Incorporating spatial correlations into multispecies mean-field models

In biology, we frequently observe different species existing within the same environment. For example, there are many cell types in a tumour, or different animal species may occupy a given habitat. In modeling interactions between such species, we often make use of the mean-field approximation, whereby spatial correlations between the locations of individuals are neglected. Whilst this approximation holds in certain situations, this is not always the case, and care must be taken to ensure the mean-field approximation is only used in appropriate settings. In circumstances where the mean-field approximation is unsuitable, we need to include information on the spatial distributions of individuals, which is not a simple task. In this paper, we provide a method that overcomes many of the failures of the mean-field approximation for an on-lattice volume-excluding birth-death-movement process with multiple species. We explicitly take into account spatial information on the distribution of individuals by including partial differential equation descriptions of lattice site occupancy correlations. We demonstrate how to derive these equations for the multispecies case and show results specific to a two-species problem. We compare averaged discrete results to both the mean-field approximation and our improved method, which incorporates spatial correlations. We note that the mean-field approximation fails dramatically in some cases, predicting very different behavior from that seen upon averaging multiple realizations of the discrete system. In contrast, our improved method provides excellent agreement with the averaged discrete behavior in all cases, thus providing a more reliable modeling framework. Furthermore, our method is tractable as the resulting partial differential equations can be solved efficiently using standard numerical techniques

Local flow management/profile descent algorithm. Fuel-efficient, time-controlled profiles for the NASA TSRV airplane

The Local Flow Management/Profile Descent (LFM/PD) algorithm designed for the NASA Transport System Research Vehicle program is described. The algorithm provides fuel-efficient altitude and airspeed profiles consistent with ATC restrictions in a time-based metering environment over a fixed ground track. The model design constraints include accommodation of both published profile descent procedures and unpublished profile descents, incorporation of fuel efficiency as a flight profile criterion, operation within the performance capabilities of the Boeing 737-100 airplane with JT8D-7 engines, and conformity to standard air traffic navigation and control procedures. Holding and path stretching capabilities are included for long delay situations

An investigation of TNAV equipped aircraft in a simulated en route metering environment

This document presents the results of an effort to estimate how often a TNAV (Time Navigation) equipped aircraft could be given a TNAV clearance in the En Route Metering (ERM) system as a function of the percentage of arriving traffic which is TNAV equipped. A fast-time simulation of Denver Stapleton international arrival traffic in the Denver Air Route Traffic Control Center route structure, including en route metering operations, was used to develop data on estimated conflicts, clearance communications and fuel usage for traffic mixes of 25, 50, 75 and 100% TNAV equipped. This study supports an overall effort by NASA to assess the benefits and required technology for using TNAV-equipped aircraft in the ERM environment

The self-assembly of DNA Holliday junctions studied with a minimal model

In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the phosphate-sugar backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately, and allows strand displacement to occur.Comment: 13 pages, 14 figure

Properties of implanted and CVD incorporated nitrogen-vacancy centers: preferential charge state and preferential orientation

The combination of the long electron state spin coherence time and the optical coupling of the ground electronic states to an excited state manifold makes the nitrogen-vacancy (NV) center in diamond an attractive candidate for quantum information processing. To date the best spin and optical properties have been found in centers deep within the diamond crystal. For useful devices it will be necessary to engineer NVs with similar properties close to the diamond surface. We report on properties including charge state control and preferential orientation for near surface NVs formed either in CVD growth or through implantation and annealing

Survival of entanglement in thermal states

We present a general sufficiency condition for the presence of multipartite entanglement in thermal states stemming from the ground state entanglement. The condition is written in terms of the ground state entanglement and the partition function and it gives transition temperatures below which entanglement is guaranteed to survive. It is flexible and can be easily adapted to consider entanglement for different splittings, as well as be weakened to allow easier calculations by approximations. Examples where the condition is calculated are given. These examples allow us to characterize a minimum gapping behavior for the survival of entanglement in the thermodynamic limit. Further, the same technique can be used to find noise thresholds in the generation of useful resource states for one-way quantum computing.Comment: 6 pages, 2 figures. Changes made in line with publication recommendations. Motivation and concequences of result clarified, with the addition of one more example, which applies the result to give noise thresholds for measurement based quantum computing. New author added with new result

Identity, community and care in online accounts of hereditary colorectal cancer syndrome

Sociological literature has explored how shifts in the point at which individuals may be designated as diseased impact upon experiences of ill health. Research has shown that experiences of being genetically “at risk” are shaped by and shape familial relations, coping strategies, and new forms of biosociality. Less is known about how living with genetic risk is negotiated in the everyday and over time, and the wider forms of identity, communities and care this involves. This article explores these arrangements drawing on online bloggers’ accounts of Familial Adenomatous Polyposis (FAP). We show how accounts of genetic risk co-exist with more palpable experiences of FAP in everyday life, notably the consequences of prophylactic surgeries. We consider how the act of blogging represents but also constitutes everyday experiences of hereditary cancer syndrome as simultaneously ordinary and exceptional, and reflect on the implications of our analysis for understanding experiences of genetic cancer risk

Reducing Sexual Risk among Racial/ethnic-minority Ninth Grade Students: Using Intervention Mapping to Modify an Evidenced-based Curriculum

Background: Racial/ethnic-minority 9th graders are at increased risk for teen pregnancy, HIV, and STIs compared to their White peers. Yet, few effective sexual health education programs exist for this population. Purpose: To apply IM Adapt—a systematic theory- and evidence-based approach to program adaptation—to modify an effective middle school sexual health education curriculum, It’s Your Game…Keep It Real! (IYG), for racial/ethnic-minority 9th graders. Methods: Following the six steps of IM Adapt, we conducted a needs assessment to describe the health problems and risk behaviors of the new population; reviewed existing evidence-based programs; assessed the fit of IYG for the new population regarding behavioral outcomes, determinants, change methods, delivery, and implementation; modified materials and activities; planned for implementation and evaluation. Results: Needs assessment findings indicated that IYG targeted relevant health and risk behaviors for racial/ethnic-minority 9th graders but required additional focus on contraceptive use, dating violence prevention, active consent, and access to healthcare services. Behavioral outcomes and matrices of change objectives for IYG were modified accordingly. Theoretical methods and practical applications were identified to address these behavioral outcomes, and new activities developed. Youth provided input on activity modifications. School personnel guided modifications to IYG’s scope and sequence, and delivery. The adapted program, Your Game, Your Life, comprised fifteen 30-minute lessons targeting determinants of sexual behavior and healthy dating relationships. Pilot-test data from 9th graders in two urban high schools indicate promising results. Conclusion: IM Adapt provides a systematic theory- and evidence-based approach for adapting existing evidence-based sexual health education curricula for a new population whilst retaining essential elements that made the original program effective. Youth and school personnel input ensured that the adapted program was age-appropriate, culturally sensitive, and responsive to the needs of the new population. IM Adapt contributes to the limited literature on systematic approaches to program adaptation

Production of oriented nitrogen-vacancy color centers in synthetic diamond

The negatively charged nitrogen-vacancy (NV-) center in diamond is an attractive candidate for applications that range from magnetometry to quantum information processing. Here we show that only a fraction of the nitrogen (typically < 0.5 %) incorporated during homoepitaxial diamond growth by Chemical Vapor Deposition (CVD) is in the form of undecorated NV- centers. Furthermore, studies on CVD diamond grown on (110) oriented substrates show a near 100% preferential orientation of NV- centers along only the [111] and [-1-11] directions, rather than the four possible orientations. The results indicate that NV centers grow in as units, as the diamond is deposited, rather than by migration and association of their components. The NV unit of the NVH- is similarly preferentially oriented, but it is not possible to determine whether this defect was formed by H capture at a preferentially aligned NV center or as a complete unit. Reducing the number of NV orientations from 4 orientations to 2 orientations should lead to increased optically-detected magnetic resonance contrast and thus improved magnetic sensitivity in ensemble-based magnetometry.Comment: 13 Pages (inlcuding suplementary information), 4 figure