http://www.hindawi.com The latest articles from Hindawi Publishing Corporation © 2013 , Hindawi Publishing Corporation . All rights reserved. Sun, 30 Dec 2012 15:41:45 +0000 http://www.hindawi.com/journals/jamop/2012/916510/ We examine the interaction between an open-shell chlorine atom and a para-H2 molecule in the region of configuration space that corresponds to a weakly bound Cl–para-H2 van der Waals dimer. By constructing and diagonalizing the Hamiltonian matrix that represents the coupled Cl atom electronic and H2 rotational degrees of freedom, we obtain one-dimensional energy curves for the Cl–para-H2 system in this region of configuration space. We find that the dimer exhibits fairly strong electronic-rotational coupling when the Cl–H2 distance R is close to ; however, this coupling does not modify substantially the positions and depths of the van der Waals wells in the dimer’s curves. An approximation in which the para-H2 fragment is treated in the strict limit thus appears to yield an accurate representation of those states of the weakly bound Cl–para-H2 dimer that correlate with H2 in the limit. Robert J. Hinde Copyright © 2012 Robert J. Hinde. All rights reserved. Thu, 27 Dec 2012 17:40:55 +0000 http://www.hindawi.com/journals/jamop/2012/469043/ The recent paper entitled by K. C. Lee et al. (2011) establishes nonlocal macroscopic quantum correlations, which they term “entanglement”, under ambient conditions. Photon(s)-phonon entanglements are established within each interferometer arm. However, our analysis demonstrates, the phonon fields between arms become correlated as a result of single-photon wavepacket path indistinguishability, not true nonlocal entanglement. We also note that a coherence expansion (as opposed to decoherence) resulted from local entanglement which was not recognized. It occurred from nearly identical Raman scattering in each arm (importantly not meeting the Born and Markovian approximations). The ability to establish nonlocal macroscopic quantum correlations through path indistinguishability rather than entanglement offers the opportunity to greatly expand quantum macroscopic theory and application, even though it was not true nonlocal entanglement. Mark E. Brezinski Copyright © 2012 Mark E. Brezinski. All rights reserved. Wed, 05 Dec 2012 10:46:12 +0000 http://www.hindawi.com/journals/jamop/2012/976376/ Industrial applications need regular testing for the lifetime, movement, strength, and performance of manufacturing machines during production process. Since speckle photography is a simple economic technique, it is used in investigating object response under mechanical and thermal effects depending on the movement of the speckle patterns with respect to the deformation strength and direction. In the present work, the cross-correlation technique is used to analyze the speckle patterns by iterative method to define both values and directions of rigid body translation and expansion. In order to check the accuracy of the cross-correlation technique, the results are compared with the displacement values given by analyzing the Young's interference fringes resulted from the Fourier transformation of the speckle patterns. This noncontact technique is found to be accurate and informative depending on the stability and sensitivity of the optical system. This method of measurement is an effective tool in studying the hard cases of objects and machines under various effects. M. Bahrawi, N. Farid, and M. Abdel-Hady Copyright © 2012 M. Bahrawi et al. All rights reserved. Sun, 25 Nov 2012 11:55:44 +0000 http://www.hindawi.com/journals/jamop/2012/689831/ The refractive indices of the cholesteric liquid crystal solution were measured using multiwavelength (visible range) refractometer for three different wavelengths. Measurements were made at different temperatures for various concentrations of the solution, mixing CLC in a soluble solvent. Vuks equation describes the wavelength and temperature dependence of refractive indices of anisotropic crystalline materials. We have used a simplified version of Vuks equation relating only to macroscopic indices and verified its validity for five-different-concentration solution at various temperatures. The result is also used to obtain molecular polarizabilities and temperature dependent material constants of our sample. Anita Kanwar and Priya S. Yadav Copyright © 2012 Anita Kanwar and Priya S. Yadav. All rights reserved. Sun, 18 Nov 2012 08:59:45 +0000 http://www.hindawi.com/journals/jamop/2012/123872/ Previously (Chen et al., 2004), it was shown that dielectric cylinder can form focal spots with small diameters and long depth. This type of focal spot was called photonic nanojet. In this paper, it was shown that dielectric cylinder of radius 595 nm (1.12 of wavelength) forms near the surface a photonic nanojet with diameter equal to 0.31 of wavelength and depth of focus equal to 0.57 of wavelength. Adding truncated concentric rings with radiuses equal to radiuses of zone plate to the cylinder increases the depth of focus to 1.18 of the wavelength. The diameter and intensity of focal spot near the cylinder surface remain unchanged. Sergey S. Stafeev and Victor V. Kotlyar Copyright © 2012 Sergey S. Stafeev and Victor V. Kotlyar. All rights reserved. Wed, 14 Nov 2012 08:29:25 +0000 http://www.hindawi.com/journals/jamop/2012/839074/ Temperature dependent phase behavior of pseudo-ternary Gemini surfactant + 1-hexanol (1 : 5 molar ratios)/oil/water systems is reported from 0°C to 65°C. The influence of nature of hydrocarbon oil and type of electrolytes (weak as well as strong) has been investigated on the temperature induced phase behavior of the ternary system. At surfactant concentration, %, a “nose-shaped” microemulsion region is observed. Below one-phase microemulsion region, phase appears. The presence of NaCl decreases the domain size of micellar region whereas oxalic acid first decreases the domain below and then increases above in the lower boundary of the phase diagram. The critical weight fraction of water decreases in presence of both electrolytes. However, increases in presence of oxalic acid and remains constant in presence of NaCl as compared to salt-free system. Furthermore, when cyclohexane was replaced by a longer straight chain hydrocarbon, dodecane, the domain of the one-phase microemulsion region is tremendously increased. Mohd Zul Helmi Rozaini Copyright © 2012 Mohd Zul Helmi Rozaini. All rights reserved. Thu, 08 Nov 2012 19:15:29 +0000 http://www.hindawi.com/journals/jamop/2012/854693/ We consider the probability that a bipartite quantum state contains phase-conjugate-state (PCS) pairs and/or identical-state pairs as signatures of quantum entanglement. While the fraction of the PCS pairs directly indicates the property of a maximally entangled state, the fraction of the identical-state pairs negatively determines antisymmetric entangled states such as singlet states. We also consider the physical limits of these probabilities. This imposes fundamental restrictions on the pair appearance of the states with respect to the local access of the physical system. For continuous-variable system, we investigate similar relations by employing the pairs of phase-conjugate coherent states. We also address the role of the PCS pairs for quantum teleportation in both discrete-variable and continuous-variable systems. Ryo Namiki Copyright © 2012 Ryo Namiki. All rights reserved. Mon, 05 Nov 2012 11:44:19 +0000 http://www.hindawi.com/journals/jamop/2012/174236/ Marek J. Wójcik, Paul Blaise, Joanna Sadlej, and Henryk Flakus Copyright © 2012 Marek J. Wójcik et al. All rights reserved. Thu, 18 Oct 2012 14:59:04 +0000 http://www.hindawi.com/journals/jamop/2012/987052/ Zeev Zalevsky, Yuval Garini, Rachela Popovtzer, and Pietro Ferraro Copyright © 2012 Zeev Zalevsky et al. All rights reserved. Thu, 11 Oct 2012 15:32:36 +0000 http://www.hindawi.com/journals/jamop/2012/137967/ We consider arbitrary angle interactions between spatial solitons and the planar boundary between two optical materials with a single power-law nonlinear refractive index. Extensive analysis has uncovered a wide range of new qualitative phenomena in non-Kerr regimes. A universal Helmholtz-Snell law describing soliton refraction is derived using exact solutions to the governing equation as a nonlinear basis. New predictions are tested through exhaustive computations, which have uncovered substantially enhanced Goos-Hänchen shifts at some non-Kerr interfaces. Helmholtz nonlinear surface waves are analyzed theoretically, and their stability properties are investigated numerically for the first time. Interactions between surface waves and obliquely incident solitons are also considered. Novel solution behaviours have been uncovered, which depend upon a complex interplay between incidence angle, medium mismatch parameters, and the power-law nonlinearity exponent. J. M. Christian, E. A. McCoy, G. S. McDonald, J. Sánchez-Curto, and P. Chamorro-Posada Copyright © 2012 J. M. Christian et al. All rights reserved. Tue, 02 Oct 2012 14:02:33 +0000 http://www.hindawi.com/journals/jamop/2012/569876/ Energies and wave functions of the states for the beryllium atom are calculated with the full-core plus correlation wave functions. Fine structures and hyperfine structures are calculated with the first-order perturbation theory. For the state, the calculated energies, fine structure, and hyperfine structure parameters are in good agreement with the latest theoretical and experimental data in the literature; it is shown that atomic parameters of the low-lying excited states for the beryllium atom can be calculated accurately using this theoretical method. For the () states, the present calculations may provide valuable reference data for future theoretical calculations and experimental measurements. Chao Chen Copyright © 2012 Chao Chen. All rights reserved. Thu, 27 Sep 2012 08:46:21 +0000 http://www.hindawi.com/journals/jamop/2012/246105/ The transition parameters such as the wavelengths, weighted oscillator strengths, and transition probabilities (or rates) for the nd , nd , np , and ng electric dipole (E1) transitions of doubly ionized lanthanum (La III, ) have been calculated using the relativistic Hartree-Fock (HFR) method. In this method, configuration interaction and relativistic effects have been included in the computations combined with a least squares fitting of the Hamiltonian eigenvalues to the observed energy levels. We have compared the results obtained from this work with the previously available calculations and experiments in literature. We have also reported new transitions with the weighted transition probabilities greater than or equal to 105. Betül Karaçoban and Leyla Özdemir Copyright © 2012 Betül Karaçoban and Leyla Özdemir. All rights reserved. Tue, 11 Sep 2012 15:47:27 +0000 http://www.hindawi.com/journals/jamop/2012/125471/ Polarized IR spectra of 2-furanacetic acid and of 2-furanacrylic acid crystals were measured at 293 K and 77 K in the 𝑣O−H and 𝑣O−H band frequency ranges. The corresponding spectra of the two individual systems strongly differ, one from the other, by the corresponding band shapes as well as by the temperature effect characterizing the bands. The crystal spectral properties remain in a close relation with the electronic structure of the two different molecular systems. We show that a vibronic coupling mechanism involving the hydrogen bond protons and the electrons on the π-electronic systems in the molecules determines the way in which the vibrational exciton coupling between the hydrogen bonds in the carboxylic acid dimers occurs. A strong coupling in 2-furanacrylic acid dimers prefers a “tail-to-head-” type Davydov coupling widespread by the π-electrons. A weak through-space coupling in 2-furanacetic acid dimers is responsible for a “side-to-side-” type coupling. The relative contribution of each exciton coupling mechanism in the dimer spectra generation is temperature and the molecular electronic structure dependent. This explains the observed difference in the temperature-induced evolution of the compared spectra. Henryk T. Flakus and Anna Jarczyk-Jędryka Copyright © 2012 Henryk T. Flakus and Anna Jarczyk-Jędryka. All rights reserved. Mon, 03 Sep 2012 12:55:26 +0000 http://www.hindawi.com/journals/jamop/2012/135708/ This study analytically analyzes the changes in the temperature profile of a homogenous and isotropic medium having the same thermal parameters as a muscular tissue, due to the heat released by a single magnetic nanoparticle (MNP) to its surroundings when subject to different magnetic field profiles. Exploring the temperature behavior of a heated MNP can be very useful predicting the temperature increment of it immediate surroundings. Therefore, selecting the most effective magnetic field profile (MFP) in order to reach the necessary temperature for cancer therapy is crucial in hyperthermia treatments. In order to find the temperature profile caused by the heated MNP immobilized inside a homogenous medium, the 3D diffusive-heat-flow equation (DHFE) was solved for three different types of boundary conditions (BCs). The change in the BC is caused by the different MF profiles (MFP), which are analyzed in this article. The analytic expressions are suitable for describing the transient temperature response of the medium for each case. The analysis showed that the maximum temperature increment surrounding the MNP can be achieved by radiating periodic magnetic pulses (PMPs) on it, making this MFP more effective than the conventional cosine profile. Brenda Dana and Israel Gannot Copyright © 2012 Brenda Dana and Israel Gannot. All rights reserved. Tue, 28 Aug 2012 08:28:36 +0000 http://www.hindawi.com/journals/jamop/2012/361947/ I present a time-dependent density functional study of the 20 low-lying excited states as well the ground states of the zinc dimer Zn2, analyze its spectrum obtained from all electrons calculations performed using time-depended density functional with a relativistic 4-component and relativistic spin-free Hamiltonian as implemented in Dirac-Package, and show a comparison of the results obtained from different well-known and newly developed density functional approximations, a comparison with the literature and experimental values as far as available. The results are very encouraging, especially for the lowest excited states of this dimer. However, the results show that long-range corrected functionals such as CAMB3LYP gives the correct asymptotic behavior for the higher states, and for which the best result is obtained. A comparable result is obtained from PBE0 functional. Spin-free Hamiltonian is shown to be very efficient for relativistic systems such as Zn2. Ossama Kullie Copyright © 2012 Ossama Kullie. All rights reserved. Wed, 22 Aug 2012 14:08:37 +0000 http://www.hindawi.com/journals/jamop/2012/363247/ Millimeter-wave rotational spectrum of trans-acrolein (propenal) (CH2CHCOH) produced by applying a DC glow discharge through a low-pressure (~10–20 mTorr) flow of allyl alcohol (CH2CHCH2OH) vapor has been observed in the ground and several excited torsional states in the frequency region: 60.0–99.0 GHz. A least-square analysis of the measured and previously reported rotational transition frequencies has produced a set of rotational and centrifugal distortion constants for the ground as well as excited torsional states. Detailed DFT calculations were also carried out with various functional and basis sets to evaluate the spectroscopic constants, dipole moment, and various structural parameters of the trans conformer of propenal for the ground state and compared with their corresponding experimental values. A linear variation of the inertia defect values with torsional quantum number (𝑣=0,1,2,3) demonstrates that the equilibrium configuration of trans-propenal is planar. A. I. Jaman and Rangana Bhattacharya Copyright © 2012 A. I. Jaman and Rangana Bhattacharya. All rights reserved. Thu, 09 Aug 2012 08:29:04 +0000 http://www.hindawi.com/journals/jamop/2012/850482/ Integrated polypyrrole, a conductive polymer, interconnects on polymeric substrates were microfabricated for flexible sensors and actuators applications. It allows manufacturing of moving polymeric microcomponents suitable, for example, for micro-optical-electromechanical (MOEMS) systems or implanted sensors. This generic technology allows producing “all polymer” components where the polymers serve as both the structural and the actuating materials. In this paper we present two possible novel architectures that integrate polypyrrole conductors with other structural polymers: (a) polypyrrole embedded into flexible polydimethylsiloxane (PDMS) matrix forming high aspect ratio electrodes and (b) polypyrrole deposited on planar structures. Self-aligned polypyrrole electropolymerization was developed and demonstrated for conducting polymer lines on either gold or copper seed layers. The electropolymerization process, using cyclic voltammetry from an electrolyte containing the monomer, is described, as well as the devices’ characteristics. Finally, we discuss the effect of integrating conducting polymers with metal seed layer, thus enhancing the device durability and reliability. Rakefet Ofek Almog, Hadar Ben-Yoav, Yelena Sverdlov, Tsvi Shmilovich, Slava Krylov, and Yosi Shacham-Diamand Copyright © 2012 Rakefet Ofek Almog et al. All rights reserved. Wed, 01 Aug 2012 10:40:45 +0000 http://www.hindawi.com/journals/jamop/2012/241051/ We consider finite-range effects when the scattering length goes to zero near a magnetically controlled Feshbach resonance. The traditional effective-range expansion is badly behaved at this point, and we therefore introduce an effective potential that reproduces the full T-matrix. To lowest order the effective potential goes as momentum squared times a factor that is well defined as the scattering length goes to zero. The potential turns out to be proportional to the background scattering length squared times the background effective range for the resonance. We proceed to estimate the applicability and relative importance of this potential for Bose-Einstein condensates and for two-component Fermi gases where the attractive nature of the effective potential can lead to collapse above a critical particle number or induce instability toward pairing and superfluidity. For broad Feshbach resonances the higher order effect is completely negligible. However, for narrow resonances in tightly confined samples signatures might be experimentally accessible. This could be relevant for suboptical wavelength microstructured traps at the interface of cold atoms and solid-state surfaces. N. T. Zinner Copyright © 2012 N. T. Zinner. All rights reserved. Wed, 01 Aug 2012 08:45:38 +0000 http://www.hindawi.com/journals/jamop/2012/985490/ Theoretical model for vibrational interactions in the hydrogen-bonded benzoic acid dimer is presented. The model takes into account anharmonic-type couplings between the high-frequency O–H and the low-frequency O⋯O stretching vibrations in two hydrogen bonds, resonance interactions between two hydrogen bonds in the dimer, and Fermi resonance between the O–H stretching fundamental and the first overtone of the O–H in-plane bending vibrations. The model is used for theoretical simulation of the O–H stretching IR absorption bands of benzoic acid dimers in the gas phase in the first excited singlet state. Ab initio CIS and CIS(D)/CIS/6-311++G(d,p) calculations have been carried out in the à state of tropolone. The grids of potential energy surfaces along the coordinates of the tunneling vibration and the low-frequency coupled vibration have been calculated. Two-dimensional model potentials have been fitted to the calculated potential energy surfaces. The tunneling splittings for vibrationally excited states have been calculated and compared with the available experimental data. The model potential energy surfaces give good estimation of the tunneling splittings in the vibrationally ground and excited states of tropolone, and explain monotonic decrease in tunneling splittings with the excitation of low-frequency out-of-plane modes and increase of the tunneling splittings with the excitation of low-frequency planar modes. Marek J. Wójcik, Marek Boczar, and Łukasz Boda Copyright © 2012 Marek J. Wójcik et al. All rights reserved. Sun, 29 Jul 2012 08:56:56 +0000 http://www.hindawi.com/journals/jamop/2012/754879/ The hydrogen bond interaction between CH3CHO, CH2FCHO, and CH3CFO and two water molecules is investigated at the B3LYP/6-311++G(d,p) level. The results are compared with the complexes involving the same carbonyl derivatives and one water molecule. The calculations involve the optimization of the structure, the harmonic vibrational frequencies, and relevant NBO (natural bond orbital) parameters such as the NBO charges, the occupation of antibonding orbitals, and intra- and intermolecular hyperconjugation energies. Two stable cyclic structures are predicted. The two structures are stabilized by C=O⋯HO hydrogen bond. The A structures are further stabilized by CH⋯O bond involving the CH3 (CH2F) group. This bond results in an elongation of the CH bond and red shift of the ν(CH) vibration. The B structures are stabilized by CH⋯O interaction involving the aldehydic CH bond. The formation of this bond results in a marked contraction of the CH bond and blue shift of the ν(CH) vibration indicating the predominance of the lone pair effect in determining the CH distances. The total interaction energies range from −12.40 to −13.50 kcal mol−1. The cooperative energies calculated at the trimer geometry are comprised between −2.30 and −2.60 kcal mol−1. Asit K. Chandra and Thérèse Zeegers-Huyskens Copyright © 2012 Asit K. Chandra and Thérèse Zeegers-Huyskens. All rights reserved. Thu, 26 Jul 2012 11:13:33 +0000 http://www.hindawi.com/journals/jamop/2012/236793/ Two forms of cyclic, doubly hydrogen-bonded dimers are discovered for crystalline 1H-pyrrolo[3,2-h]quinoline, a bifunctional molecule possessing both hydrogen bond donor and acceptor groups. One of the forms is planar, the other is twisted. Analysis of IR and Raman spectra, combined with DFT calculations, allows one to assign the observed vibrations and to single out vibrational transitions which can serve as markers of hydrogen bond formation and dimer structure. Raman spectra measured for samples submitted to high pressure indicate a transition from the planar towards the twisted structure. Formation of intermolecular hydrogen bonds leads to a large increase of the Raman intensity of the NH stretching band: it can be readily observed for the dimer, but is absent in the monomer spectrum. Alexandr Gorski, Sylwester Gawinkowski, Roman Luboradzki, Marek Tkacz, Randolph P. Thummel, and Jacek Waluk Copyright © 2012 Alexandr Gorski et al. All rights reserved. Wed, 27 Jun 2012 10:15:38 +0000 http://www.hindawi.com/journals/jamop/2012/963187/ Implantable wireless devices may allow localized real-time biomedical treating and monitoring. However, such devices require a power source, which ideally, should be self-powered and not battery dependent. In this paper, we present a novel self-powered light therapeutic device which is designed to implement blood irradiation therapy. This device is self-powered by a miniaturized turbine-based generator which uses hydraulic flow energy as its power source. The research presented in this paper may become the first step towards a new type of biomedical self-operational micromechanical devices deployed for biomedical applications. Avigail D. Amsel, Arkady Rudnitsky, and Zeev Zalevsky Copyright © 2012 Avigail D. Amsel et al. All rights reserved. Thu, 21 Jun 2012 18:30:59 +0000 http://www.hindawi.com/journals/jamop/2012/217932/ The aim of the present paper is an analysis of the hydrogen bond properties for the acid-base systems depending on the ability to the proton transfer in the formulation of the Brönsted approach. After definition of the proton transfer equilibrium expressed by using the equation log𝐾PT=𝜉Δ𝑝𝐾𝑁, various examples of different physical properties, such as dipole moments, IR spectra, and nuclear magnetic resonances, are presented which correlate with the Δ𝑝𝐾𝑁 value. In such a way, a critical state of hydrogen bonding can be defined that corresponds to the potential of the proton motion for either single minimum or double minimum with low barrier. A particular attention in this paper found electronic spectra which have not been analysed so far and the quantitative analysis of the vibrational polarizability which can reach very high values of the order of electronic polarizability. L. Sobczyk, B. Czarnik-Matusewicz, M. Rospenk, and M. Obrzud Copyright © 2012 L. Sobczyk et al. All rights reserved. Wed, 20 Jun 2012 08:57:33 +0000 http://www.hindawi.com/journals/jamop/2012/589651/ We suggest a new method for the analysis of experimental time series that can distinguish high-dimensional dynamics from stochastic motion. It is based on the idea of statistical complexity, that is, the Shannon entropy of the so-called ϵ-machine (a Markov-type model of the observed time series). This approach has been recently demonstrated to be efficient for making a distinction between a molecular trajectory in water and noise. In this paper, we analyse the difference between chaos and noise using the Chirikov-Taylor standard map as an example in order to elucidate the basic mechanism that makes the value of complexity in deterministic systems high. In particular, we show that the value of statistical complexity is high for the case of chaos and attains zero value for the case of stochastic noise. We further study the Markov property of the data generated by the standard map to clarify the role of long-time memory in differentiating the cases of deterministic systems and stochastic motion. Vladimir Ryabov and Dmitry Nerukh Copyright © 2012 Vladimir Ryabov and Dmitry Nerukh. All rights reserved. Mon, 18 Jun 2012 09:04:57 +0000 http://www.hindawi.com/journals/jamop/2012/683830/ The goal of this paper is to immobilize gold nanoparticles uniformly on a glass substrate. In order to attach gold-nanorods (GNRs) to an area of a few squared microns surface of glass substrate without preliminary coating of the GNR, 3-(Mercaptopropyl)trimethoxysilane molecules were used as linker while using different methods. These methods included placing the glass slide and the GNR (1) inside a tube without any motion; (2) inside a shaker; (3) in a fan setup. The fan setup included a tube containing the GNR solution and the glass slide at a vertical position, when the fan blows above the tube, producing turbulations in the liquid. Each method was evaluated according to the density and the homogeneousness of the GNR monolayer on the surface. The uniformity of the monolayer was demonstrated using AFM images of different areas on the slides, and the effectiveness of the protocol was demonstrated by calculating the average density of the GNR on the surface using image processing and analysis software. It was found that while both the shaker and the fan setups improved the monolayer density, the fan setup improved the density by a factor of more than two than the density found using the shaker. Hadas Weinrib, Amihai Meiri, Hamootal Duadi, and Dror Fixler Copyright © 2012 Hadas Weinrib et al. All rights reserved. Thu, 07 Jun 2012 10:12:12 +0000 http://www.hindawi.com/journals/jamop/2012/404536/ Nanoparticle-based contrast agents are expected to play a major role in the future of molecular imaging due to their many advantages over the conventional contrast agents. These advantages include prolonged blood circulation time, controlled biological clearance pathways, and specific molecular targeting capabilities. Recent studies have provided strong evidence that molecularly targeted nanoparticles can home selectively onto tumors and thereby increase the local accumulation of nanoparticles in tumor sites. However, there are almost no reports regarding the number of nanoparticles that bind per cell, which is a key factor that determines the diagnostic efficiency and sensitivity of the overall molecular imaging techniques. Hence, in this research we have quantitatively investigated the effect of the size of the nanoparticle on its binding probability and on the total amount of material that can selectively target tumors, at a single cell level. We found that 90 nm GNPs is the optimal size for cell targeting in terms of maximal Au mass and surface area per single cancer cell. This finding should accelerate the development of general design principles for the optimal nanoparticle to be used as a targeted imaging contrast agent. Vital Peretz, Menachem Motiei, Chaim N. Sukenik, and Rachela Popovtzer Copyright © 2012 Vital Peretz et al. All rights reserved. Sun, 03 Jun 2012 09:45:58 +0000 http://www.hindawi.com/journals/jamop/2012/782806/ The Wang-Landau method estimates the relative density of states (DOS) by performing random walk in energy space. However, estimation of the DOS near the ground state minimum is highly challenging because of the dearth of states in the low-energy region compared to that at the high-energy region. Ideally the derivative of the logarithm of the DOS with respect to energy, which is proportional to the inverse of temperature, should become steeper with decrease in energy. However, in actual estimation of the DOS for molecular systems, it is nontrivial to achieve this. In the current work, the accuracy of the Wang-Landau method in estimating the DOS near the ground state minimum is investigated for two peptides, Met-enkephalin and (Alanine)5. It has been found that the steepness of the DOS can be achieved if the correct ground state energy is found, the bin used to discretize the energy space is extremely small (0.1 kcal/mol was used in the current case) and the energy range used to estimate the DOS is small. The findings of this work can help in devising new protocols for calculating the DOS with high accuracy near the ground state minimum for molecular systems. Priya Singh and Pradipta Bandyopadhyay Copyright © 2012 Priya Singh and Pradipta Bandyopadhyay. All rights reserved. Mon, 14 May 2012 09:24:14 +0000 http://www.hindawi.com/journals/jamop/2012/125071/ We examine dynamics of water molecules and hydrogen bonds at the water-protein interface of the wild-type antifreeze protein from spruce budworm Choristoneura fumiferana and a mutant that is not antifreeze active by all-atom molecular dynamics simulations. Water dynamics in the hydration layer around the protein is analyzed by calculation of velocity autocorrelation functions and their power spectra, and hydrogen bond time correlation functions are calculated for hydrogen bonds between water molecules and the protein. Both water and hydrogen bond dynamics from subpicosecond to hundred picosecond time scales are sensitive to location on the protein surface and appear correlated with protein function. In particular, hydrogen bond lifetimes are longest for water molecules hydrogen bonded to the ice-binding plane of the wild type, whereas hydrogen bond lifetimes between water and protein atoms on all three planes are similar for the mutant. Yao Xu, Ramachandran Gnanasekaran, and David M. Leitner Copyright © 2012 Yao Xu et al. All rights reserved. Sun, 22 Apr 2012 11:26:23 +0000 http://www.hindawi.com/journals/jamop/2012/192613/ The 46- and 69-residue BLN model proteins both exhibit frustrated folding to β-barrel structures. We study the effect of varying the strength of nonnative interactions on the corresponding energy landscapes by introducing a parameter 𝜆, which scales the potential between the BLN (𝜆=1) and Gō-like (𝜆=0) limits. We study the effect of varying 𝜆 on the efficiency of global optimisation using basin-hopping and genetic algorithms. We also construct disconnectivity graphs for these proteins at selected values of 𝜆. Both methods indicate that the potential energy surface is frustrated for the original BLN potential but rapidly becomes less frustrated as 𝜆 decreases. For values of 𝜆≤0.9, the energy landscape is funnelled. The fastest mean first encounter time for the global minimum does not correspond to the Gō model: instead, we observe a minimum when the favourable nonnative interactions are still present to a small degree. Mark T. Oakley, David J. Wales, and Roy L. Johnston Copyright © 2012 Mark T. Oakley et al. All rights reserved. Thu, 19 Apr 2012 11:36:54 +0000 http://www.hindawi.com/journals/jamop/2012/925278/ The evolution of many systems is dominated by rare activated events that occur on timescale ranging from nanoseconds to the hour or more. For such systems, simulations must leave aside the full thermal description to focus specifically on mechanisms that generate a configurational change. We present here the activation relaxation technique (ART), an open-ended saddle point search algorithm, and a series of recent improvements to ART nouveau and kinetic ART, an ART-based on-the-fly off-lattice self-learning kinetic Monte Carlo method. Normand Mousseau, Laurent Karim Béland, Peter Brommer, Jean-François Joly, Fedwa El-Mellouhi, Eduardo Machado-Charry, Mihai-Cosmin Marinica, and Pascal Pochet Copyright © 2012 Normand Mousseau et al. All rights reserved.