Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives

Three-protein circadian oscillations in cyanobacteria sustain for weeks. To understand how cellular oscillations function robustly in stochastic fluctuating environments, we used a stochastic model to uncover two natures of circadian oscillation: the potential landscape related to steady-state probability distribution of protein concentrations; and the corresponding flux related to speed of concentration changes which drive the oscillations. The barrier height of escaping from the oscillation attractor on the landscape provides a quantitative measure of the robustness and coherence for oscillations against intrinsic and external fluctuations. The difference between the locations of the zero total driving force and the extremal of the potential provides a possible experimental probe and quantification of the force from curl flux. These results, correlated with experiments, can help in the design of robust oscillatory networks.

Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Funneled landscape leads to robustness of cellular networks: MAPK signal transduction

We uncover the underlying potential energy landscape for a cellular network. We find that the potential energy landscape of the mitogen-activated protein-kinase signal transduction network is funneled toward the global minimum. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. Funneled landscape is a realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.

A river of memory: landscape, narrative and identity in the Lee Valley, Co. Cork, Ireland

In moments of rapid social changes, as has been witnessed in Ireland in the last decade, the conditions through which people engage with their localities though memory, individually and collectively, remains an important cultural issue with key implications for questions of heritage, preservation and civic identity. In recent decades, cultural geographers have argued that landscape is more than just a view or a static text of something symbolic. The emphasis seems to be on landscape as a dynamic cultural process – an ever-evolving process being constructed and re-constructed. Hence, landscape seems to be a highly complex term that carries many different meanings. Material, form, relationships or actions have different meanings in different settings. Drawing upon recent and continuing scholarly debates in cultural landscapes and collective memory, this thesis sets out to examine the generation of collective memory and how it is employed as a cultural tool in the production of memory in the landscape. More specifically, the research considers the relationships between landscape and memory, investigating the ways in which places are produced, appropriated, experienced, sensed, acknowledged, imagined, yearned for, appropriated, re-appropriated, contested and identified with. A polyvocal-bricoleur approach aims to get below the surface of a cultural landscape, inject historical research and temporal depth into cultural landscape studies and instil a genuine sense of inclusivity of a wide variety of voices (role of monuments and rituals and voices of people) from the past and present. The polyvocal-bricoleur approach inspires a mixed method methodology approach to fieldsites through archival research, fieldwork and filmed interviews. Using a mixture of mini-vignettes of place narratives in the River Lee valley in the south of Ireland, the thesis explores a number of questions on the fluid nature of narrative in representing the story and role of the landscape in memory-making. The case studies in the Lee Valley are harnessed to investigate the role of the above questions/ themes/ debates in the act of memory making at sites ranging from an Irish War of Independence memorial to the River Lee’s hydroelectric scheme to the valley’s key religious pilgrimage site. The thesis investigates the idea that that the process of landscape extends not only across space but also across time – that the concept of historical continuity and the individual and collective human engagement and experience of this continuity are central to the processes of remembering on the landscape. In addition the thesis debates the idea that the production of landscape is conditioned by several social frames of memory – that individuals remember according to several social frames that give emphasis to different aspects of the reality of human experience. The thesis also reflects on how the process of landscape is represented by those who re-produce its narratives in various media.

Lost in Translation, book review of Urban Landscape Perspectives

In Sofia Coppola's 2003 film Lost in Translation, Bill Murray and Scarlett Johansson's characters find themselves culturally stranded and oddly mismatched as an improvised tourist couple in contemporary Tokyo. This is an urban landscape that they cannot comprehend but only temporarily experience, in a fragmented and surreptitious way that allows no possible understanding and categorizations, but offers physical inclusion, emotional participation and momentary embeddedness.

Prehistoric Pinus woodland dynamics in an upland landscape in northern Scotland: the roles of climate change and human impact

Pollen, microscopic charcoal, palaeohydrological and dendrochronological analyses are applied to a radiocarbon and tephrochronologically dated mid Holocene (ca. 8500–3000 cal B.P.) peat sequence with abundant fossil Pinus (pine) wood. The Pinus populations on peat fluctuated considerably over the period in question. Colonisation by Pinus from ca. 7900–7600 cal B.P. appears to have had no specific environmental trigger; it was probably determined by the rate of migration from particular populations. The second phase, at ca. 5000–4400 cal B.P., was facilitated by anthropogenic interference that reduced competition from other trees. The pollen record shows two Pinus declines. The first at ca. 6200–5500 cal B.P. was caused by a series of rapid and frequent climatic shifts. The second, the so-called pine decline, was very gradual (ca. 4200–3300 cal B.P.) at Loch Farlary and may not have been related to climate change as is often supposed. Low intensity but sustained grazing pressures were more important. Throughout the mid Holocene, the frequency and intensity of burning in these open Pinus–Calluna woods were probably highly sensitive to hydrological (climatic) change. Axe marks on several trees are related to the mid to late Bronze Age, i.e., long after the trees had died.

“Islands” in Holocene forests: implications for forest openness, landscape clearance and “culture-steppe” species

Human activity has undoubtedly had a major impact on Holocene forested ecosystems, with the concurrent expansion of plants and animals associated with cleared landscapes and pasture, also known as 'culture-steppe'. However, this anthropogenic perspective may have underestimated the contribution of autogenic disturbance (e.g. wind-throw, fire), or a mixture of autogenic and anthropogenic processes, within early Holocene forests. Entomologists have long argued that the north European primary forest was probably similar in structure to pasture woodland. This idea has received support from the conservation biologist Frans Vera, who has recently strongly argued that the role of large herbivores in maintaining open forests in the primeval landscapes of Europe has been seriously underestimated. This paper reviews this debate from a fossil invertebrate perspective and looks at several early Holocene insect assemblages. Although wood taxa are indeed important during this period, species typical of open areas and grassland and dung beetles, usually associated with the dung of grazing animals, are persistent presences in many early woodland faunas. We also suggest that fire and other natural disturbance agents appear to have played an important ecological role in some of these forests, maintaining open areas and creating open vegetation islands within these systems. More work, however, is required to ascertain the role of grazing animals, but we conclude that fossil insects have a significant contribution to make to this debate. This evidence has fundamental implications in terms of how the palaeoecological record is interpreted, particularly by environmental archaeologists and palaeoecologists who may be more interested in identifying human-environment interactions rather than the ecological processes which may be preserved within palaeoecological records.

A new landscape of arts-based buildings and comparative cultural policies on the island of Ireland: the curse of Jocasta's necklace

Much current cultural policy research focuses on activity traditionally viewed as arts practice: visual arts, music, literature and dance. Architecture’s role in the discussion of cultural policy is, however, less certain and thus less frequently interrogated. The study presented here both addresses this dearth of in-depth research while also contributing to the interdisciplinary discussion of cultural policy in wider terms. In seeking to better understand how architectural culture is regulated and administered in a specific case study, it unpacks how the complicated relationships of nominal and explicit policies on both sides of the Irish/Northern Irish border contributed to the significant expansion of arts-based buildings 1995-2008. It contrasts political and cultural motivations behind these projects during a period of significant economic growth, investment and inward immigration. Data has been gathered from both official published policies as well as interviews with elite actors in the decision-making field and architects who produced the buildings of interest in both countries. With the sizeable number of arts-based buildings now completed in both Republic of Ireland and Northern Ireland, one must wonder if this necklace of buildings is, like Jocasta’s, a thing of both beauty and redolent with a potential future curse. It is the goal of this project to contribute to the larger applied and critical discussion of these issues and to engage with future policy design, administration and, certainly, evaluation.

A Contested Landscape: Monuments, public memory, and post-Soviet Identity in Stavropol’, Russia

Much recent literature in cultural, political and social geography has considered the relationship between identity, memory, and the urban landscape. This paper interrogates such literature through exploring the complex materialisation of memorialisation in post-Soviet Russia. Using the example of the statue of General Alexei Ermolov in Stavropol', an analysis of the cityscape reveals interethnic tensions over differing interpretations of the life and history of the person upon whom the statue is based. The existence of a rich literature on Ermolov and the Russian colonial experience in the North Caucasus helps to explain this. The symbolic cityscape of Stavropol' plays an important role in interethnic relations in the multi-ethnic city; it is both an arena through which Russian identity is communicated with people and produced and reproduced, and an arena through which Russian citizens compete with each other for authority on historical narratives that operate at and between a number of scales. People's readings of the cityscape can reveal much about power and space in contemporary Russia.

A new landscape of arts-based buildings and comparative cultural policies on the island of Ireland: the curse of Jocasta's necklace

Much current cultural policy research focuses on activity traditionally viewed as arts practice: visual arts, music, literature and dance. Architecture’s role in the discussion of cultural policy is, however, less certain and thus less frequently interrogated. The study presented here both addresses this dearth of in-depth research while also contributing to the interdisciplinary discussion of cultural policy in wider terms. In seeking to better understand how architectural culture is regulated and administered in a specific case study, it unpacks how the complicated relationships of nominal and explicit policies on both sides of the Irish/Northern Irish border contributed to the significant expansion of arts-based buildings 1995-2008. It contrasts political and cultural motivations behind these projects during a period of significant economic growth, investment and inward immigration. Data has been gathered from both official published policies as well as interviews with elite actors in the decision-making field and architects who produced the buildings of interest in both countries. With the sizeable number of arts-based buildings now completed in both Republic of Ireland and Northern Ireland, one must wonder if this necklace of buildings is, like Jocasta’s, a thing of both beauty and redolent with a potential future curse. It is the goal of this project to contribute to the larger applied and critical discussion of these issues and to engage with future policy design, administration and, certainly, evaluation.

Efficient Architectural Design Space Exploration via Predictive Modeling

Efficiently exploring exponential-size architectural design spaces with many interacting parameters remains an open problem: the sheer number of experiments required renders detailed simulation intractable.We attack this via an automated approach that builds accurate predictive models. We simulate sampled points, using results to teach our models the function describing relationships among design parameters. The models can be queried and are very fast, enabling efficient design tradeoff discovery. We validate our approach via two uniprocessor sensitivity studies, predicting IPC with only 1–2% error. In an experimental study using the approach, training on 1% of a 250-K-point CMP design space allows our models to predict performance with only 4–5% error. Our predictive modeling combines well with techniques that reduce the time taken by each simulation experiment, achieving net time savings of three-four orders of magnitude.

Late Pleistocene climate change and landscape dynamics in the Eastern Alps: the inner-alpine Unterangerberg record (Austria)

Drill cores from the inner-alpine valley terrace of Unterangerberg, located in the Eastern Alps of Austria, offer first insights into a Pleistocene sedimentary record that was not accessible so far. The succession comprises diamict, gravel, sand, lignite and thick, fine grained sediments. Additionally, cataclastic deposits originating from two paleo-landslide events are present. Multi-proxy analyses including sedimentological and palynological investigations as well as radiocarbon and luminescence data record the onset of the last glacial period (Wurmian) at Unterangerberg at similar to 120-110 ka. This first time period, correlated to the MIS 5d, was characterised by strong fluvial aggradation under cold climatic conditions, with only sparse vegetation cover. Furthermore, two large and quasi-synchronous landslide events occurred during this time interval. No record of the first Early Wiirmian interstadial (MIS 5c) is preserved. During the second Early Wiirmian interstadial (MIS 5a), the local vegetation was characterised by a boreal forest dominated by Picea, with few thermophilous elements. The subsequent collapse of the vegetation is recorded by sediments dated to similar to 70-60 ka (i.e. MIS 4), with very low pollen concentrations and the potential presence of permafrost. Climatic conditions improved again between similar to 55 and 45 ka (MIS 3) and cold-adapted trees re-appeared during interstadials, forming an open forest vegetation. MIS 3 stadials were shorter and less severe than the MIS 4 at Unterangerberg, and vegetation during these cold phases was mainly composed of shrubs, herbs and grasses, similar to what is known from today's alpine timberline. The Unterangerberg record ended at similar to 45 ka and/or was truncated by ice during the Last Glacial Maximum. (C) 2013 Elsevier Ltd. All rights reserved.

The Landscape of Differences: Contact and Segregation in the Everyday Encounters

The article examines everyday life in Northern Ireland’s segregated communities and focus on a neglected empirical dimension of ethnic and social segregation developed within the socio-spatial relations between people and their built environment. It shows how the everyday urban encounters are reproduced through negotiating differences and the ways in which living in divided communities lead to social inequality and imbalanced use of space. The article employed qualitative research methods with individuals and community groups from the Fountain estate, a small Protestant enclave in Derry/Londonderry. Their stories were replete with cases of injustice and insights into the daily struggles that have generally occurred within theories of contact and social segregation as a whole. In fact, people in the Fountain presented their own intertextual references on what was more significant for them as a matter of routine survival and belonging, which allowed them to be more constructive about themselves. While segregation has persisted for multiple decades; time is believed to be the factor most likely to change it, as it is hoped that the younger generation will provide lasting change to Northern Ireland and eventual peace between currently segregated communities.