bluuebunny/crossref_metadata_2025 huggingface dataset:
Generation, transport, and detection of linear accelerator based femtosecond-terahertz pulses
Authors: Park Jaehun , Kim Changbum , Lee Jongseok , Yim Changmook , Kim Chul Hoon , Lee Junghwa , Jung Seonghoon , Ryu Jaehyun , Kang Heung-Sik , Joo Taiha
Published: January 2011

The generation and detection of intense terahertz (THz) radiation has drawn a great attention recently. The dramatically enhanced energy and peak electric field of the coherent THz radiation can be generated by coherent superposition of radiated fields emitted by ultrafast electron bunches. The femtosecond (fs)-THz beamline construction at the Pohang Accelerator Laboratory (PAL) was completed in the end of 2009. The fs-THz beamline at PAL can supply ultrafast and intense fs-THz radiation from a 75 MeV linear accelerator. The radiation is expected to have frequency up to 3 THz (∼100 cm−1) and the pulse width of <200 fs with pulse energy up to 10 μJ. This intense THz source has great potential for applications in nonlinear optical phenomena and fields such as material science, biomedical science, chemistry, and physics, etc.
Application of the projection operator formalism to non-Hamiltonian dynamics
Authors: Xing Jianhua , Kim K. S.
Published: January 2011

Reconstruction of equations of motion from incomplete or noisy data and dimension reduction are two fundamental problems in the study of dynamical systems with many degrees of freedom. For the latter, extensive efforts have been made, but with limited success, to generalize the Zwanzig–Mori projection formalism, originally developed for Hamiltonian systems close to thermodynamic equilibrium, to general non-Hamiltonian systems lacking detailed balance. One difficulty introduced by such systems is the lack of an invariant measure, needed to define a statistical distribution. Based on a recent discovery that a non-Hamiltonian system defined by a set of stochastic differential equations can be mapped to a Hamiltonian system, we develop such general projection formalism. In the resulting generalized Langevin equations, a set of generalized fluctuation–dissipation relations connect the memory kernel and the random noise terms, analogous to Hamiltonian systems obeying detailed balance. Lacking of these relations restricts previous application of the generalized Langevin formalism. Result of this work may serve as the theoretical basis for further technical developments on model reconstruction with reduced degrees of freedom. We first use an analytically solvable example to illustrate the formalism and the fluctuation–dissipation relation. Our numerical test on a chemical network with end-product inhibition further demonstrates the validity of the formalism. We suggest that the formalism can find wide applications in scientific modeling. Specifically, we discuss potential applications to biological networks. In particular, the method provides a suitable framework for gaining insights into network properties such as robustness and parameter transferability.
Control of structure formation in phase-separating systems
Authors: Singh Awaneesh , Mukherjee A. , Vermeulen H. M. , Barkema G. T. , Puri Sanjay
Published: January 2011

In this paper, we study the evolution of phase-separating binary mixtures which are subjected to alternate cooling and heating cycles. An initially homogeneous mixture is rapidly quenched to a temperature \documentclass[12pt]{minimal}\begin{document}$T_1 < T_c$\end{document}T1<Tc, where \documentclass[12pt]{minimal}\begin{document}$T_c$\end{document}Tc is the critical temperature. The mixture undergoes phase separation for a while and is then suddenly heated to a temperature \documentclass[12pt]{minimal}\begin{document}$T_2 > T_c$\end{document}T2>Tc. These cycles are repeated to create a domain morphology with multiple length scales, i.e., the structure factor is characterized by multiple peaks. For phase separation in d = 2 systems, we present numerical and analytical results for the emergence and growth of this multiple-scale morphology.
Free energy calculation using molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. II. Thermodynamic integration along a spatial reaction coordinate
Authors: Miyata Tatsuhiko , Ikuta Yasuhiro , Hirata Fumio
Published: January 2011

We propose the thermodynamic integration along a spatial reaction coordinate using the molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. This method provides a free energy calculation in solution along the reaction coordinate defined by the Cartesian coordinates of the solute atoms. The proposed method is based on the blue moon algorithm which can, in principle, handle any reaction coordinate as far as it is defined by the solute atom positions. In this article, we apply the present method to the complex formation process of the crown ether 18-Crown-6 (18C6) with the potassium ion in an aqueous solution. The separation between the geometric centers of these two molecules is taken to be the reaction coordinate for this system. The potential of mean force (PMF) becomes the maximum at the separation between the molecular centers being ∼4 Å, which can be identified as the free energy barrier in the process of the molecular recognition. In a separation further than the free energy barrier, the PMF is slightly reduced to exhibit a plateau. In the region closer than the free energy barrier, approach of the potassium ion to the center of 18C6 also decreases the PMF. When the potassium ion is accommodated at the center of 18C6, the free energy is lower by −5.7 ± 0.7 kcal/mol than that at the above mentioned plateau or converged state. By comparing the results with those from the free energy calculation along the coupling parameters obtained in our previous paper [T. Miyata, Y. Ikuta, and F. Hirata, J. Chem. Phys. 133, 044114 (2010)], it is found that the effective interaction in water between 18C6 and the potassium ion vanishes beyond the molecular-center-separation of 10 Å. Furthermore, the conformation of 18C6 is found to be significantly changed depending upon the 18C6–K+ distance. A proper conformational sampling and an accurate solvent treatment are crucial for realizing the accurate PMF, and we believe that the proposed method is useful to evaluate the PMF in a solution. A discussion upon the PMF in terms of the three-dimensional distribution function for the solvent is also presented.
Spectroscopic detection of the most stable carbonic acid, cis-cis H2CO3
Authors: Mori Tetsuya , Suma Kohsuke , Sumiyoshi Yoshihiro , Endo Yasuki
Published: January 2011

Carbonic acid had not been detected by any spectroscopic means for a long period. Recently, we have reported the detection of its second most stable conformer, cis-trans H2CO3, as the first spectroscopic detection of the isolated carbonic acid molecule. In the present work, the most stable conformer of carbonic acid, cis-cis H2CO3, in the gas phase has been successfully produced in a supersonic jet using a pulsed discharge nozzle, and pure rotational transitions of this molecule have been observed by a Fourier-transform microwave spectrometer. In addition to cis-cis H2CO3, its deuterated isotopologue, cis-cis D2CO3, has been observed, yielding the r0 structure of the cis-cis conformer. Furthermore, hyperfine constants of the deuterated cis-trans conformers were also determined. The two structures for the stable isolated carbonic acid molecule, those of the cis-cis and cis-trans conformers, are considered to provide basic information for the understanding of chemical reactions involving carbonic acid The present result is accurate enough to be used in radio astronomical observations, where the ortho/para ratio of cis-cis H2CO3 may be used as an important probe of interstellar chemistry.
Laser-induced UV photodissociation of 2-bromo-2-nitropropane: Dynamics of OH and Br formation
Authors: Saha Ankur , Kawade Monali , Upadhyaya Hari P. , Kumar Awadhesh , Naik Prakash D.
Published: January 2011

Photoexcitation of 2-bromo-2-nitropropane (BNP) at 248 and 193 nm generates OH, Br, and NO2 among other products. The OH fragment is detected by laser-induced fluorescence spectroscopy, and its translational and internal state distributions (vibration, rotation, spin-orbit, and Λ-doubling components) are probed. At both 248 and 193 nm, the OH fragment is produced translationally hot with the energy of 10.8 and 17.2 kcal/mol, respectively. It is produced vibrationally cold (v″ = 0) at 248 nm, and excited (v″ = 1) at 193 nm with a vibrational temperature of 1870 ± 150 K. It is also generated with rotational excitation, rotational populations of OH(v″ = 0) being characterized by a temperature of 550 ± 50 and 925 ± 100 K at 248 and 193 nm excitation of BNP, respectively. The spin-orbit components of OH(X2Π) are not in equilibrium on excitation at 193 nm, but the Λ-doublets are almost in equilibrium, implying no preference for its π lobe with respect to the plane of rotation. The NO2 product is produced electronically excited, as detected by measuring UV–visible fluorescence, at 193 nm and mostly in the ground electronic state at 248 nm. The Br product is detected employing resonance-enhanced multiphoton ionization with time-of-flight mass spectrometer for better understanding of the dynamics of dissociation. The forward convolution analysis of the experimental data has provided translational energy distributions and anisotropy parameters for both Br(2P3/2) and Br*(2P1/2). The average translational energies for the Br and Br* channels are 5.0 ± 1.0 and 6.0 ± 1.5 kcal/mol. No recoil anisotropies were observed for these products. Most plausible mechanisms of OH and Br formation are discussed based on both the experimental and the theoretical results. Results suggest that the electronically excited BNP molecules at 248 and 234 nm relax to the ground state, and subsequently dissociate to produce OH and Br through different channels. The mechanism of OH formation from BNP on excitation at 193 nm is also discussed.
Quantum state-resolved energy redistribution in gas ensembles containing highly excited N2
Authors: McCaffery Anthony J. , Pritchard Marisian , Turner John F. C. , Marsh Richard J.
Published: January 2011

A computational model is used to quantify the evolution of quantum state populations as highly vibrationally excited 14N2 (14N2*) equilibrates in various bath gases. Multicollision energy disposal follows general principles established in related single collision processes. Thus when state-to-state routes permit, maximum amounts of energy are deposited into partner species by direct vibration-to-vibration (V–V) exchange. When these pathways are absent, e.g., when Ar is the bath species, relaxation is very slow and multistaged. Conversely, in a bath of v = 0 14N2 molecules, 16 vibrational quanta (Δv = ± 8) are resonantly exchanged from (v;j) = (8;10) with vibrational equilibration so rapid that rotation and translation still lag far behind after 1000 collisions. Near-resonant V–V exchange dominates the initial phase when 15N2 forms the bath gas and although some rotational warming occurs, vibrational modes remain decoupled from, and significantly hotter than, the low heat capacity modes. These forms of behavior seem likely to characterize excited and bath species that have closely similar vibration and rotation constants. More generic in nature is 14N2 in O2 or in a mixture that closely resembles air. Here, asymmetric V–V exchange is a dominant early feature in ensemble evolution but energy differences in the key vibration and rotation quanta lead to V–V energy defects that are compensated for by the low energy modes. This results in much more rapid ensemble equilibration, generally within 400–500 collisions, when O2 is present even as a minor constituent. Our results are in good general agreement with those obtained from experimental studies of N2 plasmas both in terms of modal temperatures and initial (first collision cycle) cross-sections.
Dissipative many-electron dynamics of ionizing systems
Authors: Tremblay Jean Christophe , Klinkusch Stefan , Klamroth Tillmann , Saalfrank Peter
Published: January 2011

In this paper, we perform many-electron dynamics using the time-dependent configuration-interaction method in its reduced density matrix formulation (ρ-TDCI). Dissipation is treated implicitly using the Lindblad formalism. To include the effect of ionization on the state-resolved dynamics, we extend a recently introduced heuristic model for ionizing states to the ρ-TDCI method, which leads to a reduced density matrix evolution that is not norm-preserving. We apply the new method to the laser-driven excitation of \documentclass[12pt]{minimal}\begin{document}${\rm H}_2$\end{document}H2 in a strongly dissipative environment, for which the state-resolve lifetimes are tuned to a few femtoseconds, typical for dynamics of adsorbate at metallic surfaces. Further testing is made on the laser-induced intramolecular charge transfer in a quinone derivative as a model for a molecular switch. A modified scheme to treat ionizing states is proposed to reduce the computational burden associated with the density matrix propagation, and it is thoroughly tested and compared to the results obtained with the former model. The new approach scales favorably (\documentclass[12pt]{minimal}\begin{document}$\sim N^2$\end{document}∼N2) with the number of configurations N used to represent the reduced density matrix in the ρ-TDCI method, as compared to a \documentclass[12pt]{minimal}\begin{document}$N^3$\end{document}N3 scaling for the model in its original form.
Integral tau methods for stiff stochastic chemical systems
Authors: Yang Yushu , Rathinam Muruhan , Shen Jinglai
Published: January 2011

Tau leaping methods enable efficient simulation of discrete stochastic chemical systems. Stiff stochastic systems are particularly challenging since implicit methods, which are good for stiffness, result in noninteger states. The occurrence of negative states is also a common problem in tau leaping. In this paper, we introduce the implicit Minkowski–Weyl tau (IMW-τ) methods. Two updating schemes of the IMW-τ methods are presented: implicit Minkowski–Weyl sequential (IMW-S) and implicit Minkowski–Weyl parallel (IMW-P). The main desirable feature of these methods is that they are designed for stiff stochastic systems with molecular copy numbers ranging from small to large and that they produce integer states without rounding. This is accomplished by the use of a split step where the first part is implicit and computes the mean update while the second part is explicit and generates a random update with the mean computed in the first part. We illustrate the IMW-S and IMW-P methods by some numerical examples, and compare them with existing tau methods. For most cases, the IMW-S and IMW-P methods perform favorably.
Theoretical study of the rovibrational spectrum of H2O–H2
Authors: Wang Xiao-Gang , Carrington Tucker
Published: January 2011

In this paper we report transition frequencies and line strengths computed for ${\rm H}_2{\rm O}$H2O–${\rm H}_2$H2 and compare with the experimental observations of [M. J. Weida and D. J. Nesbitt, J. Chem. Phys. 110, 156 (1999)]. To compute the spectra we use a symmetry adapted Lanczos algorithm and an uncoupled product basis set. Our results corroborate the assignments of Weida and Nesbitt and there is good agreement between calculated and observed transitions. Possible candidates for lines that Weida and Nesbitt were not able to assign are presented. Several other bands that may be observable are also discovered. Although all the observed bands are associated with states localized near the global potential minimum, at which ${\rm H}_2{\rm O}$H2O acts as proton acceptor, a state with significant amplitude near the T-shape secondary potential minimum at which ${\rm H}_2{\rm O}$H2O acts as proton donor is identified by examining many different probability density plots.
Photoelectron imaging of several 5d and 6p Rydberg states Xe2 and improving the Xe2+ I(1/2g) potential
Authors: Shubert V. Alvin , Pratt Stephen T.
Published: January 2011

Velocity map photoelectron imaging was used to study the photoionization of Xe2 in several low-lying 5d and 6p Rydberg states. The Rydberg states were prepared by two-photon excitation and ionized by either one additional photon from the pump laser (2+1 ionization), or by one photon of a second color (2+1′ ionization). The 2+1 images and associated photoelectron spectra were consistent with previous results, although some adjustment of previously proposed equilibrium bond lengths was necessary to fit the spectra with Franck–Condon factor calculations. The 2+1′ images provided higher resolution photoelectron spectra and, in conjunction with the Xe2+ potentials reported by Zehnder and co-workers [J. Chem. Phys. 128, 234306 (2008)] and the 6p and 5d Xe2* potentials calculated by Jonin and Spiegelmann [J. Chem. Phys. 117, 3059 (2002)], provided a means for improving the Xe2* potentials. New experimental data are also presented for photoionization populating the Xe2+ I(1/2g) state, and are used to provide a better description of its potential curve.
On nonminimal ${\cal N}=4$N=4 supermultiplets in 1D and their associated σ-models
Authors: Gonzales Marcelo , Khodaee Sadi , Toppan Francesco
Published: January 2011

We construct the nonminimal linear representations of the ${\cal N}=4$N=4 extended supersymmetry in one-dimension. They act on eight bosonic and eight fermionic fields. Inequivalent representations are specified by the mass-dimension of the fields and the connectivity of the associated graphs. The oxidation to minimal ${\cal N}=5$N=5 linear representations is given. Two types of ${\cal N}=4$N=4 σ-models based on nonminimal representations are obtained: the resulting off-shell actions are either manifestly invariant or depend on a constrained prepotential. The connectivity properties of the graphs play a decisive role in discriminating inequivalent actions. These results find application in partial breaking of supersymmetric theories.
A free-space density functional theory for polymer adsorption: Influence of packing effect on conformations of polymer
Authors: Chen Xueqian , Chen Houyang , Liu Honglai , Hu Ying
Published: January 2011

We propose a free-space density functional theory for polymer adsorption. The derivation within the framework of density functional theory leads to the splitting of the intrinsic free energy into an ideal-gas term and a residual term responsible for the intrinsic energy and the nonbonded interactions between monomers, respectively. A more reasonable treatment is adopted for the residual free energy to count for the monomer–monomer correlation underestimated by the local density approximation. An approach using propagators is proposed to calculate the single-chain partition function and the segment-density distributions, the three adsorption conformations as trains, loops, and tails are further described by propagators. Dirac's bra-ket notation used makes the derivation simpler and provides clearer physical meanings. The theoretical calculations for the adsorption of hard-sphere chains onto a nonadsorbing and an adsorbing hard wall show that the structure of the adsorption layer is strongly affected by the packing effect which has been underestimated by the previous lattice adsorption theory.
Fast motion in molecular solids at low temperatures: Evidence from a pulsed electron paramagnetic resonance study of nitroxyl radical relaxation
Authors: Kveder Marina , Jokić Milan , Rakvin Boris
Published: January 2011

We have investigated the electron phase-memory relaxation time of the nitroxyl radical 2,2,6,6-tetramethylpiperidine-1-oxyl at temperatures between 5 and 80 K in crystalline and glassy states of ethanol using pulsed X-band electron paramagnetic resonance spectroscopy. The results indicate that the transition from the slow to fast motion regimes of the paramagnetic center occurs upon further cooling of the sample below ∼20 K. We provide experimental evidence that this phenomenon cannot be ascribed to the impact of hyperfine interactions with methyl protons in the system, but it can be instead a signature of the coupling of the electron spin with the boson peak excitations of the lattice.
Multilayer multiconfiguration time-dependent Hartree method: Implementation and applications to a Henon–Heiles Hamiltonian and to pyrazine
Authors: Vendrell Oriol , Meyer Hans-Dieter
Published: January 2011

The multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method is discussed and a fully general implementation for any number of layers based on the recursive ML-MCTDH algorithm given by Manthe [J. Chem. Phys. 128, 164116 (2008)] is presented. The method is applied first to a generalized Henon–Heiles (HH) Hamiltonian. For 6D HH the overhead of ML-MCTDH makes the method slower than MCTDH, but for 18D HH ML-MCTDH starts to be competitive. We report as well 1458D simulations of the HH Hamiltonian using a seven-layer scheme. The photoabsorption spectrum of pyrazine computed with the 24D Hamiltonian of Raab et al. [J. Chem. Phys. 110, 936 (1999)] provides a realistic molecular test case for the method. Quick and small ML-MCTDH calculations needing a fraction of the time and resources of reference MCTDH calculations provide already spectra with all the correct features. Accepting slightly larger deviations, the calculation can be accelerated to take only 7 min. When pushing the method toward convergence, results of similar quality than the best available MCTDH benchmark, which is based on a wavepacket with \documentclass[12pt]{minimal}\begin{document}$4.6\break \times 10^7$\end{document}4.6×107time-dependent coefficients, are obtained with a much more compact wavefunction consisting of only \documentclass[12pt]{minimal}\begin{document}$4.5\times 10^5$\end{document}4.5×105 coefficients and requiring a shorter computation time.
Phase-field modeling of two-dimensional solute precipitation/dissolution: Solid fingers and diffusion-limited precipitation
Authors: Xu Zhijie , Meakin Paul
Published: January 2011

Two-dimensional dendritic growth due to solute precipitation was simulated using a phase-field model reported earlier [Z. Xu and P. Meakin, J. Chem. Phys. 129, 014705 (2008)]. It was shown that diffusion-limited precipitation due to the chemical reaction at the solid–liquid interface has similarities with diffusion-limited aggregation (DLA). The diffusion-limited precipitation is attained by setting the chemical reaction rate much larger compared to the solute diffusion to eliminate the effect of the interface growth kinetics. The phase-field simulation results were in reasonable agreement with the analytical solutions. The fractal solid fingers can be formed in the diffusion-limited precipitation and have a fractal dimension measured $d_f = 1.68$df=1.68, close to 1.64, the fractal dimensionality of large square lattice DLA clusters.
The coupled cluster approach with a hybrid treatment of connected triple excitations based on the restricted Hartree–Fock reference
Authors: Shen Jun , Kou Zhuangfei , Xu Enhua , Li Shuhua
Published: January 2011

A generalization of the coupled cluster (CC) singles, doubles, and a hybrid treatment of connected triples [denoted as CCSD(T)-h] [Shen et al., J. Chem. Phys. 132, 114115 (2010)] to the restricted Hartree–Fock (RHF) reference is presented. In this approach, active (or pseudoactive) RHF orbitals are constructed automatically by performing unitary transformations of canonical RHF orbitals so that they spatially mimic the natural orbitals of the unrestricted Hartree–Fock reference. The present RHF-based CCSD(T)-h approach has been applied to study the potential energy surfaces in several typical bond breaking processes and the singlet–triplet gaps in a diradical (HFH)−1. For all systems under study, the overall performance of CCSD(T)-h is very close to that of the corresponding CCSD(T) (CC singles, doubles, and triples), and much better than that of CCSD(T) (CC singles, doubles, and perturbative triples).
A multidimensional pseudospectral method for optimal control of quantum ensembles
Authors: Ruths Justin , Li Jr-Shin
Published: January 2011

In our previous work, we have shown that the pseudospectral method is an effective and flexible computation scheme for deriving pulses for optimal control of quantum systems. In practice, however, quantum systems often exhibit variation in the parameters that characterize the system dynamics. This leads us to consider the control of an ensemble (or continuum) of quantum systems indexed by the system parameters that show variation. We cast the design of pulses as an optimal ensemble control problem and demonstrate a multidimensional pseudospectral method with several challenging examples of both closed and open quantum systems from nuclear magnetic resonance spectroscopy in liquid. We give particular attention to the ability to derive experimentally viable pulses of minimum energy or duration.
Debye process and dielectric state of an alcohol in a nonpolar solvent
Authors: Power G. , Nagaraj Mamatha , Vij J. K. , Johari G. P.
Published: January 2011

To investigate the origin of the first order molecular kinetics of the most prominent, Debye-type polarization, a detailed dielectric relaxation study of 66.5, 40, and 20 mole% solutions of 5-methyl-2-hexanol in 2-methylpentane (2:1, 0.67:1, and 0.25:1 molar ratios) was performed. The Debye-type polarization remains prominent in the solutions, despite the extensive loss of intermolecular hydrogen bonds. At high temperatures, its contribution to permittivity extrapolates close to the statistically scaled values for the 2:1 solution. For others, the measured values of its contribution crossover the scaled values in a temperature plane. The faster relaxation process of about 4% magnitude has an asymmetric distribution of times in the solutions and, relative to those of the pure alcohol, their values decrease on heating more at high temperatures and less at low. This is attributed to an increase in the alcohol cluster size by consumption of monomers as well as the growth of smaller clusters as the solution is cooled. It is argued that structural fluctuation in solutions, as in the pure alcohol, is determined by the rates of both the Debye-type and the faster polarizations in the ultraviscous state.
Nonequilibrium restructuring in two-dimensional Lennard-Jones system induced by a simple square start configuration
Authors: Karbowniczek Paweł , Chrzanowska Agnieszka
Published: January 2011

In the present paper, we report a molecular dynamics simulation of two-dimensional Lennard-Jones system with a simple square start configuration. Mean square displacement was computed showing interesting dependence on high pressure conditions in short time scale, corresponding to an abrupt restructurization. This paper is the first to report the qualitative and quantitative details of this phenomenon.
A Hamiltonian replica exchange method for building protein–protein interfaces applied to a leucine zipper
Authors: Cukier Robert I.
Published: January 2011

Leucine zippers consist of alpha helical monomers dimerized (or oligomerized) into alpha superhelical structures known as coiled coils. Forming the correct interface of a dimer from its monomers requires an exploration of configuration space focused on the side chains of one monomer that must interdigitate with sites on the other monomer. The aim of this work is to generate good interfaces in short simulations starting from separated monomers. Methods are developed to accomplish this goal based on an extension of a previously introduced [Su and Cukier, J. Phys. Chem. B 113, 9595, (2009)] Hamiltonian temperature replica exchange method (HTREM), which scales the Hamiltonian in both potential and kinetic energies that was used for the simulation of dimer melting curves. The new method, HTREM_MS (MS designates mean square), focused on interface formation, adds restraints to the Hamiltonians for all but the physical system, which is characterized by the normal molecular dynamics force field at the desired temperature. The restraints in the nonphysical systems serve to prevent the monomers from separating too far, and have the dual aims of enhancing the sampling of close in configurations and breaking unwanted correlations in the restrained systems. The method is applied to a 31-residue truncation of the 33-residue leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. The monomers are initially separated by a distance that is beyond their capture length. HTREM simulations show that the monomers oscillate between dimerlike and monomerlike configurations, but do not form a stable interface. HTREM_MS simulations result in the dimer interface being faithfully reconstructed on a 2 ns time scale. A small number of systems (one physical and two restrained with modified potentials and higher effective temperatures) are sufficient. An in silico mutant that should not dimerize because it lacks charged residues that provide electrostatic stabilization of the dimer does not with HTREM_MS, giving confidence in the method. The interface formation time scale is sufficiently short that using HTREM_MS as a screening tool to validate leucine zipper design methods may be feasible.
Communication: Reactions and adsorption at the surface of silver nanoparticles probed by second harmonic generation
Authors: Gan Wei , Gonella Grazia , Zhang Min , Dai Hai-Lung
Published: January 2011

Even though nanoparticles have dimensions much smaller than the optical wavelength and shapes commonly with inversion symmetry, we show, for the first time, direct experimental evidence that second harmonic generation (SHG) can be detected from the surface layer of metallic nanoparticles, in this case 40 nm radius Ag particles. The SH intensity detected is shown to substantially decrease upon chemical bonding of thiol molecules to the Ag particle surface. The surface generated SH intensity can be used for probing properties and processes at the nanoparticle surface.
Scanning tunneling microscope with two-dimensional translator
Authors: Nichols J. , Ng K.-W.
Published: January 2011

Since the invention of the scanning tunneling microscope (STM), it has been a powerful tool for probing the electronic properties of materials. Typically STM designs capable of obtaining resolution on the atomic scale are limited to a small area which can be probed. We have built an STM capable of coarse motion in two dimensions, the z- and x-directions which are, respectively, parallel and perpendicular to the tip. This allows us to image samples with very high resolution at sites separated by macroscopic distances. This device is a single unit with a compact design making it very stable. It can operate in either a horizontal or vertical configuration and at cryogenic temperatures.
Phase measurement in nondegenerate three-wave mixing spectroscopy
Authors: Jena Kailash C. , Covert Paul A. , Hore Dennis K.
Published: January 2011

A detailed model is presented that describes the temporal and spectral interference patterns resulting from phase-recovery infrared–visible sum-frequency spectroscopy. Included in this model are the effects of dispersive elements other than the phase shifting unit placed between the sample and local oscillator signals. This inclusion is critical when considering the interference patterns arising from studies of buried interfaces. Furthermore, in the midinfrared where it is difficult to have high visibility of the fringes, it is demonstrated that local field corrections have a significant effect on the shape of the interference pattern. By collecting and subsequently fitting a two-dimensional interference pattern displaying both temporal and spectral fringes, a complete characterization of all these effects is possible.
Recycling of a defective metal insulator semiconductor solar cell by hot phosphoric acid
Authors: Fathi M. , Mougas A.
Published: January 2011

With the rapid development of silicon photovoltaic power generation systems in recent years, the silicon wafer material becomes more and more expensive. Large quantities of defective solar cells are rejected from production lines. By this study, we explore the methods for reusing silicon wafers of defective solar cells using metal insulator semiconductor (MIS) technology. For this, the insulating layers and the electrically conductive contacts must be totally etched. Also, we have to assure the removal of all alkali metal ions. In order to provide new operating MIS solar cells, we have deposited new layers into the etched silicon base material. These recycled wafers are chemically polished beforehand to remove all impurities and defects. Optionally, the layers to be stripped off can be etched selectively. We have applied hot phosphoric (H3PO4) acidic solution for MIS solar cells delayering. To permit a time-saving process, H3PO4 solution is heated at temperature around 120 °C. By using this process, all insulating and contact layers are stripped off.
Investigating synapse formation and function using human pluripotent stem cell-derived neurons
Authors: Kim Ji-Eun , O'Sullivan Matthew L. , Sanchez Christopher A. , Hwang Minju , Israel Mason A. , Brennand Kristen , Deerinck Thomas J. , Goldstein Lawrence S. B. , Gage Fred H. , Ellisman Mark H. , Ghosh Anirvan
Published: January 2011

A major goal of stem-cell research is to identify conditions that reliably regulate their differentiation into specific cell types. This goal is particularly important for human stem cells if they are to be used for in vivo transplantation or as a platform for drug development. Here we describe the establishment of procedures to direct the differentiation of human embryonic stem cells and human induced pluripotent stem cells into forebrain neurons that are capable of forming synaptic connections. In addition, HEK293T cells expressing Neuroligin (NLGN) 3 and NLGN4, but not those containing autism-associated mutations, are able to induce presynaptic differentiation in human induced pluripotent stem cell-derived neurons. We show that a mutant NLGN4 containing an in-frame deletion is unable to localize correctly to the cell surface when overexpressed and fails to enhance synapse formation in human induced pluripotent stem cell-derived neurons. These findings establish human pluripotent stem cell-derived neurons as a viable model for the study of synaptic differentiation and function under normal and disorder-associated conditions.
Normal gut microbiota modulates brain development and behavior
Authors: Heijtz Rochellys Diaz , Wang Shugui , Anuar Farhana , Qian Yu , Björkholm Britta , Samuelsson Annika , Hibberd Martin L. , Forssberg Hans , Pettersson Sven
Published: February 2011

Microbial colonization of mammals is an evolution-driven process that modulate host physiology, many of which are associated with immunity and nutrient intake. Here, we report that colonization by gut microbiota impacts mammalian brain development and subsequent adult behavior. Using measures of motor activity and anxiety-like behavior, we demonstrate that germ free (GF) mice display increased motor activity and reduced anxiety, compared with specific pathogen free (SPF) mice with a normal gut microbiota. This behavioral phenotype is associated with altered expression of genes known to be involved in second messenger pathways and synaptic long-term potentiation in brain regions implicated in motor control and anxiety-like behavior. GF mice exposed to gut microbiota early in life display similar characteristics as SPF mice, including reduced expression of PSD-95 and synaptophysin in the striatum. Hence, our results suggest that the microbial colonization process initiates signaling mechanisms that affect neuronal circuits involved in motor control and anxiety behavior.
Rab GTPase–Myo5B complexes control membrane recycling and epithelial polarization
Authors: Roland Joseph T. , Bryant David M. , Datta Anirban , Itzen Aymelt , Mostov Keith E. , Goldenring James R.
Published: February 2011

The Rab GTPases are the largest family of proteins regulating membrane traffic. Rab proteins form a nidus for the assembly of multiprotein complexes on distinct vesicle membranes to regulate particular membrane trafficking pathways. Recent investigations have demonstrated that Myosin Vb (Myo5B) is an effector for Rab8a, Rab10, and Rab11a, all of which are implicated in regulating different pathways for recycling of proteins to the plasma membrane. It remains unclear how specific interactions of Myo5B with individual Rab proteins can lead to specificity in the regulation of alternate trafficking pathways. We examined the relative contributions of Rab/Myo5B interactions with specific pathways using Myo5B mutants lacking binding to either Rab11a or Rab8a. Myo5B Q1300L and Y1307C mutations abolished Rab8a association, whereas Myo5B Y1714E and Q1748R mutations uncoupled association with Rab11a. Expression of Myo5B tails containing these mutants demonstrated that Rab11a, but not Rab8a, was required for recycling of transferrin in nonpolarized cells. In contrast, in polarized epithelial cyst cultures, Myo5B was required for apical membrane trafficking and de novo lumen formation, dependent on association with both Rab8a and Rab11a. These data demonstrate that different combinations of Rab GTPase association with Myo5B control distinct membrane trafficking pathways.
Word lengths are optimized for efficient communication
Authors: Piantadosi Steven T. , Tily Harry , Gibson Edward
Published: January 2011

We demonstrate a substantial improvement on one of the most celebrated empirical laws in the study of language, Zipf's 75-y-old theory that word length is primarily determined by frequency of use. In accord with rational theories of communication, we show across 10 languages that average information content is a much better predictor of word length than frequency. This indicates that human lexicons are efficiently structured for communication by taking into account interword statistical dependencies. Lexical systems result from an optimization of communicative pressures, coding meanings efficiently given the complex statistics of natural language use.
Widespread establishment and regulatory impact of Alu exons in human genes
Authors: Shen Shihao , Lin Lan , Cai James J. , Jiang Peng , Kenkel Elizabeth J. , Stroik Mallory R. , Sato Seiko , Davidson Beverly L. , Xing Yi
Published: February 2011

The Alu element has been a major source of new exons during primate evolution. Thousands of human genes contain spliced exons derived from Alu elements. However, identifying Alu exons that have acquired genuine biological functions remains a major challenge. We investigated the creation and establishment of Alu exons in human genes, using transcriptome profiles of human tissues generated by high-throughput RNA sequencing (RNA-Seq) combined with extensive RT-PCR analysis. More than 25% of Alu exons analyzed by RNA-Seq have estimated transcript inclusion levels of at least 50% in the human cerebellum, indicating widespread establishment of Alu exons in human genes. Genes encoding zinc finger transcription factors have significantly higher levels of Alu exonization. Importantly, Alu exons with high splicing activities are strongly enriched in the 5′-UTR, and two-thirds (10/15) of 5′-UTR Alu exons tested by luciferase reporter assays significantly alter mRNA translational efficiency. Mutational analysis reveals the specific molecular mechanisms by which newly created 5′-UTR Alu exons modulate translational efficiency, such as the creation or elongation of upstream ORFs that repress the translation of the primary ORFs. This study presents genomic evidence that a major functional consequence of Alu exonization is the lineage-specific evolution of translational regulation. Moreover, the preferential creation and establishment of Alu exons in zinc finger genes suggest that Alu exonization may have globally affected the evolution of primate and human transcriptomes by regulating the protein production of master transcriptional regulators in specific lineages.
N
ε
-lysine acetylation determines dissociation from GAP junctions and lateralization of connexin 43 in normal and dystrophic heart
Authors: Colussi Claudia , Rosati Jessica , Straino Stefania , Spallotta Francesco , Berni Roberta , Stilli Donatella , Rossi Stefano , Musso Ezio , Macchi Emilio , Mai Antonello , Sbardella Gianluca , Castellano Sabrina , Chimenti Cristina , Frustaci Andrea , Nebbioso Angela , Altucci Lucia , Capogrossi Maurizio C. , Gaetano Carlo
Published: February 2011

Wanting to explore the epigenetic basis of Duchenne cardiomyopathy, we found that global histone acetylase activity was abnormally elevated and the acetylase P300/CBP-associated factor (PCAF) coimmunoprecipitated with connexin 43 (Cx43), which was N
ε
-lysine acetylated and lateralized in mdx heart. This observation was paralleled by Cx43 dissociation from
N
-cadherin and zonula occludens 1, whereas pp60-c-Src association was unaltered. In vivo treatment of mdx with the pan-histone acetylase inhibitor anacardic acid significantly reduced Cx43 N
ε
-lysine acetylation and restored its association to GAP junctions (GJs) at intercalated discs. Noteworthy, in normal as well as mdx mice, the class IIa histone deacetylases 4 and 5 constitutively colocalized with Cx43 either at GJs or in the lateralized compartments. The class I histone deacetylase 3 was also part of the complex. Treatment of normal controls with the histone deacetylase pan-inhibitor suberoylanilide hydroxamic acid (MC1568) or the class IIa-selective inhibitor 3-{4-[3-(3-fluorophenyl)-3-oxo-1-propen-1-yl]-1-methyl-1H-pyrrol-2-yl}-N-hydroxy-2-propenamide (MC1568) determined Cx43 hyperacetylation, dissociation from GJs, and distribution along the long axis of ventricular cardiomyocytes. Consistently, the histone acetylase activator pentadecylidenemalonate 1b (SPV106) hyperacetylated cardiac proteins, including Cx43, which assumed a lateralized position that partly reproduced the dystrophic phenotype. In the presence of suberoylanilide hydroxamic acid, cell to cell permeability was significantly diminished, which is in agreement with a Cx43 close conformation in the consequence of hyperacetylation. Additional experiments, performed with Cx43 acetylation mutants, revealed, for the acetylated form of the molecule, a significant reduction in plasma membrane localization and a tendency to nuclear accumulation. These results suggest that Cx43 N
ε
-lysine acetylation may have physiopathological consequences for cell to cell coupling and cardiac function.
pH-induced metal-ligand cross-links inspired by mussel yield self-healing polymer networks with near-covalent elastic moduli
Authors: Holten-Andersen Niels , Harrington Matthew J. , Birkedal Henrik , Lee Bruce P. , Messersmith Phillip B. , Lee Ka Yee C. , Waite J. Herbert
Published: January 2011

Growing evidence supports a critical role of metal-ligand coordination in many attributes of biological materials including adhesion, self-assembly, toughness, and hardness without mineralization [Rubin DJ, Miserez A, Waite JH (2010)
Advances in Insect Physiology: Insect Integument and Color
, eds Jérôme C, Stephen JS (Academic Press, London), pp 75–133]. Coordination between Fe and catechol ligands has recently been correlated to the hardness and high extensibility of the cuticle of mussel byssal threads and proposed to endow self-healing properties [Harrington MJ, Masic A, Holten-Andersen N, Waite JH, Fratzl P (2010)
Science
328:216–220]. Inspired by the pH jump experienced by proteins during maturation of a mussel byssus secretion, we have developed a simple method to control catechol-Fe
3+
interpolymer cross-linking via pH. The resonance Raman signature of catechol-Fe
3+
cross-linked polymer gels at high pH was similar to that from native mussel thread cuticle and the gels displayed elastic moduli (G′) that approach covalently cross-linked gels as well as self-healing properties.
Exercise training increases size of hippocampus and improves memory
Authors: Erickson Kirk I. , Voss Michelle W. , Prakash Ruchika Shaurya , Basak Chandramallika , Szabo Amanda , Chaddock Laura , Kim Jennifer S. , Heo Susie , Alves Heloisa , White Siobhan M. , Wojcicki Thomas R. , Mailey Emily , Vieira Victoria J. , Martin Stephen A. , Pence Brandt D. , Woods Jeffrey A. , McAuley Edward , Kramer Arthur F.
Published: February 2011

The hippocampus shrinks in late adulthood, leading to impaired memory and increased risk for dementia. Hippocampal and medial temporal lobe volumes are larger in higher-fit adults, and physical activity training increases hippocampal perfusion, but the extent to which aerobic exercise training can modify hippocampal volume in late adulthood remains unknown. Here we show, in a randomized controlled trial with 120 older adults, that aerobic exercise training increases the size of the anterior hippocampus, leading to improvements in spatial memory. Exercise training increased hippocampal volume by 2%, effectively reversing age-related loss in volume by 1 to 2 y. We also demonstrate that increased hippocampal volume is associated with greater serum levels of BDNF, a mediator of neurogenesis in the dentate gyrus. Hippocampal volume declined in the control group, but higher preintervention fitness partially attenuated the decline, suggesting that fitness protects against volume loss. Caudate nucleus and thalamus volumes were unaffected by the intervention. These theoretically important findings indicate that aerobic exercise training is effective at reversing hippocampal volume loss in late adulthood, which is accompanied by improved memory function.
Magnetosome-like ferrimagnetic iron oxide nanocubes for highly sensitive MRI of single cells and transplanted pancreatic islets
Authors: Lee Nohyun , Kim Hyoungsu , Choi Seung Hong , Park Mihyun , Kim Dokyoon , Kim Hyo-Cheol , Choi Yoonseok , Lin Shunmei , Kim Byung Hyo , Jung Hye Seung , Kim Hyeonjin , Park Kyong Soo , Moon Woo Kyung , Hyeon Taeghwan
Published: February 2011

For ultrasensitive magnetic resonance imaging (MRI), magnetic nanoparticles with extremely high r2 relaxivity are strongly desired. Magnetosome-like nanoparticles were prepared by coating polyethylene glycol-phospholipid (PEG-phospholipid) onto ferrimagnetic iron oxide nanocubes (FIONs). FIONs exhibited a very high relaxivity (r2) of 324 mM
-1
 s
-1
, allowing efficient labeling of various kinds of cells. The magnetic resonance (MR) imaging of single cells labeled with FIONs is demonstrated not only in vitro but also in vivo. Pancreatic islet grafts and their rejection could be imaged using FIONs on a 1.5 T clinical MRI scanner. The strong contrast effect of FIONs enabled MR imaging of transplanted islets in small rodents as well as in large animals. Therefore, we expect that MR imaging of pancreatic islet grafts using FIONs has the potentials for clinical applications. Furthermore, FIONs will enable highly sensitive noninvasive assessment after cell transplantation.