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Quasi-optical theory of microwave plasma heating in open magnetic trap
https://cds.cern.ch/record/2210814
Microwave heating of a high-temperature plasma confined in a large-scale open magnetic trap, including all important wave effects like diffraction, absorption, dispersion and wave beam aberrations, is described for the first time within the first-principle technique based on consistent Maxwell's equations. With this purpose, the quasi-optical approach is generalized over weakly inhomogeneous gyrotrotropic media with resonant absorption and spatial dispersion, and a new form of the integral quasi-optical equation is proposed. An effective numerical technique for this equation's solution is developed and realized in a new code QOOT, which is verified with the simulations of realistic electron cyclotron heating scenarios at the Gas Dynamic Trap at the Budker Institute of Nuclear Physics (Novosibirsk, Russia).Shalashov, A GBalakin, A AGospodchikov, E DKhusainov, T ASat, 27 Aug 2016 06:54:47 GMT25 Aug 2016arXiv:1608.07273https://cds.cern.ch/record/2210814['arXiv:1608.07273']arXiv:1608.07273Leibnizian relationalism for general relativistic physics
https://cds.cern.ch/record/2210813
An ontology of Leibnizian relationalism, consisting in distance relations among sparse matter points and their change only, is well recognized as a serious option in the context of classical mechanics. In this paper, we investigate how this ontology fares when it comes to general relativistic physics. Using a Humean strategy, we regard the gravitational field as a means to represent the overall change in the distance relations among point particles in a way that achieves the best combination of being simple and being informative.Vassallo, AntonioEsfeld, MichaelSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07257https://cds.cern.ch/record/2210813['arXiv:1608.07257']arXiv:1608.07257Meissner-like effect for synthetic gauge field in multimode cavity QED
https://cds.cern.ch/record/2210812
Previous realizations of synthetic gauge fields for ultracold atoms do not allow the spatial profile of the field to evolve freely. We propose a scheme which overcomes this restriction by using the light in a multimode cavity, in conjunction with Raman coupling, to realize an artificial magnetic field which acts on a Bose-Einstein condensate of neutral atoms. We describe the evolution of such a system, and present the results of numerical simulations which show dynamical coupling between the effective field and the matter on which it acts. Crucially, the freedom of the spatial profile of the field is sufficient to realize a close analogue of the Meissner effect, where the magnetic field is expelled from the superfluid. This back-action of the atoms on the synthetic field distinguishes the Meissner-like effect described here from the Hess-Fairbank suppression of rotation in a neutral superfluid observed elsewhere.Ballantine, Kyle ELev, Benjamin LKeeling, JonathanSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07246https://cds.cern.ch/record/2210812['arXiv:1608.07246']arXiv:1608.07246One-step Patterning of Sub-wavelength Plasmonic Gratings in Metal-Polymer Composites
https://cds.cern.ch/record/2210811
2D and 3D micro/nano fabrication based on two-photon polymerization (TPP) has emerged as a strong contender for additive manufacturing for wide variety of applications. In this manuscript we report one step patterning of structurally stable, subwavelength 2D and 3D gold nanostructures using femto-second laser by incorporating single photon photoinitiator only in pure and metal precursor doped polymers. The metal polymer composite nanostructures are written directly by in-situ reduction of gold precursor within the photoresist using femto-second laser irradiation. The photo-initiator triggers the reduction of gold precursor and induces simultaneous polymerization of the photoresist based on two-photon absorption phenomenon. Diffraction gratings with varied loading of gold precursors in photoresist have been fabricated and characterized by measuring their diffraction efficiencies in the infrared region. Minimum line width of 390 nm has been achieved for 5 wt% gold loaded polymers. Systematic studies of the effect of laser power, metal precursor loading etc. on the line-widths have also been performed. These investigations are expected to pave way for exploration of new material combinations for development of simple fabrication for fabrication of metal composite functional structures at significantly low cost and with high-throughput.Chaudhary, Raghvendra PUmmethala, GovindJaiswal, ArunHawal, Suyog RSaxena, SumitShukla, ShobhaSat, 27 Aug 2016 06:54:46 GMT24 Aug 2016arXiv:1608.07245https://cds.cern.ch/record/2210811['arXiv:1608.07245']arXiv:1608.07245The Griffiths Phase on Hierarchical Modular Networks with Small-world Edges
https://cds.cern.ch/record/2210810
The Griffiths phase has been proposed to induce a stretched critical regime that facilitates self organizing of brain networks for optimal function. This phase stems from the intrinsic structural heterogeneity of brain networks, such as the hierarchical modular structure. In this work, we extend this concept to modified hierarchical networks with small-world connections based on Hanoi networks [1]. Through extensive simulations, we identify the essential role played by the exponential distribution of the inter-moduli connectivity probability across hierarchies on the emergence of the Griffiths phase in this network. Additionally, the spectral analysis on the adjacency matrix of the relevant networks [2] shows that a localized principle eigenvector is not necessarily the fingerprint of the Griffiths phase.Li, ShanshanSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07231https://cds.cern.ch/record/2210810['arXiv:1608.07231']arXiv:1608.07231The specific shapes of gender imbalance in scientific authorships: a network approach
https://cds.cern.ch/record/2210809
Gender differences in collaborative research have received little attention when compared with the growing importance that women hold in academia and research. Unsurprisingly, most of bibliometric databases have a strong lack of directly available information by gender. Although empirical-based network approaches are often used in the study of research collaboration, the studies about the influence of gender dissimilarities on the resulting topological outcomes are still scarce. Here, networks of scientific subjects are used to characterize patterns that might be associated to five categories of authorships which were built based on gender. We find enough evidence that gender imbalance in scientific authorships brings a peculiar trait to the networks induced from papers published in Web of Science (WoS) indexed journals of Economics over the period 2010-2015 and having at least one author affiliated to a Portuguese institution. Our results show the emergence of a specific pattern when the network of co-occurring subjects is induced from a set of papers exclusively authored by men. Such a male-exclusive authorship condition is found to be the solely responsible for the emergence that particular shape in the network structure. This peculiar trait might facilitate future network analyses of research collaboration and interdisciplinarity.Araújo, TanyaFontainha, ElsaSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07224https://cds.cern.ch/record/2210809['arXiv:1608.07224']arXiv:1608.07224Pattern formation in polymerising actin flocks: spirals, spots and waves without nonlinear chemistry
https://cds.cern.ch/record/2210808
We propose a model solely based on actin treadmilling and polymerisation which describes many characteristic states of actin wave formation: spots, spirals and travelling waves. In our model, as in experiments on cell recovering motility following actin depolymerisation, we choose an isotropic low density initial condition; polymerisation of actin filaments then raises the density towards the Onsager threshold where they align. We show that this alignment, in turn, destabilizes the isotropic phase and generically induces transient actin spots or spirals as part of the dynamical pathway towards a polarized phase which can either be uniform or consist of a series of actin-wave trains (flocks). Our results uncover a universal route to actin wave formation in the absence of any system specific nonlinear biochemistry, and it may help understand the mechanism underlying the observation of actin spots and waves in vivo. They also suggest a minimal setup to design similar patterns in vitro.Goff, Thomas LeLiebchen, BennoMarenduzzo, DavideSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07218https://cds.cern.ch/record/2210808['arXiv:1608.07218']arXiv:1608.07218Analysis of fluid velocity vector field divergence $\nabla\cdot\vec{u}$ in function of variable fluid density $\rho(\vec{x},t)\neq const$ and conditions for vanishing viscosity of compressible Navier-Stokes equations
https://cds.cern.ch/record/2210807
In this paper, we perform analysis of the fluid velocity vector field divergence $\nabla \cdot \vec{u}$ derived from the continuity equation, and we explore its application in the Navier-Stokes equations for compressible fluids $\rho (\vec{x},t)\ne const$, occupying all of $\vec{x}\in R^{3} $ space at any $t\geq 0$. The resulting velocity vector field divergence $\nabla \cdot \vec{u}=-\frac{1}{\rho } (\frac{\partial \rho }{\partial t} +\vec{u}\cdot \nabla \rho )$ is a direct consequence of the fluid density rate of change over time $\frac{\partial \rho }{\partial t}$ and over space $\nabla \rho $, in addition to the fluid velocity vector field $\vec{u}(\vec{x},t)$ and the fluid density $\rho (\vec{x},t)$ itself. We derive the conditions for the divergence-free fluid velocity vector field $\nabla \cdot \vec{u}=0$ in scenarios when the fluid density is not constant $\rho(\vec{x},t)\neq const$ over space nor time, and we analyze scenarios of the non-zero divergence $\nabla \cdot \vec{u}\ne 0$. We apply the statement for divergence in the Navier-Stokes equation for compressible fluids, and we deduct the condition for vanishing (zero) viscosity term of the compressible Navier-Stokes equation: $\nabla (\frac{1}{\rho } (\frac{\partial \rho }{\partial t} +\vec{u}\cdot \nabla \rho ))=-3\Delta \vec{u}$. In addition to that, we derive even more elementary condition for vanishing viscosity, stating that vanishing viscosity is triggered once scalar function $d(\vec{x},t)=-\frac{1}{\rho } (\frac{\partial \rho }{\partial t} +\vec{u}\cdot \nabla \rho )$ is harmonic function. Once that condition is satisfied, the viscosity related term of the Navier-Stokes equations for compressible fluids equals to zero, which is known as related to turbulent fluid flows.Kovacevic, DejanSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07214https://cds.cern.ch/record/2210807['arXiv:1608.07214']arXiv:1608.07214Dynamics of atomic spin-orbit-state wave packets produced by short-pulse laser photodetachment
https://cds.cern.ch/record/2210806
We analyse the experiment by Hultgren et al. [Phys. Rev. A {\bf 87}, 031404 (2013)] on orbital alignment and quantum beats in coherently excited atomic fine-structure manifolds produced by short-pulse laser photodetachment of C$^-$, Si$^-$ and Ge$^-$ negative ions, and derive a formula that describes the beats. Analysis of the experimental data enables us to extract the non-coherent background contribution for each species, and indicates the need for a full density matrix treatment of the problem.Law, S M KGribakin, G FSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07211https://cds.cern.ch/record/2210806['arXiv:1608.07211']arXiv:1608.07211Ambiguity in deriving Larmor's formula from the LAD equation of motion
https://cds.cern.ch/record/2210805
Larmor's formula provides the power radiated by an accelerated electric charge. This can be derived from the Li\'enard-Wiechert retarded potential. However, extracting the same result from the Lorentz-Abraham-Dirac equation of motion is ambiguous. The present letter discusses this difficulty and reviews other problems of the LAD equation.Faci, SofianeHelayël-Neto, José ASat, 27 Aug 2016 06:54:46 GMT23 Aug 2016arXiv:1608.07177https://cds.cern.ch/record/2210805['arXiv:1608.07177']arXiv:1608.07177On Particles and Primes
https://cds.cern.ch/record/2210804
Primes in the two complete associative normed division algebras C and H have affinities with structures seen in the standard model of particle physics. On the integers in the two algebras, there are two equivalence relations: a strong one, related to a U(1) and SU(3) symmetry allowing to permute and switch signs of the coordinates of the integers, as well as a weak relation with origins from units U(1),SU(2) in the algebra. Weak equivalence classes within the strong equivalence classes of odd primes in C case relate to leptons, the inert ones being neutrino like, and the split ones resembling electron-positron pairs. In the H case, for odd primes, the equivalence classes come in groups of two or three, leading to a caricature of hadrons featuring either mesons built by a quark pair or then baryons obtained by quark triplets. We can now list for every rational prime p all these particles and attach fractional charges to its constituents.Knill, OliverSat, 27 Aug 2016 06:54:46 GMT21 Aug 2016arXiv:1608.07175https://cds.cern.ch/record/2210804['arXiv:1608.07175']arXiv:1608.07175Coupling quantum Monte Carlo and independent-particle calculations: self-consistent constraint for the sign problem based on density or density matrix
https://cds.cern.ch/record/2210803
The vast majority of quantum Monte Carlo (QMC) calculations in interacting fermion systems require a constraint to control the sign problem. The constraint involves an input trial wave function which restricts the random walks. We introduce a systematically improvable constraint which relies on the fundamental role of the density or one-body density matrix. An independent-particle calculation is coupled to an auxiliary-field QMC calculation. The independent-particle solution is used as the constraint in QMC, which then produces the input density or density matrix for the next iteration. The constraint is optimized by the self-consistency between the many-body and independent-particle calculations. The approach is demonstrated in the two-dimensional Hubbard model by accurately determining the spin densities when collective modes separated by tiny energy scales are present in the magnetic and charge correlations. Our approach also provides an ab initio way to predict effective "U" parameters for independent-particle calculations.Qin, MingpuShi, HaoZhang, ShiweiSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07154https://cds.cern.ch/record/2210803['arXiv:1608.07154']arXiv:1608.07154High Order Moment Model for Polydisperse Evaporating Sprays Towards Interfacial Geometry
https://cds.cern.ch/record/2210802
In this paper we propose a new Eulerian modeling and related accurate and robust numerical methods, describing polydisperse evaporating sprays, based on high order moment methods in size. The main novelty of this model is its capacity to describe some geometrical variables of the droplet-gas interface, by analogy with the liquid-gas interface in interfacial flows. For this purpose, we use fractional size-moments, where the size variable is taken as the droplet surface. In order to evaluate the evaporation of the polydisperse spray, we use a smooth reconstruction which maximizes the Shannon entropy. However, the use of fractional moments introduces some theoretical and numerical difficulties, which need to be tackled. First, relying on a study of the moment space, we extend the Maximum Entropy (ME) reconstruction of the size distribution to the case of fractional moments. Then, we propose a new accurate and realizable algorithm to solve the moment evolution due to evaporation, which preserves the structure of the moment space. This algorithm is based on a mathematical analysis of the kinetic evolution due to evaporation, where it shown that the evolution of some negative order fractional moments have to be properly predicted, a peculiarity related to the use of fractional moments. The present model and numerical schemes yield an accurate and stable evaluationof the moment dynamics with minimal number of variables, as well as a minimal computational cost as with the EMSM model, but with the very interesting additional capacity of coupling with diffuse interface model and transport equation of averaged geometrical interface variables, which are essential in oder to describe atomization.Essadki, MohamedDe Chaisemartin, StephaneLaurent, FrédériqueMassot, MarcSat, 27 Aug 2016 06:54:46 GMT25 Aug 2016arXiv:1608.07148https://cds.cern.ch/record/2210802['arXiv:1608.07148']arXiv:1608.07148Time-dependent solutions for a stochastic model of gene expression with molecule production in the form of a compound Poisson process
https://cds.cern.ch/record/2210801
We study a stochastic model of gene expression, in which protein production has a form of random bursts whose size distribution is arbitrary, whereas protein decay is a first-order reaction. We find exact analytical expressions for the time evolution of the cumulant-generating function for the most general case when both the burst size probability distribution and the model parameters depend on time in an arbitrary (e.g. oscillatory) manner, and for arbitrary initial conditions. We show that in the case of periodic external activation and constant protein degradation rate, the response of the gene is analogous to the RC low-pass filter, where slow oscillations of the external driving have a greater effect on gene expression than the fast ones. We also demonstrate that the $n$-th cumulant of the protein number distribution depends on the $n$-th moment of the burst size distribution. We use these results to show that different measures of noise (coefficient of variation, Fano factor, fractional change of variance) may vary in time in a different manner. Therefore, any biological hypothesis of evolutionary optimization based on the nonmonotonicity of a chosen measure of noise must justify why it assumes that biological evolution quantifies noise in that particular way. Finally, we show that not only for exponentially distributed burst sizes but also for a wider class of burst size distributions (e.g. Dirac delta and gamma) the control of gene expression level by burst frequency modulation gives rise to proportional scaling of variance of the protein number distribution to its mean, whereas the control by amplitude modulation implies proportionality of protein number variance to the mean squared.Jędrak, JakubOchab-Marcinek, AnnaSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07139https://cds.cern.ch/record/2210801['arXiv:1608.07139']arXiv:1608.07139On the Hierarchical Preconditioning of the PMCHWT Integral Equation on Simply and Multiply Connected Geometries
https://cds.cern.ch/record/2210799
We present a hierarchical basis preconditioning strategy for the Poggio-Miller-Chang-Harrington-Wu-Tsai (PMCHWT) integral equation considering both simply and multiply connected geometries.To this end, we first consider the direct application of hierarchical basis preconditioners, developed for the Electric Field Integral Equation (EFIE), to the PMCHWT. It is notably found that, whereas for the EFIE a diagonal preconditioner can be used for obtaining the hierarchical basis scaling factors, this strategy is catastrophic in the case of the PMCHWT since it leads to a severly ill-conditioned PMCHWT system in the case of multiply connected geometries. We then proceed to a theoretical analysis of the effect of hierarchical bases on the PMCHWT operator for which we obtain the correct scaling factors and a provably effective preconditioner for both low frequencies and mesh refinements. Numerical results will corroborate the theory and show the effectiveness of our approach.Guzman, J E OrtizAdrian, S BMitharwal, RBeghein, YEibert, T FCools, KAndriulli, F PSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07129https://cds.cern.ch/record/2210799['arXiv:1608.07129']arXiv:1608.07129Dynamics of a single trapped ion immersed in a buffer gas
https://cds.cern.ch/record/2210798
We provide a comprehensive theoretical framework for describing the dynamics of a single trapped ion interacting with a neutral buffer gas, thus extending our previous studies on buffer-gas cooling of ions beyond the critical mass ratio [B. H\"oltkemeier et al., Phys. Rev. Lett. 116, 233003 (2016)]. By transforming the collisional processes into a frame, where the ion's micromotion is assigned to the buffer gas atoms, our model allows one to investigate the influence of non-homogeneous buffer gas configurations as well as higher multipole orders of the radio-frequency trap in great detail. Depending on the neutral-to-ion mass ratio, three regimes of sympathetic cooling are identified which are characterized by the form of the ion's energy distribution in equilibrium. We provide analytic expressions and numerical simulations of the ion's energy distribution, spatial profile and cooling rates for these different regimes. Based on these findings, a method for actively decreasing the ion's energy by reducing the spatial expansion of the buffer gas arises (Forced Sympathetic Cooling).Höltkemeier, BastianWeckesser, PascalLópez-Carrera, HenryWeidemüller, MatthiasSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07120https://cds.cern.ch/record/2210798['arXiv:1608.07120']arXiv:1608.07120Modelling Chemical Reasoning to Predict Reactions
https://cds.cern.ch/record/2210797
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph containing 14.4 million molecules and 8.2 million binary reactions, which represents the bulk of all chemical reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180,000 randomly selected binary reactions. We show that our data-driven model generalises even beyond known reaction types, and is thus capable of effectively (re-) discovering novel transformations (even including transition-metal catalysed reactions). Our model enables computers to infer hypotheses about reactivity and reactions by only considering the intrinsic local structure of the graph, and because each single reaction prediction is typically achieved in a sub-second time frame, our model can be used as a high-throughput generator of reaction hypotheses for reaction discovery.Segler, Marwin H SWaller, Mark PSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07117https://cds.cern.ch/record/2210797['arXiv:1608.07117']arXiv:1608.07117Modelling the effect of curvature on the collective behaviour of cells growing new tissue
https://cds.cern.ch/record/2210796
The growth of several biological tissues is known to be controlled in part by local geometrical features, such as the curvature of the tissue interface. This control leads to changes in tissue shape that in turn can affect the tissue's evolution. Understanding the cellular basis of this control is highly significant for bioscaffold tissue engineering, the evolution of bone microarchitecture, wound healing, and tumour growth. While previous models have proposed geometrical relationships between tissue growth and curvature, the role of cell density and cell vigor remains poorly understood. We propose a cell-based mathematical model of tissue growth to investigate the systematic influence of curvature on the collective crowding or spreading of tissue-synthesising cells induced by changes in local tissue surface area during the motion of the interface. Depending on the strength of diffusive damping, the model exhibits complex growth patterns such as undulating motion, efficient smoothing of irregularities, and the generation of cusps. We compare this model with in-vitro experiments of tissue deposition in bioscaffolds of different geometries. By accounting for the depletion of active cells, the model is able to capture both smoothing of initial substrate geometry and tissue deposition slowdown as observed experimentally.Alias, AlmieBuenzli, Pascal RSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07108https://cds.cern.ch/record/2210796['arXiv:1608.07108']arXiv:1608.07108Influence of the electron beam emittance on the polarization of a laser--electron X-ray generator
https://cds.cern.ch/record/2210795
In this paper we analyze the polarization of the X-ray radiation coming from laser--electron X-ray generator (LEXG). We obtain general relations connecting the polarization state of outgoing X-ray radiation to the polarization state of laser beam as well as to the parameters of electron beam. We demonstrate that finite electron beam emittance causes a partial depolarization of initially fully polarized X-ray radiation even when the laser beam is fully polarized. We demonstrate with a number of numerical experiments that finite electron beam emittance can in some cases fundamentally alter the polarization state of X-ray radiation as compared to the polarization state of X-ray radiation scattered by electron beam with a zero emittance. Possible applications of polarized LEXG's radiation are discussed.Artyukov, I AVinogradov, A VFeshchenko, R MSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07106https://cds.cern.ch/record/2210795['arXiv:1608.07106']arXiv:1608.07106Measurement of the magnetic field profile in the atomic fountain clock FoCS-2 using Zeeman spectroscopy
https://cds.cern.ch/record/2210794
We report the evaluation of the second order Zeeman shift in the continuous atomic fountain clock FoCS-2. Because of the continuous operation and its geometrical constraints, the methods used in pulsed fountain are not applicable. We use here time-resolved Zeeman spectroscopy to probe the magnetic field profile in the clock. The pulses of ac magnetic excitation allow us to measure the Zeeman frequency with spatial resolution and to evaluate the Zeeman shift with an uncertainty smaller than 10E-16 in relative units.Laurent, DevenogesGianni, Di DomenicoAndré, StefanovAntoine, JallageasJacques, MorelThomas, SüdmeyerPierre, ThomannSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07099https://cds.cern.ch/record/2210794['arXiv:1608.07099']arXiv:1608.07099Charge Transport in Dendrimer Melt using Multiscale Modeling Simulation
https://cds.cern.ch/record/2210793
In this paper we present a theoretical calculation of the charge carrier mobility in two different dendrimeric melt system (Dendritic phenyl azomethine with Triphenyl amine core and Dendritic Carbazole with Cyclic Phenylazomethine as core), which have recently been reported1 to increase the efficiency of Dye-Sensitized solar cells (DSSCs) by interface modification. Our mobility calculation, which is a combination of molecular dynamics simulation, first principles calculation and kinetic Monte Carlo simulation, leads to mobilities that are in quantitative agreement with available experimental data. We also show how the mobility depends on the dendrimer generation. Furthermore, we examine the variation of mobility with external electric field and external reorganization energy. Physical mechanisms behind observed electric field and generation dependencies of mobility are also explored.Bag, SaientanJain, ManishMaiti, Prabal KSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07098https://cds.cern.ch/record/2210793['arXiv:1608.07098']arXiv:1608.07098Dramatic changes in DNA Conductance with stretching: Structural Polymorphism at a critical extension
https://cds.cern.ch/record/2210792
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out multiscale modeling, to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2 attachments we find an abrupt jump in the current within a very short stretching length (6 $ \AA $ or 17 %) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32$ \AA $ (84 %) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We find that the dramatically different conductance behaviors for two different pulling protocols arise from the nature of how hydrogen bonds of DNA base pairs break.Bag, SaientanMogurampelly, SantoshGoddard, William AMaiti, Prabal KSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07092https://cds.cern.ch/record/2210792['arXiv:1608.07092']arXiv:1608.07092PALMA, an improved algorithm for DOSY signal processing
https://cds.cern.ch/record/2210790
NMR is a tool of choice for the measure of diffusion coefficients of species in solution. The DOSY experiment, a 2D implementation of this measure, has proven to be particularly useful for the study of complex mixtures, molecular interactions, polymers, etc. However, DOSY data analysis requires to resort to inverse Laplace transform, in particular for polydisperse samples. This is a known difficult numerical task, for which we present here a novel approach. A new algorithm based on a splitting scheme and on the use of proximity operators is introduced. Used in conjunction with a Maximum Entropy and $\ell_1$ hybrid regularisation, this algorithm converges rapidly and produces results robust against experimental noise. This method has been called PALMA. It is able to reproduce faithfully monodisperse as well as polydisperse systems, and numerous simulated and experimental examples are presented. It has been implemented on the server http://palma. labo.igbmc.fr where users can have their datasets processed automatically.Cherni, AfefChouzenoux, EmilieDelsuc, Marc-AndréSat, 27 Aug 2016 06:54:45 GMT25 Aug 2016arXiv:1608.07055https://cds.cern.ch/record/2210790['arXiv:1608.07055']arXiv:1608.07055The interaction of intense ultrashort laser pulses with cryogenic He jets
https://cds.cern.ch/record/2210789
We study the interaction of intense ultrashort laser pulses with cryogenic He jets using 2d/3v relativistic Particle-in-Cell simulations (XOOPIC). Of particular interest are laser intensities $(10^{15}-10^{20})$ W/cm$^2$, pulse lengths $\le 100$ fs, and the frequency regime $\sim 800$ nm for which the jets are initially transparent and subsequently not homogeneously ionized. Pulses $\ge 10^{16}$ W/cm$^2$ are found to drive ionization along the jet and outside the laser spot, the ionization-front propagates along the jet at a fraction of the speed of light. Within the ionized region, there is a highly transient field, which may be interpreted as two-surface wave decay and as a result of the charge-neutralizing disturbance at the jet-vacuum interface. The ionized region has solid-like densities and temperatures of few to hundreds of eV, i.e., warm and hot dense matter regimes. Such extreme conditions are relevant for high-energy densities as found, e.g., in shock-wave experiments and inertial confinement fusion studies. The temporal evolution of the ionization is studied considering theoretically a pump-probe x-ray Thomson scattering (XRTS) scheme. We observe plasmon and non-collective modes that are generated in the jet, and their amplitude is proportional to the ionized volume. Our theoretical findings could be tested at free-electron laser facilities such as FLASH and the European XFEL (Hamburg) and the LCLS (Stanford).Shihab, MBornath, TRedmer, RSat, 27 Aug 2016 06:54:44 GMT25 Aug 2016arXiv:1608.07052https://cds.cern.ch/record/2210789['arXiv:1608.07052']arXiv:1608.07052Characterization of charge-exchange collisions between ultracold $\rm{^6Li}$ atoms and $\rm{^{40}Ca^+}$ ions
https://cds.cern.ch/record/2210788
We investigate the energy dependence and the internal-state dependence of the charge-exchange collision cross sections in a mixture of $^6$Li atoms and $^{40}$Ca$^+$ ions in the collision energy range from 0.2 mK to 1 K. Deliberately excited ion micromotion is used to control the collision energy of atoms and ions. The energy dependence of the charge-exchange collision cross section obeys the Langevin model in the temperature range of the current experiment, and the measured magnitude of the cross section is correlated to the internal state of the $^{40}$Ca$^+$ ions. Revealing the relationship between the charge-exchange collision cross sections and the interaction potentials is an important step toward the realization of the full quantum control of the chemical reactions at an ultralow temperature regime.Saito, RHaze, SSasakawa, MNakai, RRaoult, MSilva, H DaDulieu, OMukaiyama, TSat, 27 Aug 2016 06:54:44 GMT25 Aug 2016arXiv:1608.07043https://cds.cern.ch/record/2210788['arXiv:1608.07043']arXiv:1608.07043