On Ito's formula for elliptic diffusion processes

Bardina and Jolis [Stochastic process. Appl. 69 (1997) 83-109] prove an extension of Ito's formula for F(Xt, t), where F(x, t) has a locally square-integrable derivative in x that satisfies a mild continuity condition in t and X is a one-dimensional diffusion process such that the law of Xt has a density satisfying certain properties. This formula was expressed using quadratic covariation. Following the ideas of Eisenbaum [Potential Anal. 13 (2000) 303-328] concerning Brownian motion, we show that one can re-express this formula using integration over space and time with respect to local times in place of quadratic covariation. We also show that when the function F has a locally integrable derivative in t, we can avoid the mild continuity condition in t for the derivative of F in x.

Salting kinetics and salt diffusivities in farmed Pantanal caiman muscle

The legal Pantanal caiman (Caiman crocodilus yacare) farming, in Brazil, has been stimulated and among meat preservation techniques the salting process is a relatively simple and low-cost method. The objective of this work was to study the sodium chloride diffusion kinetics in farmed caiman muscle during salting. Limited volumes of brine were employed, with salting essays carried at 3, 4 and 5 brine/muscle ratios, at 15%, 20% and 25% w/w brine concentrations, and brine temperatures of 10, 15 and 20ºC. The analytical solution of second Fick's law considering one-dimensional diffusion through an infinite slab in contact with a well-stirred solution of limited volume was used to calculate effective salt diffusion coefficients and to predict the sodium chloride content in the fillets. A good agreement was obtained between the considered analytical model and experimental data. Salt diffusivities in fillets were found to be in the range of 0.47x10-10 to 9.62x10-10 m²/s.

A combined computational and functional approach identifies new residues involved in pH-dependent gating of ASIC1a.

Acid-sensing ion channels (ASICs) are key receptors for extracellular protons. These neuronal nonvoltage-gated Na(+) channels are involved in learning, the expression of fear, neurodegeneration after ischemia, and pain sensation. We have applied a systematic approach to identify potential pH sensors in ASIC1a and to elucidate the mechanisms by which pH variations govern ASIC gating. We first calculated the pK(a) value of all extracellular His, Glu, and Asp residues using a Poisson-Boltzmann continuum approach, based on the ASIC three-dimensional structure, to identify candidate pH-sensing residues. The role of these residues was then assessed by site-directed mutagenesis and chemical modification, combined with functional analysis. The localization of putative pH-sensing residues suggests that pH changes control ASIC gating by protonation/deprotonation of many residues per subunit in different channel domains. Analysis of the function of residues in the palm domain close to the central vertical axis of the channel allowed for prediction of conformational changes of this region during gating. Our study provides a basis for the intrinsic ASIC pH dependence and describes an approach that can also be applied to the investigation of the mechanisms of the pH dependence of other proteins.

Weakly linked binary mixtures of F = 1 87Rb Bose-Einstein condensates

We present a study of binary mixtures of Bose-Einstein condensates confined in a double-well potential within the framework of the mean field Gross-Pitaevskii (GP) equation. We re-examine both the single component and the binary mixture cases for such a potential, and we investigate what are the situations in which a simpler two-mode approach leads to an accurate description of their dynamics. We also estimate the validity of the most usual dimensionality reductions used to solve the GP equations. To this end, we compare both the semi-analytical two-mode approaches and the numerical simulations of the one-dimensional (1D) reductions with the full 3D numerical solutions of the GP equation. Our analysis provides a guide to clarify the validity of several simplified models that describe mean-field nonlinear dynamics, using an experimentally feasible binary mixture of an F = 1 spinor condensate with two of its Zeeman manifolds populated, m = ±1.

Weakly linked binary mixtures of F = 1 87Rb Bose-Einstein condensates

We present a study of binary mixtures of Bose-Einstein condensates confined in a double-well potential within the framework of the mean field Gross-Pitaevskii (GP) equation. We re-examine both the single component and the binary mixture cases for such a potential, and we investigate what are the situations in which a simpler two-mode approach leads to an accurate description of their dynamics. We also estimate the validity of the most usual dimensionality reductions used to solve the GP equations. To this end, we compare both the semi-analytical two-mode approaches and the numerical simulations of the one-dimensional (1D) reductions with the full 3D numerical solutions of the GP equation. Our analysis provides a guide to clarify the validity of several simplified models that describe mean-field nonlinear dynamics, using an experimentally feasible binary mixture of an F = 1 spinor condensate with two of its Zeeman manifolds populated, m = ±1.

The Effects of Headcut and Knickpoint Propagation on Bridges in Iowa, TR-541, 2008

The overarching goal of the proposed research was to provide a predictive tool for knickpoint propagation within the HCA (Hungry Canyon Alliance) territory. Knickpoints threaten the stability of bridge structures in Western Iowa. The study involved detailed field investigations over two years in order to monitor the upstream migration of a knickpoint on Mud Creek in Mills County, IA and identify the key mechanisms triggering knickpoint propagation. A state-of-the-art laser level system mounted on a movable truss provided continuous measurements of the knickpoint front for different flow conditions. A pressure transducer found in proximity of the truss provided simultaneous measurements of the flow depth. The laser and pressure transducer measurements led to the identification of the conditions at which the knickpoint migration commences. It was suggested that negative pressures developed by the reverse roller flow near the toe of the knickpoint face triggered undercutting of the knickpoint at this location. The pressure differential between the negative pressure and the atmospheric pressure also draws the impinging jet closer to the knickpoint face producing scour. In addition, the pressure differential may induce suction of sediment from the face. Other contributing factors include slump failure, seepage effects, and local fluvial erosion due to the exerted fluid shear. The prevailing flow conditions and soil information along with the channel cross-sectional geometry and gradient were used as inputs to a transcritical, one dimensional, hydraulic/geomorphic numerical model, which was used to map the flow characteristics and shear stress conditions near the knickpoint. Such detailed flow calculations do not exist in the published literature. The coupling of field and modeling work resulted in the development of a blueprint methodology, which can be adopted in different parts of the country for evaluating knickpoint evolution. This information will assist local government agencies in better understanding the principal factors that cause knickpoint propagation and help estimate the needed response time to control the propagation of a knickpoint after one has been identified.

Dynamics of F=1 87Rb condensates at finite temperatures

We investigate the dynamics of a F=1 spinor Bose-Einstein condensate of 87Rb atoms confined in a quasi-one-dimensional trap both at zero and at finite temperature. At zero temperature, we observe coherent oscillations between populations of the various spin components and the formation of multiple domains in the condensate. We study also finite temperature effects in the spin dynamics taking into account the phase fluctuations in the Bogoliubov-de Gennes framework. At finite T, despite complex multidomain formation in the condensate, population equipartition occurs. The length scale of these spin domains seems to be determined intrinsically by nonlinear interactions.

Predicting spinor condensate dynamics from simple principles

We study the spin dynamics of quasi-one-dimensional F=1 condensates both at zero and finite temperatures for arbitrary initial spin configurations. The rich dynamical evolution exhibited by these nonlinear systems is explained by surprisingly simple principles: minimization of energy at zero temperature and maximization of entropy at high temperature. Our analytical results for the homogeneous case are corroborated by numerical simulations for confined condensates in a wide variety of initial conditions. These predictions compare qualitatively well with recent experimental observations and can, therefore, serve as a guidance for ongoing experiments.

First-passage and escape problems in the Feller process

The Feller process is an one-dimensional diffusion process with linear drift and state-dependent diffusion coefficient vanishing at the origin. The process is positive definite and it is this property along with its linear character that have made Feller process a convenient candidate for the modeling of a number of phenomena ranging from single-neuron firing to volatility of financial assets. While general properties of the process have long been well known, less known are properties related to level crossing such as the first-passage and the escape problems. In this work we thoroughly address these questions.

Entropic transport: kinetics, scaling, and control mechanisms

We show that transport in the presence of entropic barriers exhibits peculiar characteristics which makes it distinctly different from that occurring through energy barriers. The constrained dynamics yields a scaling regime for the particle current and the diffusion coefficient in terms of the ratio between the work done to the particles and available thermal energy. This interesting property, genuine to the entropic nature of the barriers, can be utilized to effectively control transport through quasi-one-dimensional structures in which irregularities or tortuosity of the boundaries cause entropic effects. The accuracy of the kinetic description has been corroborated by simulations. Applications to different dynamic situations involving entropic barriers are outlined.

Aminoterminal amphipathic α-helix AH1 of hepatitis C virus nonstructural protein 4B possesses a dual role in RNA replication and virus production.

Nonstructural protein 4B (NS4B) is a key organizer of hepatitis C virus (HCV) replication complex formation. In concert with other nonstructural proteins, it induces a specific membrane rearrangement, designated as membranous web, which serves as a scaffold for the HCV replicase. The N-terminal part of NS4B comprises a predicted and a structurally resolved amphipathic α-helix, designated as AH1 and AH2, respectively. Here, we report a detailed structure-function analysis of NS4B AH1. Circular dichroism and nuclear magnetic resonance structural analyses revealed that AH1 folds into an amphipathic α-helix extending from NS4B amino acid 4 to 32, with positively charged residues flanking the helix. These residues are conserved among hepaciviruses. Mutagenesis and selection of pseudorevertants revealed an important role of these residues in RNA replication by affecting the biogenesis of double-membrane vesicles making up the membranous web. Moreover, alanine substitution of conserved acidic residues on the hydrophilic side of the helix reduced infectivity without significantly affecting RNA replication, indicating that AH1 is also involved in virus production. Selective membrane permeabilization and immunofluorescence microscopy analyses of a functional replicon harboring an epitope tag between NS4B AH1 and AH2 revealed a dual membrane topology of the N-terminal part of NS4B during HCV RNA replication. Luminal translocation was unaffected by the mutations introduced into AH1, but was abrogated by mutations introduced into AH2. In conclusion, our study reports the three-dimensional structure of AH1 from HCV NS4B, and highlights the importance of positively charged amino acid residues flanking this amphipathic α-helix in membranous web formation and RNA replication. In addition, we demonstrate that AH1 possesses a dual role in RNA replication and virus production, potentially governed by different topologies of the N-terminal part of NS4B.

1008-003 White Oak Watershed Final Report

Whit Oak Lake was listed on the 2008 Section 303(d) List if impaired waters in four categories. The first phase of the project has already helped to affect approximately 60% of the watershed. There has been an estimated sediment reduction of 609 tons per year with phase one. The structure being planned for the South end of the lake, (phase two) will affect nearly all of the remaining 40%. If we can accomplish similar results, we can expect a sediment reduction of approximately 273 tons additional per year. We have been working with the Mahaska County NRCS office, Snyder & Associates (engineers) and private landowners in the watershed to make this project a reality.

GPS to LRM: Integration of Spatial Point Features with Linear Referencing Methods, 2001

Global positioning systems (GPS) offer a cost-effective and efficient method to input and update transportation data. The spatial location of objects provided by GPS is easily integrated into geographic information systems (GIS). The storage, manipulation, and analysis of spatial data are also relatively simple in a GIS. However, many data storage and reporting methods at transportation agencies rely on linear referencing methods (LRMs); consequently, GPS data must be able to link with linear referencing. Unfortunately, the two systems are fundamentally incompatible in the way data are collected, integrated, and manipulated. In order for the spatial data collected using GPS to be integrated into a linear referencing system or shared among LRMs, a number of issues need to be addressed. This report documents and evaluates several of those issues and offers recommendations. In order to evaluate the issues associated with integrating GPS data with a LRM, a pilot study was created. To perform the pilot study, point features, a linear datum, and a spatial representation of a LRM were created for six test roadway segments that were located within the boundaries of the pilot study conducted by the Iowa Department of Transportation linear referencing system project team. Various issues in integrating point features with a LRM or between LRMs are discussed and recommendations provided. The accuracy of the GPS is discussed, including issues such as point features mapping to the wrong segment. Another topic is the loss of spatial information that occurs when a three-dimensional or two-dimensional spatial point feature is converted to a one-dimensional representation on a LRM. Recommendations such as storing point features as spatial objects if necessary or preserving information such as coordinates and elevation are suggested. The lack of spatial accuracy characteristic of most cartography, on which LRM are often based, is another topic discussed. The associated issues include linear and horizontal offset error. The final topic discussed is some of the issues in transferring point feature data between LRMs.

Nonequilibrium phase transition in a model for the propagation of innovations among economic agents

We characterize the different morphological phases that occur in a simple one-dimensional model of propagation of innovations among economic agents [X. Guardiola et al., Phys. Rev E 66, 026121 (2002)]. We show that the model can be regarded as a nonequilibrium surface growth model. This allows us to demonstrate the presence of a continuous roughening transition between a flat (system size independent fluctuations) and a rough phase (system size dependent fluctuations). Finite-size scaling studies at the transition strongly suggest that the dynamic critical transition does not belong to directed percolation and, in fact, critical exponents do not seem to fit in any of the known universality classes of nonequilibrium phase transitions. Finally, we present an explanation for the occurrence of the roughening transition and argue that avalanche driven dynamics is responsible for the novel critical behavior.

Observation of a continuous interior crisis in the Hindmarsh-Rose neuron model.

Interior crises are understood as discontinuous changes of the size of a chaotic attractor that occur when an unstable periodic orbit collides with the chaotic attractor. We present here numerical evidence and theoretical reasoning which prove the existence of a chaos-chaos transition in which the change of the attractor size is sudden but continuous. This occurs in the Hindmarsh¿Rose model of a neuron, at the transition point between the bursting and spiking dynamics, which are two different dynamic behaviors that this system is able to present. Moreover, besides the change in attractor size, other significant properties of the system undergoing the transitions do change in a relevant qualitative way. The mechanism for such transition is understood in terms of a simple one-dimensional map whose dynamics undergoes a crossover between two different universal behaviors