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No / In this paper we investigate the use of general topological spaces in connection with a generalised variant of membrane systems. We provide an approach which produces a fine grain description of local operations occurring simultaneously in sets of compartments of the system by restricting the interactions between objects. This restriction is given by open sets of a topology and multisets of objects associated with them, which dynamically change during the functioning of the system and which together define a notion of vicinity for the objects taking part in the interactions. / The first, the second, and the third authors were partially supported under the Royal Society International Exchanges Scheme (ref. IE110369). The second author was also partially supported by the project MuVet, Romanian National Authority for Scientific Research (CNCS – UEFISCDI) grant number PNII- ID-PCE-2011-3-0688. This work was partially completed whilst the third author was a visiting fellow at the Isaac Newton Institute for the Mathematical Sciences in the programme ‘Semantics & Syntax: A Legacy of Alan Turing’. The work of the first and the fourth author was also supported in part by the Hungarian Scientific Research Fund (OTKA), Grant no. K75952. The fourth author was supported by the European Union through the T´AMOP-4.2.2.C-11/1/KONV-2012-0001 project which is co-financed by the European Social Fund.

In the process of translation, ribosomes, a type of macromolecules, read the genetic code on a messenger RNA template (mRNA) and assemble amino acids into a polypeptide chain which folds into a functioning protein product. The ribosomes perform discrete directed motion that is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. We incorporate the essential components of the translation process: Ribosomes, cognate tRNA concentrations, and mRNA templates correspond to particles (covering ell > 1 sites), hopping rates, and the underlying lattice, respectively. As the hopping rates in an mRNA are given by its sequence (in the unit of codons), we are especially interested in the effects of a finite number of slow codons to the overall stationary current. To study this matter systematically, we first explore the effects of local inhomogeneities, i.e., one or two slow sites of hopping rate q<1 in TASEP for particles of size ell > 1(in the unit of lattice site) using Monte Carlo simulation. We compare the results of ell =1 and ell >1 and notice that the existence of local defects has qualitatively similar effects to the steady state. We focus on the stationary current as well as the density profiles. If there is only a single slow site in the system, we observe a significant dependence of the current on the location of the slow site for both ell =1 and ell >1 cases. In particular, we notice a novel "edge" effect, i.e., the interaction of a single slow codon with the system boundary. When two slow sites are introduced, more intriguing phenomena such as dramatic decreases in the current when the two are close together emerge. We analyze the simulation results using several different levels of mean-field theory. A finite-segment mean-field approximation is especially successful in understanding the "edge effect." If we consider the systems with finite defects as "contrived mRNA's", the real mRNA's are of more biological significance. Inspired by the previous results, we study several mRNA sequences from Escherichia coli. We argue that an effective translation rate including the context of each codon needs to be taken into consideration when seeking an efficient strategy to optimize the protein production. / Ph. D.

Open land has historically been considered an expendable resource. This concept has abetted the sprawl which occurs in all urbanizing areas of our country. With the United States urbanizing at a rate of more than a million acres a year, this concept can no longer be tolerated. In the last fifteen years, urban development has consumed approximately two-thirds as much new land as it did in all the previous years in the history of our country. Virginia has not been an innocent bystander in this process. This thesis points up the necessity for immediate action to preserve open space in the State of Virginia. It examines the human as well as the economic values that can be derived from open space through an analysis of both the active and passive uses to which open space or low-density use lands can be put. This is accomplished through the establishment and critical analysis of the goals and objectives of an open space program for Virginia. The law on open space in Virginia is a mass of detail buried in traditional legal categories developed for other purposes. This thesis has examined the existing constitutional and statutory powers available to local governmental subdivisions for developing an open space program. In addition, it examines and appraises significant proposals for acquiring and controlling open space. From this analysis, alternative programs for open space acquisition and control are presented including the acquisition of development rights, the land bank, fresh concepts of zoning and subdivision regulations, and expanded concepts in the use of the taxing power. / Master of Science

Yes / The present study investigates the turbulent hydrodynamics in an open channel flow with an emergent and sparse vegetation patch placed in the middle of the channel. The dimensions of the rigid vegetation patch are 81 cm long and 24 cm wide and it is prepared by a 7× 10 array of uniform acrylic cylinders by maintaining 9 cm and 4 cm spacing between centers of two consecutive cylinders along streamwise and lateral directions respectively. From the leading edge of the patch, the observed nature of time averaged flow velocities along streamwise, lateral and vertical directions is not consistent up to half length of the patch; however the velocity profiles develop a uniform behavior after that length. In the interior of the patch, the magnitude of vertical normal stress is small in comparison to the magnitudes of streamwise and lateral normal stresses. The magnitude of Reynolds shear stress profiles decreases with increasing downstream length from the leading edge of the vegetation patch and the trend continues even in the wake region downstream of the trailing edge. The increased magnitude of turbulent kinetic energy profiles is noticed from leading edge up to a certain length inside the patch; however its value decreases with further increasing downstream distance. A new mathematical model is proposed to predict time averaged streamwise velocity inside the sparse vegetation patch and the proposed model shows good agreement with the experimental data. / Debasish Pal received financial assistance from SRIC Project of IIT Kharagpur (Project code: FVP)

Yes / Effective and efficient healthcare not only depends on good interpersonal communication but also on the ability of organisations to communicate successfully and professionally. Yet organisations can become entrenched in rules, regulations and expected behaviours that stifle creative responses to work situations. Deep-seated bureaucracy can alienate the personal, and is made even more challenging if the organisation has multi-sites. This chapter will examine the many varied structures of organisation, and how communication flow within organisations can limit or expand inclusion of staff members within its boundaries. This chapter offers several barriers to good organisational communication and suggests ways these hurdles can be overcome. The ethics of healthcare practice is discussed in relation to the effect on the individual and the organisation, highlighting how both parties could respond to avoid conflict, clash and threats to professionalism. Above all, this chapter emphasises how open and honest personcentred communication in an organisation can lead to healthy outcomes for staff and patients alike.

Intelligence analysts today are faced with many challenges, chief among them being the need to fuse disparate streams of data and rapidly arrive at analytical decisions and quantitative predictions for use by policy makers. A forecasting tool to anticipate key events of interest is an invaluable aid in helping analysts cut through the chatter. We present the design of user interfaces for the EMBERS system, an anticipatory intelligence system that ingests myriad open source data streams (e.g., news, blogs, tweets, economic and financial indicators, search trends) to generate forecasts of significant societal-level events such as disease outbreaks, protests, and elections. A key research issue in EMBERS is not just to generate high-quality forecasts but provide interfaces for analysts so they can understand the rationale behind these forecasts and pose why, what-if, and other exploratory questions. This thesis presents the design and implementation of three visualization interfaces for EMBERS. First, we illustrate how the rationale behind forecasts can be presented to users through the use of an audit trail and its associated visualization. The audit trail enables an analyst to drill-down from a final forecast down to the raw (and processed) data sources that contributed to the forecast. Second, we present a forensics tool called Reverse OSI that enables analysts to investigate if there was additional information either in existing or new data sources that can be used to improve forecasting. Unlike the audit trail which captures the transduction of data from raw feeds into alerts, Reverse OSI enables us to posit connections from (missed) forecasts back to raw feeds. Finally, we present an interactive machine learning approach for analysts to steer the construction of machine learning mod-els. This provides fine-grained control into tuning tradeoffs underlying EMBERS. Together, these three interfaces support a range of functionality in EMBERS, from visualization of algorithm output to a complete framework for user feedback via a tight human-algorithm loop. They are currently being utilized by a range of user groups in EMBERS: analysts, social scientists, and machine learning developers, respectively. / Master of Science

The design of public open spaces frequently does not address the physical and psychological needs of their users with regard to their ages. This research gathered and restated the needs and preferences of teenagers, as an understudied group, in public open spaces, with an emphasis on neighborhood parks. Utilizing a neighborhood park in Roanoke, Virginia, the study developed findings that can influence the design of public open spaces, with the goals of providing social and physical benefits of neighborhood parks for teenagers. This research was conducted through two phases of interviews. The first phase of interviews took place with professionals who had experience in working with teenagers. The data collected in the first phase of interviews with adults were utilized for the second phase of interviews, which were with teenagers. Experimental models of the study site were created for the second phase to assist the interviewees in visualizing the various designs. In the second phase, the design options were presented to the teenaged study group in response to teenagers' characteristics and needs as determined by the outcomes of the first phase of interviews. The teenagers were asked to state their preferences among the design options. The different options for designing neighborhood parks utilized a neighborhood park in Roanoke, Virginia, as a study site. The findings of this research suggest that teenagers prefer to utilize spaces closer to the front of the park, by its edges, entrances, and exits, and the parking lot. These findings suggest that there may be no need to design specific spaces dedicated for teenagers in public spaces; however teenager's preferences should be considered in the design process of public spaces. Based on the findings of this research and the suggested relationships among the design attributes of neighborhood parks and teenagers' use of space, this research suggests that providing public spaces is linked with increased opportunities for the social development of teenagers. The primary implications of the findings of this research could help inform landscape architects and urban planners in their designs of future public open spaces that address the needs of teenagers. / Master of Landscape Architecture