A few selected applications of surface nonlinear optical spectroscopy.

As a second-order nonlinear optical process, sum-frequency generation is highly surface-specific and accordingly has been developed into a very powerful and versatile surface spectroscopic tool. It has found many unique applications in different disciplines and thus provided many exciting new research opportunities in surface and surface-related science. Selected examples are discussed here to illustrate the power of the technique.

Nonlinear dynamics in ventricular fibrillation.

Electrogram recordings of ventricular fibrillation appear complex and possibly chaotic. However, sequences of beat-to-beat intervals obtained from these recordings are generally short, making it difficult to explicitly demonstrate nonlinear dynamics. Motivated by the work of Sugihara on atmospheric dynamics and the Durbin-Watson test for nonlinearity, we introduce a new statistical test that recovers significant dynamical patterns from smoothed lag plots. This test is used to show highly significant nonlinear dynamics in a stable canine model of ventricular fibrillation.

Photocleavable biotin derivatives: a versatile approach for the isolation of biomolecules.

While the strong biotin-avidin interaction has been widely used for the detection of biomolecules, its irreversibility complicates their isolation. We report the synthesis of a photocleavable biotin derivative (PCB) which eliminates many limitations of existing methods. This reagent contains a biotin moiety linked through a spacer arm to a photocleavable moiety, which reacts selectively with primary amino groups on any substrate. In experiments using [leucine]-enkephalin as a model substrate, we show that PCB retains its high affinity toward avidin/streptavidin and allows rapid (< 5 min) and efficient (> 99%) photorelease of the substrate in a completely unaltered form. Photocleavable biotins should be useful in numerous applications involving the isolation of proteins, nucleic acids, lipids, and cells.

MINLP Model for the Synthesis of Heat Exchanger Networks with Handling Pressure of Process Streams

This paper introduces a new mathematical model for the simultaneous synthesis of heat exchanger networks (HENs), wherein the handling pressure of process streams is used to enhance the heat integration. The proposed approach combines generalized disjunctive programming (GDP) and mixed-integer nonlinear programming (MINLP) formulation, in order to minimize the total annualized cost composed by operational and capital expenses. A multi-stage superstructure is developed for the HEN synthesis, assuming constant heat capacity flow rates and isothermal mixing, and allowing for streams splits. In this model, the pressure and temperature of streams must be treated as optimization variables, increasing further the complexity and difficulty to solve the problem. In addition, the model allows for coupling of compressors and turbines to save energy. A case study is performed to verify the accuracy of the proposed model. In this example, the optimal integration between the heat and work decreases the need for thermal utilities in the HEN design. As a result, the total annualized cost is also reduced due to the decrease in the operational expenses related to the heating and cooling of the streams.

2C-Cas9: a versatile tool for clonal analysis of gene function

CRISPR/Cas9-mediated targeted mutagenesis allows efficient generation of loss-of-function alleles in zebrafish. To date this technology has been primarily used to generate genetic knockout animals. Nevertheless, the study of the function of certain loci might require tight spatiotemporal control of gene inactivation. Here, we show that tissue-specific gene disruption can be achieved by driving Cas9 expression with the Gal4/UAS system. Furthermore, by combining the Gal4/UAS and Cre/loxP systems, we establish a versatile tool to genetically label mutant cell clones, enabling their phenotypic analysis. Our technique has the potential to be applied to diverse model organisms, enabling tissue-specific loss-of-function and phenotypic characterization of live and fixed tissues.

Dynamic D-Vine copula model with applications to Value-at-Risk (VaR)

Regular vine copulas are multivariate dependence models constructed from pair-copulas (bivariate copulas). In this paper, we allow the dependence parameters of the pair-copulas in a D-vine decomposition to be potentially time-varying, following a nonlinear restricted ARMA(1,m) process, in order to obtain a very flexible dependence model for applications to multivariate financial return data. We investigate the dependence among the broad stock market indexes from Germany (DAX), France (CAC 40), Britain (FTSE 100), the United States (S&P 500) and Brazil (IBOVESPA) both in a crisis and in a non-crisis period. We find evidence of stronger dependence among the indexes in bear markets. Surprisingly, though, the dynamic D-vine copula indicates the occurrence of a sharp decrease in dependence between the indexes FTSE and CAC in the beginning of 2011, and also between CAC and DAX during mid-2011 and in the beginning of 2008, suggesting the absence of contagion in these cases. We also evaluate the dynamic D-vine copula with respect to Value-at-Risk (VaR) forecasting accuracy in crisis periods. The dynamic D-vine outperforms the static D-vine in terms of predictive accuracy for our real data sets.

(Table 1) Age model of sediment core MD03-2705

A reconstruction of northwest African summer monsoon strength during the cold marine isotopic stage (MIS) 6 indicates a link to the seasonal migration of the Intertropical Convergence Zone (ITCZ). High-resolution studies of eolian dust supply and sea surface temperature recorded in marine core MD03-2705, on the Mauritanian margin, provide a better understanding about the penultimate glacial history of northwestern African aridity/humidity and upwelling coastal activity. Today, site MD03-2705 experiences increased upwelling and dust flux during the winter months, when the ITCZ is in a southerly position. Analyses of foraminifera isotopic composition suggest that during MIS 6.5 (180-168 ka) the average position of the ITCZ migrated north, marked by an increase in the strength of the summer monsoon, which decreased eolian dust transport and the coastal upwelling activity. The northward migration is in phase with a specific orbital combination of a low precessional index with a high obliquity signal. High-resolution analysis of stable isotopes (d18O and d13C) and microscale resolution geochemical (Ti/Al and quartz grain counts) determinations reveal that the transition between monsoonal humid (MIS 6.5) and dry (MIS 6.4) conditions has occurred in less than 1.3 ka. Such rapid changes suggest a nonlinear link between the African monsoonal rainfall system and environmental changes over the continent. This study provides new insights about the influence of vegetation and oceanic temperature feedbacks on the onset of African summer monsoon and demonstrates that, during the penultimate glacial period, changes in tropical dynamics had regional and global impacts.

Quantum transport and integrability of the Anderson model for a quantum dot with multiple leads

We show that an Anderson Hamiltonian describing a quantum dot connected to multiple leads is integrable. A general expression for the nonlinear conductance is obtained by combining the Bethe ansatz exact solution with Landauer-Buttiker theory. In the Kondo regime, a closed form expression is given for the matrix conductance at zero temperature and when all the leads are close to the symmetric point. A bias-induced splitting of the Kondo resonance is possible for three or more leads. Specifically, for N leads, with each at a different chemical potential, there can be N-1 Kondo peaks in the conductance.

Functionality, Robustness and Control of Nonlinear Network Dynamics: Modeling and Understanding the C. elegans Connectome

Thesis (Ph.D.)--University of Washington, 2016-06

Ground water model calibration using pilot points and regularization

Use of nonlinear parameter estimation techniques is now commonplace in ground water model calibration. However, there is still ample room for further development of these techniques in order to enable them to extract more information from calibration datasets, to more thoroughly explore the uncertainty associated with model predictions, and to make them easier to implement in various modeling contexts. This paper describes the use of pilot points as a methodology for spatial hydraulic property characterization. When used in conjunction with nonlinear parameter estimation software that incorporates advanced regularization functionality (such as PEST), use of pilot points can add a great deal of flexibility to the calibration process at the same time as it makes this process easier to implement. Pilot points can be used either as a substitute for zones of piecewise parameter uniformity, or in conjunction with such zones. In either case, they allow the disposition of areas of high and low hydraulic property value to be inferred through the calibration process, without the need for the modeler to guess the geometry of such areas prior to estimating the parameters that pertain to them. Pilot points and regularization can also be used as an adjunct to geostatistically based stochastic parameterization methods. Using the techniques described herein, a series of hydraulic property fields can be generated, all of which recognize the stochastic characterization of an area at the same time that they satisfy the constraints imposed on hydraulic property values by the need to ensure that model outputs match field measurements. Model predictions can then be made using all of these fields as a mechanism for exploring predictive uncertainty.

Nonlinear quantum optical computing via measurement

We show how the measurement induced model of quantum computation proposed by Raussendorf and Briegel ( 2001, Phys. Rev. Letts., 86, 5188) can be adapted to a nonlinear optical interaction. This optical implementation requires a Kerr nonlinearity, a single photon source, a single photon detector and fast feed forward. Although nondeterministic optical quantum information proposals such as that suggested by KLM ( 2001, Nature, 409, 46) do not require a Kerr nonlinearity they do require complex reconfigurable optical networks. The proposal in this paper has the benefit of a single static optical layout with fixed device parameters, where the algorithm is defined by the final measurement procedure.

An experimental and finite element poroelastic creep response analysis of an intervertebral hydrogel disc model in axial compression

A hydrogel intervertebral disc (lVD) model consisting of an inner nucleus core and an outer anulus ring was manufactured from 30 and 35% by weight Poly(vinyl alcohol) hydrogel (PVA-H) concentrations and subjected to axial compression in between saturated porous endplates at 200 N for 11 h, 30 min. Repeat experiments (n = 4) on different samples (N = 2) show good reproducibility of fluid loss and axial deformation. An axisymmetric nonlinear poroelastic finite element model with variable permeability was developed using commercial finite element software to compare axial deformation and predicted fluid loss with experimental data. The FE predictions indicate differential fluid loss similar to that of biological IVDs, with the nucleus losing more water than the anulus, and there is overall good agreement between experimental and finite element predicted fluid loss. The stress distribution pattern indicates important similarities with the biological lVD that includes stress transference from the nucleus to the anulus upon sustained loading and renders it suitable as a model that can be used in future studies to better understand the role of fluid and stress in biological IVDs. (C) 2005 Springer Science + Business Media, Inc.

A probabilistic switch model of information flow in social networks: Application for virtual circuits to organizational design

Network building and exchange of information by people within networks is crucial to the innovation process. Contrary to older models, in social networks the flow of information is noncontinuous and nonlinear. There are critical barriers to information flow that operate in a problematic manner. New models and new analytic tools are needed for these systems. This paper introduces the concept of virtual circuits and draws on recent concepts of network modelling and design to introduce a probabilistic switch theory that can be described using matrices. It can be used to model multistep information flow between people within organisational networks, to provide formal definitions of efficient and balanced networks and to describe distortion of information as it passes along human communication channels. The concept of multi-dimensional information space arises naturally from the use of matrices. The theory and the use of serial diagonal matrices have applications to organisational design and to the modelling of other systems. It is hypothesised that opinion leaders or creative individuals are more likely to emerge at information-rich nodes in networks. A mathematical definition of such nodes is developed and it does not invariably correspond with centrality as defined by early work on networks.

General foundation for the nonlinear ponderomotive four-force in laser-plasma interactions

The interaction of electromagnetic radiation with plasmas is studied in relativistic four-vector formalism. A gauge and Lorentz invariant ponderomotive four-force is derived from the time dependent nonlinear three-force of Hora (1985). This four-force, due to its Lorentz invariance, contains new magnetic field terms. A new gauge and Lorentz invariant model of the response of plasma to electromagnetic radiation is then devised. An expression for the dispersion relation is obtained from this model. It is then proved that the magnetic permeability of plasma is unity for a general reference frame. This is an important result since it has been previously assumed in many plasma models.