Energy transport for biomolecular networks (Vol. 43 No. 1)

Recent experimental demonstrations of long-lived quantum coherence in certain photosynthetic light-harvesting structures have launched a flurry of controversy over the role of coherence in biological function. An ongoing investigation into the astonishingly high-energy transport efficiency of these structures suggests that nature takes advantage of quantum coherent dynamics.
We inquire on the fundamental principles of quantum coherent energy transport in ensembles of spatially disordered molecular networks subjected to dephasing noise. De-phasing reduces the coherence between individual network nodes and has already been shown to assist transport substantially provided that quantum coherence is disadvantageous by reason of destructive interference, e.g. in the presence of disorder and quantum localization. In a statistical survey, we map the probability landscape of transport efficiency for the whole ensemble of disordered networks, in search of specially adapted molecular conformations that nature may select in order to facilitate energy transport: We thus find certain optimal molecular configurations that by virtue of constructive quantum interference yield the highest transport efficiencies in the absence of dephasing noise. Moreover, the transport efficiencies realized by these optimal configurations are systematically higher than the noise-assisted efficiencies mentioned above. As discussed in the article, this defines a clear incentive to select configurations for which quantum coherence can be harnessed.
The optimization topography of exciton transport
T. Scholak, T. Wellens and A. Buchleitner, EPL, 96, 10001 (2011)
[Abstract]
Enigmatic Nematics (Vol. 44 No. 1)
The law of hydrodynamics governing the way internally driven systems such as biological cells and bacteria behave could explain their complex structure and their inherent properties. Hydrodynamics is used here to understand the physical mechanism responsible for changes in the long-range order of groups of particles. The present work concerns ordered groups of elongated self-propelled particles, studying the breakdown of long-range order due to fluctuations that render them unstable and give rise to complex structures.
The authors coined the term self-propelled nematics to refer to internally driven elongated particles that spontaneously align head to tail, like tinned sardines. These are characterised by an ordered state that is stationary on average. This means that there is a long-range order, whereas the locally preferred direction may vary throughout the medium due to local strains or disturbances.
It is found here that a uniform nematic state can be disturbed by density fluctuations associated with an upward current of active particles. Since the density in turn controls the onset of nematic order, this phenomenon is self-regulating and universal.
It is also found that instability could be triggered by a local distortion of particles’ orientation. Such a distortion results in local currents that in turn amplify the distortion, leading to instability deep inside the nematic state.
Ultimately, this work may help us gain a deeper understanding of pattern formation and dynamics in a variety of internally driven systems, from epithelial cells and soil bacteria such as Myxococcus xanthus, to colloidal self-propelled nanorods.
A. Baskaran and M. C. Marchetti, ‘Self-regulation in self-propelled nematic fluids’, Eur. Phys. J. E 35, 95 (2012)
[Abstract]
Entanglement or separability: factorisation of density matrix algebra (Vol. 43 No. 1)

The present theoretical description of teleportation phenomena in sub-atomic scale physical systems proves that mathematical tools let free to choose how to separate out the constituting matter of a complex physical system by selectively analysing its so-called quantum state. That is the state in which the system is found when performing measurement, being either entangled or not. The state of entanglement corresponds to a complex physical system in a definite (pure) state, while its parts taken individually are not. This concept of entanglement used in quantum information theory applies when measurement in laboratory A (called Alice) depends on the definite measurement in laboratory B (called Bob), as both measurements are correlated. This phenomenon cannot be observed in larger-scale physical systems.
The findings show that the entanglement or separability of a quantum state -whether its sub-states are separable or not; i.e., whether Alice and Bob were able to find independent measurements - depends on the perspective used to assess its status.
A so-called density matrix is used to mathematically describe a quantum state. To assess this state's status, the matrix can be factorised in different ways, similar to the many ways a cake can be cut. The Vienna physicists have shown that by choosing a particular factorisation, it may lead to entanglement or separability; this can, however, only be done theoretically, as experimentally the factorisation is fixed by experimental conditions.
This is applied to model physical systems of quantum information including the theoretical study of teleportation, which is the transportation of a single quantum state. Other practical applications include gaining a better understanding of K-meson creation and decay in particle physics, and of the quantum Hall effect, where electric conductivity takes quantified values.
Entanglement or separability: the choice of how to factorise the algebra of a density matrix
W. Thirring, R.A. Bertlmanna, P. Köhler and H. Narnhofer, Eur. Phys. J. D, 64/2, 181 (2011)
[Abstract]
Enterococcus faecalis biofilm in an air plasma jet

Enterococcus faecalis is a gram-positive bacterium, which often infects root canals during endodontic dental treatments and is among the most antibiotic- and heat-resistant pathogens, which strongly resist calcium hydroxide treatment. Inactivation of these pathogens is particularly challenging because they form thick self-organized biofilms. Effective inactivation of a record thick 25.2 µm-thick biofilm by using a handheld, 12 V DC battery-operated plasma jet device is reported. The plasma jet, called the Plasma Flashlight operates in open air at atmospheric pressure and does not require any external gas supply or wall power. This makes the Plasma Flashlight suitable for various point-of-care applications, such as in ambulance emergency outcalls, natural disaster rescue and military combat operations, treatments in remote locations, etc. It produces a plasma plume with the temperature of 20-28°C, which is very close to room temperature. The device is extremely energy efficient and only 60 mW DC power is required to sustain the discharge. The figure shows the results of inactivation of the Enterococcus faecalis bacteria in each of the 17 layers within a 25.2 µm-thick biofilm. These results advance our ability to effectively inactivate biofilms formed by notoriously drug- and treatment-resistant pathogens. The reported mobile, handheld plasma jet device may also be used for surface treatment and functionalization in nanotechnology, device fabrication, and several other applications where surface temperature sensitivity is an issue.
Inactivation of a 25.5 µm Enterococcus faecalis biofilm by a room-temperature, battery-operated, handheld air plasma jet
X. Pei, X. Lu, J. Liu, D. Liu, Y. Yang, K. Ostrikov, Paul K. Chu and Y. Pan, J. Phys. D: Appl. Phys., 45, 165205 (2012)
[Abstract]
Ephemeral vacuum particles induce speed-of-light fluctuations (Vol. 44 No. 4)

New research shows that the speed of light may not be fixed after all, but rather fluctuates, while its value could be set by the total number of elementary particles in nature. Two EPJ D neighbour papers challenge established wisdom about the nature of vacuum. Vacuum is one of the most intriguing concepts in physics. When observed at the quantum level, vacuum is not empty. It is filled with continuously appearing and disappearing particle pairs such as electron-positron or quark-antiquark pairs.
In the study of article 1, the authors established, for the first time, a detailed quantum mechanism that would explain the magnetisation and polarisation of the vacuum, referred to as vacuum permeability and permittivity, and the finite speed of light. This finding is relevant because it suggests the existence of a limited number of ephemeral particles per unit volume in a vacuum. As a result, there is a theoretical possibility that the speed of light is not fixed, as conventional physics has assumed. Instead, this speed would be dependent on variations in the vacuum properties of space or time.
In the work of article 2, the other authors found that a specific property of vacuum called the impedance, which is crucial in determining the speed of light, depends only on the sum of the square of the electric charges of particles’ pair but not on their masses. If their idea is correct, the value of the speed of light combined with the value of vacuum impedance gives an indication of the total number of charged elementary particles existing in nature.
M. Urban, F. Couchot, X. Sarazin and A. Djannati-Atai, ‘The quantum vacuum as the origin of the speed of light’, Eur. Phys. J. D, 67, 58 (2013)
[Abstract]
G. Leuchs and L. L. Sánchez-Soto ‘A sum rule for charged elementary particles’, Eur. Phys. J. D, 67, 57 (2013)
[Abstract]
Evidence for a Bose-Einstein condensate of excitons (Vol. 45 No.5-6)

At sufficiently low temperatures, boson-like quantum particles can condense in the ground-state of the system and then form a particular realm called a Bose-Einstein condensate. Semiconductor excitons, i.e. electron-hole pairs bound by Coulomb attraction, shall undergo Bose-Einstein condensation under a priori easily accessible experimental conditions, e.g. below a few Kelvins. However, due to their composite nature, excitons exhibit a dark ground-state, i.e. optically inactive, which has certainly contributed to the lack of signature of exciton condensation obtained through conventional optical probes.
In this letter, the authors reveal the dark nature of excitons Bose-Einstein condensation. They report an excitonic quantum statistical distribution marked by a dominant (~ 90%) fraction of dark excitons at sub-Kelvin temperatures. The exciton condensate emits a weak photoluminescence with macroscopic spatial coherence and linear polarization. These signal a multi-component exciton condensation, with a weak bright component coherently coupled to a dominant dark part, as theoretically predicted.
M. Alloing et al., “Evidence for a Bose-Einstein condensate of excitons”, EPL, 107, 10012 (2014)
[Abstract]
Evidence of Long-range Correlations in Shallow Earthquakes (Vol. 49 No.4)

Earthquakes are one of the most devastating natural disasters by the number of casualties and the negative economic impact. Seismic phenomena have been studied from the viewpoint of complex systems, where complex patterns arise from nonlinear interactions between their elements. One of such ways is using networks of geographical sites; we introduce a new methodology to construct networks of epicenters and applied it to global catalogs of shallow earthquakes. It involves essentially the introduction of a time window, which works as a temporal filter for vertices connections. The resulting network constructed has small-world properties and presents scale-free properties in its connectivity distribution, which we proved to be invariant with respect to the value of the time window adopted. Vertices with larger connectivity in the network correspond to areas with very intense seismic activity in the period considered. These new results constitute evidences of possible spatial and temporal long-range correlations between earthquakes.
D. Ferreira, J. Ribeiro, A. Papa and R. Menezes, Towards evidence of long-range correlations in shallow seismic activities, EPL 121, 58003 (2018)
[Abstract]
Exact formula now available for measuring scientific success (Vol. 47 No. 2)

https://eu.fotolia.com/id/84276789 © treenabeena
Physicists team has developed equations governing the growth of authors’ h-index using an agent-based model.
Scientometrics research is the science of evaluating scientific performance. Physics methods designed to predict growth based on a scale-free network have rarely been applied to this field. Now, the authors have developed an analytical method using a previously developed agent-based model to predict the h-index, probably the most popular citation-based scientific measurement, using bibliometric data. They are the very first to succeed in developing an exact formula to calculate the number of external citations and self-citations for each paper written by an author. These findings have just been published by the authors. It opens the door to applying this growth analysis to social network users or citations from different scientific fields.
B. Żogała-Siudem, G. Siudem, A. Cena and M. Gagolewski, Agent-based model for the h-index – exact solution, Eur. Phys. J. B 8, 21 (2016)
[Abstract]
Exploiting cavity optomechanics for phonon lasing (Vol. 48 No. 1)

Phonon lasing in a mechanical resonator is a regime in which its oscillations are self-sustained, monochromatic, coherent and of high-amplitude. The main limitations of conventional sources of coherent mechanical waves are that they are not self-sustained nor operate efficiently above a few tens of gigahertz. Phonon lasers overcome the former by definition, while the latter is one of the challenges being tackled to make a real technological impact. Phonon lasers based on optomechanical devices may provide a way out, where advances of nanofabrication techniques help push-up the frequency of the vibration modes that can be tailored and driven by radiation pressure forces, while integration into a high-quality optical cavity allows a dramatic increase of power efficiencies.
This work reviews several mechanisms and techniques that can drive a mechanical mode into the lasing regime by exploiting the radiation pressure force in optomechanical cavities. The authors pay special attention to circular microresonators and optomechanical photonic crystal cavities. The former were the pioneer optomechanical setups demonstrating phonon lasing action while the latter can be chip-integrated enabling straightforward connection to phononic waveguides or membranes for out-coupling the phonon lasing signal.
D. Navarro-Urrios, J. Gomis-Bresco, F. Alzina, N. E. Capuj, P. D. García, M. F. Colombano, E. Chavez-Angel and C. M. Sotomayor-Torres, Self-sustained coherent phonon generation in optomechanical cavities, J. Opt. 18, 094006 (2016)
[Abstract]
Exploiting Slow Light for Stimulated Brillouin Scattering (Vol. 50, No. 3)

Stimulated Brillouin scattering (SBS) is an important third-order nonlinear process. The main challenge of utilizing SBS in silicon photonic waveguides is that the SBS gain coefficient is too weak to generate efficient power conversion between optical waves and acoustic waves.
In a recent study, the authors show how to improve the SBS process in a periodic suspended silicon waveguide by exploiting the slow light characteristic. They focus on tuning the structural parameters and working wavelength of the device to exploiting the resonance enhancement effect to amplify the weak SBS phenomenon. The calculated SBS gain coefficient is shown to be in the order of 106 W-1m-1. They also prove the feasibility of the device design using standard silicon-on-insulator wafers. The slow-light waveguide provides a powerful platform for light-sound interaction through SBS process.
Y. Xu, L. Zhou, L. Lu, J. Chen, and B. M. A. Rahman, Enhanced forward stimulated Brillouin scattering in silicon photonic slot waveguide Bragg grating, J. Phys. D: Appl. Phys. 52, 184001 (2019)
[Abstract]
Exploring charge transport in nitride heterostructures (Vol. 43 No. 2)
One of the most fundamental properties of nitride semiconductors is the presence of strong electronic polarization fields due to its wurtzite crystal structure. A variety of electronic and optoelectronic devices use or are adversely affected by the presence of polarization fields and charges at heterojunctions. For example, high GaN electron mobility transistors (HEMTs) use the high-density 2-dimensional electron gases induced by polarization discontinuity as the conductive channel. Optical devices such as light emitting diodes (LEDs) and lasers have to be designed by taking the presence of high polarization fields and quantum-confined Stark-effect into account. As investigations of non-polar and semi-polar orientations of GaN heterostructures mature for device applications, a comparative study of charge transport properties for various polar orientations in III-Nitride semiconductors is especially timely.
This article presents such a comparative study. Carrier transport is anisotropic in semi-polar and non-polar nitrides compared to the polar orientations. New phenomena such as interface charge scattering due to polarization discontinuity emerge for non-polar heterostructures. It is shown that for quantum well LEDs, the nitrogen-polar structure has the best carrier injection properties into the wells, while the non-polar structure has the highest electron-hole wave function overlap, enhancing the efficiency of light emission. Thus, depending on the dopant activation energies, polarization can help improve LED performance if the direction is chosen carefully. The study also reveals that by vertically injecting the high-energy electrons from AlGaN into GaN, the negative mass region of the GaN band structure can be accessed leading to current instabilities and current oscillation in the time domain. This process can be a recipe for generating ac power at high frequencies. This study will help to design high-mobility enhancement-mode transistors, efficient quantum well LEDs and possibly open up routes to nitride-based terahertz generation and detection.
Charge transport in non-polar and semi-polar III-V nitride heterostructures
A. Konar, A. Verma, Tian Fang, Pei Zhao, R. Jana and D. Jena, Semicond. Sci. Technol. 27, 024018 (2012)
[Abstract]
Extreme UV spectroscopy of highly charged xenon (Vol. 44 No. 2)

Spectra of highly ionized xenon have been studied exhaustively in a wide variety of high-temperature devices, such as tokamaks and electron beam ion traps (EBITs), through the past several decades. Due to its large mass that significantly reduces the Doppler broadening, xenon is routinely used for spectra calibration, and therefore its accurately measured and identified spectra would have immediate application in diagnostics of hot plasmas.
The measurements of extreme ultraviolet Xe spectra were performed on the NIST EBIT at six electron beam energies between 1.51 keV and 5.93 keV. These energies were chosen to enhance expected ion species based on our collisional-radiative modelling of the EBIT plasma. With a flat-field grazing-incidence spectrometer operating in the range 4.5-19.5 nm, we observed and classified 50 lines of Xe ranging from 26-times ionized to 43-times ionized. Thirty of these lines were entirely new, and eight of those are due to forbidden (magnetic-dipole and electric-quadrupole) transitions. By using well-known lines as references, we measured the wavelengths of the new lines to an accuracy of 0.0025 nm. An example of agreement between the measured spectra and our large-scale collisional-radiative calculations used to identify spectral lines is presented in the figure. The theory is seen to be capable of correctly predicting not only the spectral line wavelengths but also their intensities.
D. Osin, J. Reader, J. D. Gillaspy, and Yu. Ralchenko, ‘Extreme ultraviolet spectra of highly charged xenon observed with an electron beam ion trap’, J. Phys. B: At. Mol. Opt. Phys. 45, 245001 (2012)
[Abstract]
Factors affecting turbulence scaling (Vol. 50, No. 1)

Study focuses on hydrodynamic effects of external disturbances on fluids at critical points, including inconsistent turbulence in all directions, or anisotropy, and varying degrees of compressibility
Fluids exhibiting scaling behaviour can be found in diverse physical phenomena occurring both in the laboratory and in real-world conditions. For instance, they occur at the critical point when a liquid becomes a vapour, at the phase transition of superfluids, and at the phase separation of binary liquids whose components exhibit two different types of behaviour. Until now, models have not fully taken the effect of external turbulences into account. In a recent study published recently, the authors investigate the influence of ambient turbulent speed fluctuations in physical systems when they reach a critical point. These fluctuations are found to be the result of a lack of spatial regularity in these systems, or anisotropy, and of the compressibility of fluids. What is unique about this study is that the turbulence introduced in the model is novel and helps to elucidate the extent to which the speed of these fluctuations affects their scaling behaviour.
M. Hnatič, G. Kalagov, and T. Lučivjanský, Scaling behavior in interacting systems: joint effect of anisotropy and compressibility, Eur. Phys. J. B, 91, 269 (2018)
[Abstract]
Fast domain-wall propagation in magnetic nanotracks (Vol. 42, No. 5)

Magnetic domain walls are the interfaces separating magnetic domains of opposite magnetizations, which are used to store binary information in magnetic media. The current developments of magnetic data storage and processing technologies make highly desirable to control a fast and reproducible motion of these domain walls in nanoscale magnetic tracks. This can be performed using either magnetic field, or electrical current.
For this purpose, nanotracks defined in ultrathin magnetic films with out-of-plane magnetic anisotropy seem to be particularly good candidates to obtain an efficient propagation under a low excitation. However, in most of the out-of-plane metallic nanosystems that were studied up to now, domain-wall pinning on the track’s defects was shown to significantly reduce the domain-wall velocity, as compared to the one measured in the corresponding plain magnetic film.
In this work, nanotracks are etched in a Pt/Co/Pt thin film with out-of-plane magnetic anisotropy, where pinning has been artificially reduced by weak He+-ion irradiation. It is shown that in these tracks, domain walls propagate as fast and under magnetic field as low as in the corresponding plain irradiated film.
Moreover, when magnetic-field and electrical-current pulses are simultaneously applied to the track, a considerably faster magnetization reversal is observed, which is due to a Joule-heating-induced thermomagnetic effect when current flows into the track.
Fast propagation of weakly pinned domain walls and current-assisted magnetization reversal in He+-irradiated Pt/Co/Pt nanotracks
M. Cormier, A. Mougin, J. Ferré, J.-P. Jamet, R. Weil, J. Fassbender, V. Baltz and B. Rodmacq, J. Phys. D: Appl. Phys. 44, 215002 (2011)
[Abstract]
Fast growth of high mobility ZnO:Al by cathodic arc deposition (Vol. 42, No. 5)

Transparent conducting oxides (TCOs) are increasingly important materials as the demand for high efficiency solar cells, displays, and smart windows increases. Currently, indium tin oxide (ITO) is the preferred material for its properties of low resistance and high visible light transmittance. Excessive indium demand justifies the search for abundant and low cost alternative materials to satisfy the growing need of coating (>108 m2/year). The best ZnO films doped with Ga or Al typically deposited at low rate by magnetron sputtering, are attractive but their performance is usually inferior to ITO.
Using a lesser known technique, called dc filtered cathodic arc deposition, we have shown that very high quality Al-doped ZnO (AZO) can be grown at rates 10 times higher than the rates for sputtering. Filtered cathodic arc produces a flux of fully ionized material, in stark contrast to sputtering which occurs at much lower power and predominantly produces a flux of neutral atoms. The arc-produced ions bring significant potential and kinetic energies to the surface, which leads to heating of the growing film just where the growth occurs while the substrate as a whole can remain at a much lower temperature. If the ion flux is high, the surface heat accumulates and anneals the film as it grows. The result is high quality AZO with electron mobility approaching the theoretical limit for polycrystalline AZO films. High electron mobility is what allows TCOs to transmit light throughout the solar spectrum while maintaining high conductivity since the electron concentration does not have to be very high.
Achieving high mobility ZnO:Al at very high growth rates by dc filtered cathodic arc deposition
R.J. Mendelsberg, S.H.N. Lim, Y.K. Zhu, J. Wallig, D.J. Milliron and A. Anders, J. Phys. D: Appl. Phys. 44, 232003 (2011)
[Abstract]
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