Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.

In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations.

Numerical study of the laser-tip coupling in surface plasmon assisted stacked-double-gate field emitter arrays

Recently, sub-wavelength-pitch stacked double-gate metal nanotip arrays have been proposed to realize high current, high brightness electron bunches for ultrabright cathodes for x-ray free-electron laser applications. With the proposed device structure, ultrafast field emission of photoexcited electrons is efficiently driven by vertical incident near infrared laser pulses, via near field coupling of the surface plasmon polariton resonance of the gate electrodes with the nanotip apex. In this work, in order to gain insight in the underlying physical processes, the authors report detailed numerical studies of the proposed device. The results indicate the importance of the interaction of the double-layer surface plasmon polariton, the position of the nanotip, as well as the incident angle of the near infrared laser pulses.

Direct-Drive Shock-Ignition for the Laser Megajoule.

We present a review of direct-drive shock ignition studies done as alternative for the Laser Mega-Joule to achieve high thermonuclear gain. One-dimensional analysis of HiPER-like Shock-ignited target designs is presented. It is shown that high gain can be achieved with shock ignition for designs which do not ignite only from the laser compression. Shock ignition is achieved for different targets of the fast ignition family which are driven by an absorbed energy between 100 kJ and 850kJ and deliver thermonuclear energies between 10-130 MJ. Shock-Ignition of Direct-Drive Double-Shell non-cryogenic target is also addressed. 2D results concerning the LMJ irradiation geometry are presented. Few systematic analyses are performed for the fuel assembly irradiation uniformity using the whole LMJ configuration or a part of the facility, and for the ignitor spike uniformity. Solutions for fuel assembly and shock ignition on LMJ using 2D calculations are presented. It is shown that high-gain shock-ignition is possible with intensity of each quad less than 1e15 W/cm2but low modes asymmetries displace the ignitor power in the spike towards higher powers.

The use of the ESS Bilbao installations for laser fusion studies

In this work the use of ESS-Bilbao fast neutron lines for irradiation of materials for nuclear fusion is studied. For the comparison of ESS-Bilbao with an inertial fusion facility a simplified model of HiPER chamber has been used. Several positions for irradiation at ESS-Bilbao have been also compared. The material chosen for the damage analysis is silica due to its importance on IFC optics. In this work a detailed comparison between the two facilities for silica irradiation is given. The comparison covers the neutron fluxes, doses, defect production and PKA spectra. This study is also intended as a methodological approach or guideline for future works on other materials.

Probabilistic reasoning with an enzyme-driven DNA device

We present a biomolecular probabilistic model driven by the action of a DNA toolbox made of a set of DNA templates and enzymes that is able to perform Bayesian inference. The model will take single-stranded DNA as input data, representing the presence or absence of a specific molecular signal (the evidence). The program logic uses different DNA templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (DNA polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded DNA species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes? law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagno- sis. Thanks to the inherent amplification capability of this DNA toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.

Experimental implementation of a biometric laser synaptic sensor

We fabricate a biometric laser fiber synaptic sensor to transmit information from one neuron cell to the other by an optical way. The optical synapse is constructed on the base of an erbium-doped fiber laser, whose pumped diode current is driven by a pre-synaptic FitzHugh–Nagumo electronic neuron, and the laser output controls a post-synaptic FitzHugh–Nagumo electronic neuron. The implemented laser synapse displays very rich dynamics, including fixed points, periodic orbits with different frequency-locking ratios and chaos. These regimes can be beneficial for efficient biorobotics, where behavioral flexibility subserved by synaptic connectivity is a challenge.

Fast ignition driven by quasi-monoenergetic ions: Optimal ion type and reduction of ignition energies with an ion beam array

Fast ignition of inertial fusion targets driven by quasi-monoenergetic ion beams is investigated by means of numerical simulations. Light and intermediate ions such as lithium, carbon, aluminum and vanadium have been considered. Simulations show that the minimum ignition energies of an ideal configuration of compressed Deuterium-Tritium are almost independent on the ion atomic number. However, they are obtained for increasing ion energies, which scale, approximately, as Z2, where Z is the ion atomic number. Assuming that the ion beam can be focused into 10 ?m spots, a new irradiation scheme is proposed to reduce the ignition energies. The combination of intermediate Z ions, such as 5.5 GeV vanadium, and the new irradiation scheme allows a reduction of the number of ions required for ignition by, roughly, three orders of magnitude when compared with the standard proton fast ignition scheme.

A photosystem I reaction center driven by chlorophyll d in oxygenic photosynthesis

A far-red type of oxygenic photosynthesis was discovered in Acaryochloris marina, a recently found marine prokaryote that produces an atypical pigment chlorophyll d (Chl d). The purified photosystem I reaction center complex of A. marina contained 180 Chl d per 1 Chl a with PsaA–F, -L, -K, and two extra polypeptides. Laser excitation induced absorption changes of reaction center Chl d that was named P740 after its peak wavelength. A midpoint oxidation reduction potential of P740 was determined to be +335 mV. P740 uses light of significantly low quantum energy (740 nm = 1.68 eV) but generates a reducing power almost equivalent to that produced by a special pair of Chl a (P700) that absorbs red light at 700 nm (1.77 eV) in photosystem I of plants and cyanobacteria. The oxygenic photosynthesis based on Chl d might either be an acclimation to the far-red light environments or an evolutionary intermediate between the red-absorbing oxygenic and the far-red absorbing anoxygenic photosynthesis that uses bacteriochlorophylls.

The photoreceptor sensory rhodopsin I as a two-photon-driven proton pump.

Proton translocation experiments with intact cells of Halobacterium salinarium overproducing sensory rhodopsin I (SRI) revealed transport activity of SRI in a two-photon process. The vectoriality of proton translocation depends on pH, being outwardly directed above, and inwardly directed below, pH 5.7. Activation of the transport cycle requires excitation of the initial dark state of SRI, SRI590, to form the intermediate SRI380. Action spectra identify the photocycle intermediates SRI380 and SRI520 as the two photochemically reactive species in the outwardly directed transport process. As shown by flash photolysis experiments, SRI520 undergoes a so-far unknown photochemical reaction to SRI380 with a half-time of <200 micros. Mutation of SRI residue Asp-76, the residue which is equivalent to the proton acceptor Asp-85 in bacteriorhodopsin, to asparagine leads to inactivation of proton translocation. This demonstrates that the underlying mechanisms of proton transport in both retinal proteins share similar features. However, SRI is to our knowledge the first case where photochemical reactions between two thermally unstable photoproducts of a retinal protein constitute a catalytic ion transport cycle.

Nearly spherical constant power detonation waves driven by focused radiation /

"Prepared by Cornell University ... for Lewis Research Center."

Introduction of routine outcome measures: staff reactions and issues for consideration

The aim of this study was to explore clinician reactions to (i) the introduction of routine outcome measures and (ii) the utility of outcomes data in clinical practice. Focus group discussions (n = 34) were conducted with mental health staff (n = 324) at approximately 8 months post implementation of routine outcome measures. A semi-structured interview schedule was used to collect data on two key issues; reactions to the introduction of outcome measures and factors influencing the utility of outcomes data in clinical practice. Data from the discussion groups were analysed using content analysis to isolate emerging themes. While the majority of participants endorsed the collection and utilization of outcomes data, many raised questions about the merits of the initiative. Ambivalence, competing work demands, lack of support from senior medical staff, questionable evidence to support the use of outcome measures, and fear of how outcomes data might be used emerged as key issues. At 8 months post implementation a significant number of clinical staff remained ambivalent about the benefits of outcome measurement and had not engaged in the process. The shift to a service model driven by outcomes and case-mix data will take time and resources to achieve. Implications for nursing staff are discussed.

Cobalt complexes of tripodal hexadentate ligands: Electrochemically driven rearrangements

The Co-III complexes of the hexadentate tripodal ligands HOsen (3-(2'-aminoethylamino)-2,2-bis((2 ''-aminoethylamino) methyl) propan-1-ol) and HOten (3-(2'-aminoethylthia)-2,2-bis((2 ''-aminoethylthia) methyl) propan-1-ol) have been synthesized and fully characterized. The crystal structures of [Co(HOsen)]Cl-3 center dot H2O and [Co(HOten)](ClO4)Cl-2 are reported and in both cases the ligands coordinate as tripodal hexadentate N-6 and N3S3 donors, respectively. Cyclic voltammetry of the N3S3 coordinated complex [Co(HOten)](3+) is complicated and electrode dependent. On a Pt working electrode an irreversible Co-III/II couple ( formal potential - 157 mV versus Ag-AgCl) is seen, which is indicative of dissociation of the divalent complex formed at the electrode. The free HOten released by the dissociation of [Co(HOten)](2+) can be recaptured by Hg as shown by cyclic voltammetry experiments on a static Hg drop electrode ( or in the presence of Hg2+ ions), which leads to the formation of an electroactive Hg-II complex of the N3S3 ligand (formal potential + 60 mV versus Ag-AgCl). This behaviour is in contrast to the facile and totally reversible voltammetry of the hexaamine complex [Co(HOsen)](3+) ( formal potential (Co-III/II) - 519 mV versus Ag-AgCl), which is uncomplicated by any coupled chemical reactions. Akinetic and thermodynamic analysis of the [Co(HOten)](2+)/[Hg(HOten)](2+) system is presented on the basis of digital simulation of the experimental voltammetric data.

Q-switched induced gain switching of a twotransition cascade laser

A gain-switched laser transition, of a two-laser-transition cascade laser, that is driven by the adjacent laser transition which is Q-switched is demonstrated using a Ho3+ -doped fluoride fiber laser. Q-switching the 5|6 ? 5|7 transition at 3.002 µm produces stable gain-switched pulses from the 5|7 ? 5|8 transition at 2.074 µm; however, Q-switching the 5|7 ? 5|8 transition produced multiple gain switched pulses from the 5|6 ? 5|7 transition. The gain-switched pulses were measured to be of a similar duration to the Q-switched pulses suggesting that much shorter pulses of closer duration could be generated at pump power higher levels.

THz emission from quantum dot-based THz antennas pumped by a tunable quantum-dot laser diode

The THz optoelectronics field is now maturing and semiconductor-based THz antenna devices are becoming more widely implemented as analytical tools in spectroscopy and imaging. Photoconductive (PC) THz switches/antennas are driven optically typically using either an ultrashort-pulse laser or an optical signal composed of two simultaneous longitudinal wavelengths which are beat together in the PC material at a THz difference frequency. This allows the generation of (photo)carrier pairs which are then captured over ultrashort timescales usually by defects and trapping sites throughout the active material lattice. Defect-implanted PC materials with relatively high bandgap energy are typically used and many parameters such as carrier mobility and PC gain are greatly compromised. This paper demonstrates the implementation of low bandgap energy InAs quantum dots (QDs) embedded in standard crystalline GaAs as both the PC medium and the ultrafast capture mechanism in a PC THz antenna. This semiconductor structure is grown using standard MBE methods and allows the device to be optically driven efficiently at wavelengths up to ~1.3 µm, in this case by a single tunable dual-mode QD diode laser.

Structure, energetics and reactions of metal cation complexes of dipeptides in the gas phase

Structure, energetics and reactions of ions in the gas phase can be revealed by mass spectrometry techniques coupled to ions activation methods. Ions can gain enough energy for dissociation by absorbing IR light photons introduced by an IR laser to the mass spectrometer. Also collisions with a neutral molecule can increase the internal energy of ions and provide the dissociation threshold energy. Infrared multiple photon dissociation (IRMPD) or sustained off-resonance irradiation collision-induced dissociation (SORI-CID) methods are combined with Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometers where ions can be held at low pressures for a long time. The outcome of ion activation techniques especially when it is compared to the computational methods results is of great importance since it provides useful information about the structure, thermochemistry and reactivity of ions of interest. In this work structure, energetics and reactivity of metal cation complexes with dipeptides are investigated. Effect of metal cation size and charge as well as microsolvation on the structure of these complexes has been studied. Structures of bare and hydrated Na and Ca complexes with isomeric dipeptides AlaGly and GlyAla are characterized by means of IRMPD spectroscopy and computational methods. At the second step unimolecular dissociation reactions of singly charged and doubly charged multimetallic complexes of alkaline earth metal cations with GlyGly are examined by CID method. Also structural features of these complexes are revealed by comparing their IRMPD spectra with calculated IR spectra of possible structures. At last the unimolecular dissociation reactions of Mn complexes are studied. IRMPD spectroscopy along with computational methods is also employed for structural elucidation of Mn complexes. In addition the ion-molecule reactions of Mn complexes with CO and water are explored in the low pressures obtained in the ICR cell.