329</link> | |
| <description><p>We present an adaptive resolution simulation of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">protein</span> G in multiscale water. We couple atomistic water around the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">protein</span> with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">model</span> via a 4-to-1 molecule coarse-grain mapping by using bundled water <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">models,</span> i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">molecular dynamics simulations,</span> we observe within our error bars no differences between <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">structural</span> (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">solvent</span> accessible surface area) and dynamical <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">properties</span> of the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">protein</span> in the adaptive resolution approach compared to the fully atomistically solvated <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">model.</span> Our multiscale <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">model</span> is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">biomolecular</span> simulations.</p></description> | |
| <dc:date>2014-02-06T16:53:37Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863992"> | |
| <title>A coarse-grained model for the simulations of biomolecular interactions in cellular environments</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863992</link> | |
| <description><p>The <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">interactions</span> of bio-molecules constitute the key steps of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">cellular</span> functions. However, <span class="jp-italic">in vivo</span> binding properties differ significantly from their <span class="jp-italic">in vitro</span> measurements due to the heterogeneity of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">cellular</span> environments. Here we introduce a coarse-grained <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">model</span> based on rigid-body representation to study how factors such as <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">cellular</span> crowding and <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">membrane</span> confinement affect molecular binding. The macroscopic parameters such as the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">equilibrium constant</span> and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">model</span> parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">cellular</span> environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion</span> and diffusion-limited <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">reactions.</span> Furthermore, the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">binding constants</span> of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">membrane proteins</span> are currently difficult to measure. We provide quantitative estimations about how the binding of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">membrane proteins</span> deviates from <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">soluble</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">proteins</span> under different degrees of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">membrane</span> confinements. The simulation results provide biological insights to the functions of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">membrane</span> receptors on <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">cell</span> surfaces. Overall, our studies establish a connection between the details of molecular <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">interactions</span> and the heterogeneity of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">cellular</span> environments.</p></description> | |
| <dc:date>2014-02-06T16:53:29Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863995"> | |
| <title>Anomalous diffusion with transient subordinators: A link to compound relaxation laws</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863995</link> | |
| <description><p>This paper deals with a problem of transient anomalous <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion</span> which is currently found to emerge from a wide range of complex processes. The nonscaling behavior of such phenomena reflects changes in time-scaling exponents of the mean-squared displacement through time domain – a more general picture of the anomalous <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion</span> observed in nature. Our study is based on the identification of some transient subordinators responsible for transient anomalous <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion.</span> We derive the corresponding fractional <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">equation</span> and provide links to the corresponding compound <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">relaxation</span> laws supported by this case generalizing many empirical dependencies well-known in <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">relaxation</span> investigations.</p></description> | |
| <dc:date>2014-02-06T16:53:19Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863444"> | |
| <title>Charge/mass dynamic structure factors of water and applications to dielectric friction and electroacoustic conversion</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863444</link> | |
| <description><p>We determine time <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">correlation functions</span> and dynamic structure factors of the number and <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">charge density</span> of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">liquid</span> water from <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">molecular dynamics simulations.</span> Using these <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">correlation functions</span> we consider <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">dielectric</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">friction</span> and electro-acoustic coupling <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">effects</span> via linear response theory. From charge-charge correlations, the drag force on a moving point charge is derived and found to be maximal at a velocity of around 300 m/s. Strong deviations in the resulting <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">friction</span> coefficients from approximate theory employing a single Debye relaxation mode are found that are due to non-Debye-like resonances at high frequencies. From charge-mass cross-correlations the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">ultrasonic</span> vibration potential is derived, which characterizes the conversion of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">acoustic waves</span> into electric time-varying potentials. Along the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">dispersion relation</span> for normal sound waves in water, the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">ultrasonic</span> vibration potential is shown to strongly vary and to increase for larger wavelengths.</p></description> | |
| <dc:date>2014-02-06T16:18:12Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4862689"> | |
| <title>Theoretical analysis of aqueous solutions of mixed strong electrolytes by a smaller-ion shell electrostatic model</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4862689</link> | |
| <description><p>In spite of the great importance of mixed <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">electrolytes</span> in science and technology, no compelling <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">theoretical</span> explanation has been offered yet for the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">thermodynamic</span> behavior of such systems, such as their deviation from ideality and the variation of their excess functions with ionic composition and concentration. Using the newly introduced Smaller-ion Shell treatment – an extension of the Debye–Hückel <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">theory</span> to ions of dissimilar size (hence DH–SiS) – simple analytic mathematical expressions can be derived for the mean and single-ion activity coefficients of binary <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">electrolyte</span> components of ternary ionic systems. Such expressions are based on modifying the parallel DH–SiS equations for pure binary ionic systems, by adding to the three ion-size parameters – <span class="jp-italic">a</span> (of counterions), <span class="jp-italic">b</span> <span class="jp-sub">+</span> (of positive coions), and <span class="jp-italic">b</span> <span class="jp-sub">−</span> (of negative coions) – a fourth parameter. For the (+ + −) system, this is “<span class="jp-italic">b</span> <span class="jp-sub">++</span>,” the contact distance between non-coion cations. <span class="jp-italic">b</span> <span class="jp-sub">++</span> is derived from fits with experiment and, like the other <span class="jp-italic">b</span>’s, is constant at varying ion concentration and combination. Four case studies are presented: (1) HCl–NaCl–H<span class="jp-sub">2</span>O, (2) HCl–NH<span class="jp-sub">4</span>Cl–H<span class="jp-sub">2</span>O, (3) (0.01 M H<span class="jp-italic">X</span>)–<span class="jp-italic">MX</span>–H<span class="jp-sub">2</span>O with <span class="jp-italic">X</span> = Cl, Br, and with <span class="jp-italic">M</span> = Li, <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Na,</span> K, Cs, and (4) HCl–<span class="jp-italic">M</span>Cl<span class="jp-sub"> <span class="jp-italic">n</span> </span>–H<span class="jp-sub">2</span>O with <span class="jp-italic">n</span> = 2, <span class="jp-italic">M</span> = Sr, Ba; and <span class="jp-italic">n</span> = 3, <span class="jp-italic">M</span> = Al, Ce. In all cases, <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">theory</span> is fully consistent with experiment when using <span class="jp-italic">a</span> of the measured binary <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">electrolyte</span> as the sole fitting parameter. DH–SiS is thus shown to explain known “mysteries” in the behavior of ternary <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">electrolytes,</span> including Harned rule, and to adequately predict the pH of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">acid</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">solutions</span> in which ionized salts are present at different concentrations.</p></description> | |
| <dc:date>2014-02-06T16:18:00Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863918"> | |
| <title>Multiscale modeling of polyisoprene on graphite</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863918</link> | |
| <description><p>The local <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">dynamics</span> and the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">conformational</span> properties of polyisoprene next to a smooth <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">graphite</span> <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">surface</span> constructed by <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">graphene</span> layers are studied by a multiscale methodology. First, fully atomistic <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">molecular dynamics simulations</span> of oligomers next to the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">surface</span> are performed. Subsequently, <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Monte Carlo simulations</span> of a systematically derived coarse-grained model generate numerous uncorrelated <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">structures</span> for <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">polymer</span> systems. A new reverse backmapping strategy is presented that reintroduces atomistic detail. Finally, multiple extensive fully atomistic simulations with large systems of long macromolecules are employed to examine local <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">dynamics</span> in proximity to <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">graphite.</span> Polyisoprene repeat units arrange close to a parallel configuration with chains exhibiting a distribution of contact lengths. Efficient Monte Carlo algorithms with the coarse-grain model are capable of sampling these distributions for any molecular weight in quantitative agreement with predictions from atomistic models. Furthermore, <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">molecular dynamics simulations</span> with well-equilibrated systems at all length-scales support an increased <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">dynamic</span> heterogeneity that is emerging from both intermolecular interactions with the flat <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">surface</span> and intramolecular cooperativity. This study provides a detailed comprehensive picture of polyisoprene on a flat <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">surface</span> and consists of an effort to characterize such systems in atomistic detail.</p></description> | |
| <dc:date>2014-02-06T16:11:52Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863331"> | |
| <title>Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863331</link> | |
| <description><p>In this contribution, we develop a coarse-graining methodology for mapping specific <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">block copolymer</span> systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">Monte Carlo simulations</span> of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">characteristic</span> features of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">block copolymer</span> systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diblock copolymer,</span> namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.</p></description> | |
| <dc:date>2014-02-06T16:11:46Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863998"> | |
| <title>Mixed alkaline earth effect in the compressibility of aluminosilicate glasses</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4863998</link> | |
| <description><p>The mixed modifier effect (MME) in oxide <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">glasses</span> manifests itself as a non-additive variation in certain <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">properties</span> when one modifier oxide species is substituted by another one at constant total modifier content. However, the structural and topological origins of the MME are still under debate. This study provides new insights into the MME by investigating the effect of isostatic compression on density and <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">hardness</span> of mixed MgO/CaO <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">sodium</span> aluminosilicate <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">glasses.</span> This is done using a specially designed setup allowing isostatic compression of bulk <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">glass</span> samples up to 1 GPa at elevated temperature. A mixed alkaline earth effect is found in the compressibility and relative change of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">hardness,</span> viz., a local maximum of density as a function of Mg/Ca ratio appears following compression, whereas a local minimum of <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">hardness</span> in the uncompressed <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">glasses</span> nearly disappears after compression. Moreover, the densification of these <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">glasses</span> is found to occur at temperatures much below the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">glass transition</span> temperature, indicating that a non-viscous mechanism is at play. This is further supported by the fact that density relaxes in a stretched exponential manner upon subsequent annealing at ambient <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">pressure</span> with an exponent of ∼0.62. This is close to the Phillips value of 3/5 for relaxation in three dimensions when both short- and long-range interactions are activated.</p></description> | |
| <dc:date>2014-02-06T16:07:07Z</dc:date> | |
| </item> | |
| <item rdf:about="http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864189"> | |
| <title>Determination of the molecular diffusion coefficients in ternary mixtures by the sliding symmetric tubes technique</title> | |
| <link>http://scitation.aip.org/content/aip/journal/jcp/140/5/10.1063/1.4864189</link> | |
| <description><p>A new analytical methodology has been developed to determine the diagonal and cross-diagonal molecular <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion</span> coefficients in ternary mixtures by the Sliding Symmetric Tubes technique. The analytical <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">solution</span> is tested in binary mixtures obtaining good agreement with the results of the literature. Results are presented for the ternary mixture formed by tetralin, isobutylbenzene, and dodecane with an equal mass fraction for all the components (1–1–1) which is held at 25 °C. Diagonal and cross-diagonal coefficients are determined for the three possible orders of components, in order to compare the results with those available in the literature. A comparison with published results shows a good agreement for the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">eigenvalues</span> of the <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion</span> matrix, and a reasonable agreement for the diagonal molecular <span xmlns="http://pub2web.metastore.ingenta.com/ns/" class="named-content">diffusion</span> coefficients.</p></description> | |
| <dc:date>2014-02-06T16:03:31Z</dc:date> | |
| </item> | |
| </rdf:RDF> |
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