Steady state equivalence among autocatalytic peroxidase-oxidase reactions
Peroxidase-oxidase is an enzymaticreaction that can exhibit dynamical scenarios such as bistability, sustained oscillations, and Shilnikovchaos. In this work, we apply the chemicalreactionnetwork theory approach to find kinetic constants such that the associated mass action kinetics ordinary differential equations induced by three four dimensional structurally different enzymaticreaction systems can support the same steady states for several chemical species despite differences in their chemical nature. (Source: Journal of Chemical Physics)
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Jos é Méndez-González and Ricardo Femat Source Type: research
Single-chain-in-mean-field simulations of weak polyelectrolyte brushes
Structural properties of brushes which are composed of weak acidic and basicpolyelectrolytes are studied in the framework of a particle-based approach that implicitly accounts for thesolvent quality. Using a semi-grandcanonical partition function in the framework of the Single-Chain-in-Mean-Field (SCMF) algorithm, the weakpolyelectrolyte is conceived as a supramolecular mixture of polymers in differentdissociation states, which are explicitly treated in the partition function and sampled by the SCMF procedure. One obtains a local expression for the equilibrium acid-basereaction responsible for the regulation of the charged...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: F. L éonforte, U. Welling and M. Müller Source Type: research
Water dynamics in rigid ionomer networks
The dynamics of water within ionic polymer networks formed by sulfonated poly(phenylene) (SPP), as revealed by quasi-elastic neutron scattering (QENS), is presented. These polymers are distinguished from other ionic macromolecules by their rigidity and therefore in their network structure. QENS measurements as a function of temperature as the fraction of ionic groups and humidity were varied have shown that the polymer molecules are immobile while absorbed water molecules remain dynamic. The water molecules occupy multiple sites, either bound or loosely constrained, and bounce between the two. With increasing temperature a...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: N. C. Osti, T. N. Etampawala, U. M. Shrestha, D. Aryal, M. Tyagi, S. O. Diallo, E. Mamontov, C. J. Cornelius and D. Perahia Source Type: research
A DFT+U study of the structural, electronic, magnetic, and mechanical properties of cubic and orthorhombic SmCoO3
SmCoO3 is aperovskitematerial that has gained attention as a potential substitute for La1 −xSrxMnO3 −d as asolid oxide fuel cell cathode. However, a number ofproperties have remained unknown due to the complexity of thematerial. For example, we know from experimental evidence that thisperovskite exists in two differentcrystal structures, cubic and orthorhombic, and that thecobalt ion changes its spin state at high temperatures, leading to a semiconductor-to-metal transition. However, little is known about the precise magneticstructure that causes the metallic behavior or the spin state of the Co centers at high tempera...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Emilia Olsson, Xavier Aparicio-Angl ès and Nora H. de Leeuw Source Type: research
Phase behavior of decorated soft disks in two dimensions
Molecular dynamics simulations are used to investigate the phase behavior of disks decorated with small ligands in two-dimensional films. We consider disks with four ligands, which are fixed at vertices of a square or slide over the circle delimiting the core. For selected model systems,phase diagrams are evaluated and discussed. We show that ligand mobility can change the topology ofphase diagrams. In particular, it can affect fluid-solidtransitions, changing thesolid phase symmetry. Moreover, the mobility of ligands can either hamper or facilitatecrystallization. (Source: Journal of Chemical Physics)
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: M. Bor ówko, W. Rżysko, S. Sokołowski and T. Staszewski Source Type: research
Thermopower of molecular junctions: Tunneling to hopping crossover in DNA
We study the electrical conductanceG and the thermopowerS of single-moleculejunctions and reveal signatures of differenttransport mechanisms: off-resonanttunneling, on-resonantcoherent(ballistic) motion, and multi-stephopping. These mechanisms are identified by studying the behavior ofG andS while varying molecular length and temperature. Based on a simple one-dimensional model for molecularjunctions, we derive approximate expressions for the thermopower in these different regimes. Analytical results are compared to numerical simulations, performed using a variant of B üttiker’s probe technique, the so-called voltage-te...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Roman Korol, Michael Kilgour and Dvira Segal Source Type: research
Quantum effects in graphene monolayers: Path-integral simulations
Path-integralmolecular dynamics (PIMD) simulations have been carried out to study the influence of quantumdynamics ofcarbon atoms on theproperties of a singlegraphene layer. Finite-temperatureproperties were analyzed in the range from 12 to 2000 K, by using the LCBOPII effective potential. To assess the magnitude ofquantum effects in structural andthermodynamic properties ofgraphene, classicalmolecular dynamics simulations have been also performed. Particular emphasis has been laid on the atomic vibrations along the out-of-plane direction. Even thoughquantum effects are present in these vibrational modes, we show that at a...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Carlos P. Herrero and Rafael Ram írez Source Type: research
The angularly resolved O 1s ion-yield spectrum of O2 revisited
The high-resolution photoabsorption spectrum of O2 below the O1sσ−1 ionization threshold has been reanalyzed by using a sophisticated fit approach. For the vibrational substates of the O1sσu−1(4∑u−)3sσg(3∑u−) Rydberg state Fano lineshapes are observed indicating an interaction with the O1sσg−1(4∑g−)3σu∗(3∑u−) core-to-valence excited state. In the angularly resolved ion-yield spectrum recorded at 90 ° relative to the polarization direction of the synchrotron radiation clear evidence for the O1sσg−1(2∑g−)3σu∗(3∑u−) and the O1sσu−1(2∑u−)3sσg(3∑u−) state was found. This o...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: R. P üttner and K. Ueda Source Type: research
The d3 Π state of LiRb
We report ourspectroscopic studies of thed3Π state of ultra-cold7Li85Rb usingresonantly enhanced multi-photon ionization and depletionspectroscopy with bound-to-bound transitions originating from the metastablea3Σ+ state. We evaluate the potential of this state for use as the intermediate state in a stimulated-Raman-adiabatic-passage transfer scheme from triplet Feshbach LiRb molecules to theX1Σ+ground state and find that the lowest several vibrational levels possess the requisite overlap with initial and final states, as well as convenient energies. Using depletion measurements, we measured the well depth and spin-orbi...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: I. C. Stevenson, D. B. Blasing, A. Altaf, Y. P. Chen and D. S. Elliott Source Type: research
Comparison of flow-controlled calcium and barium carbonate precipitation patterns
Various precipitation patterns can be obtained in flow conditions when injecting a solution of sodium carbonate in a confined geometry initially filled with a solution of either barium or calcium chloride. We compare here the barium and calcium carbonate precipitate structures as a function of initial concentrations and injection flow rate. We show that, in some part of the parameter space, the patterns are similar and feature comparable properties indicating that barium and calcium behave similarly in the related flow-controlled precipitation conditions. For other values of parameters though, the precipitate structures ar...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: G. Schuszter and A. De Wit Source Type: research
Semi-empirical estimation of ion-specific cross sections in electron ionization of molecules
Partialionization cross sections are the absolute yields of specific ions from an electron-molecule collision. They are necessary for modelingplasmas and determining the sensitivity ofmass spectrometers, among other applications. They can be predicted semi-empirically when experimental data are available for channel-specific oscillator strengths. However, such data are seldom available because they are obtained using specialized apparatus. Here, an alternative semi-empirical method is proposed that exploits experimental data obtained using ordinarymass spectrometers, as corrected for mass discrimination. Data are presented...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Karl K. Irikura Source Type: research
Potential energy landscape of the apparent first-order phase transition between low-density and high-density amorphous ice
The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics to describe supercooled liquids and glasses. Here we use the PEL formalism and computer simulations to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) at different temperatures. We employ the ST2 water model for which the LDA-HDA transformations are remarkably sharp, similar to what is observed in experiments, and reminiscent of a first-order phase transition. Our results are consistent with the view that LDA and HDA configurations are associated with two...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Nicolas Giovambattista, Francesco Sciortino, Francis W. Starr and Peter H. Poole Source Type: research
Quantum electron-vibrational dynamics at finite temperature: Thermo field dynamics approach
Quantum electron-vibrationaldynamics in molecular systems at finite temperature is described using an approach based on the thermo fielddynamicstheory. This formulation treats temperature effects in theHilbert space without introducing the Liouville space. A comparison with thetheoretically equivalent density matrix formulation shows the key numerical advantages of the present approach. The solution of thermo fielddynamicsequations with a novel technique for the propagation oftensor trains (matrix product states) is discussed. Numerical applications to model spin-boson systems show that the present approach is a promising ...
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Raffaele Borrelli and Maxim F. Gelin Source Type: research
Communication: Length-dependent thermopower of single-molecule junctions
In the present work, we theoretically study the length dependence of thermopower of asingle-molecule junction with a chain-like molecular bridge of an arbitrary length using a tight-binding model. Weanalyze conditions bringing a nonlinear growth of the thermopower accompanying the extension of the bridge length. Also, we show that the thermopower may decrease with increasing molecular length provided that the molecular bridge is sufficiently long. (Source: Journal of Chemical Physics)
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Natalya A. Zimbovskaya Source Type: research
Editorial: The Future of Chemical Physics Conference 2016
(Source: Journal of Chemical Physics)
Source: Journal of Chemical Physics - December 8, 2016 Category: Physics Authors: Angelos Michaelides, David E. Manolopoulos, Carlos Vega, Peter Hamm, David W. Chandler, Erinn C. Brigham and Marsha I. Lester Source Type: research
