Demonstrating the Transferability and the Descriptive Power of Sketch-Map

Increasingly, it is recognized that new automated forms of analysis are required to understand the high-dimensional output obtained from atomistic simulations. Recently, we introduced a new dimensionality reduction algorithm, sketch-map, that was designed specifically to work with data from molecular dynamics trajectories. In what follows, we provide more details on how this algorithm works and on how to set its parameters. We also test it on two well-studied Lennard-Jones clusters and show that the coordinates we extract using this algorithm are extremely robust. In particular, we demonstrate that the coordinates constructed for one particular Lennard-Jones cluster can be used to describe the configurations adopted by a second, different cluster and even to tell apart different phases of bulk Lennard-Jonesium.

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

Simplifying the representation of complex free-energy landscapes using sketch-map

A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.

Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

This work examines the conformational ensemble involved in β-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, and this complex energy landscape is sampled by means of parallel tempering metadynamics simulations. The ensemble of configurations explored is analyzed using the recently proposed sketch-map algorithm. Further simulations allow us to probe how mutations affect the structures adopted by this protein. We find that many of the configurations adopted by a mutant are the same as those adopted by the wild-type protein. Furthermore, certain mutations destabilize secondary-structure-containing configurations by preventing the formation of hydrogen bonds or by promoting the formation of new intramolecular contacts. Our analysis demonstrates that machine-learning techniques can be used to study the energy landscapes of complex molecules and that the visualizations that are generated in this way provide a natural basis for examining how the stabilities of particular configurations of the molecule are affected by factors such as temperature or structural mutations.

Bringing sounds into use: Thinking of sounds as materials and a sketch of auditory affordances

We live in a richly structured auditory environment. From the sounds of cars charging towards us on the street to the sounds of music filling a dancehall, sounds like these are generally seen as being instances of things we hear but can also be understood as opportunities for action. In some circumstances, the sound of a car approaching towards us can provide critical information for the avoidance of harm. In the context of a concert venue, sociocultural practices like music can equally afford coordinated activities of movement, such as dancing or music making. Despite how evident the behavioral effects of sound are in our everyday experience, they have been sparsely accounted for within the field of psychology. Instead, most theories of auditory perception have been more concerned with understanding how sounds are passively processed and represented or how they convey information of world, neglecting how this information can be used for anything. Here, we argue against these previous rationalizations, suggesting instead that information is instantiated through use and, therefore, is an emergent effect of a perceiver’s interaction with their environment. Drawing on theory from psychology, philosophy and anthropology, we contend that by thinking of sounds as materials, theorists and researchers alike can get to grips with the vast array of auditory affordances that we purposefully bring into use when interacting with the environment.

The Equalization of Effective Communicative Freedom: Democratic Justice in the Constitutional State and Beyond

Jurgen Habermas takes the realization of rights through the democratic self-organization of legal communities to be the normative core of emancipatory politics. In this article I explore the implications of this claim in relation to the requirements of justice. I argue that Habermas's discourse theory of democratic legitimacy presupposes a substantive principle of justice that demands the equalization of effective communicative freedom for all structurally constituted social groups in any constitutional state. This involves the elimination of a range of structural injustices rooted in the complex interrelationships between political, economic and cultural orders. In the final section I sketch briefly the implications of this analysis in the context of ongoing globalization processes. It is suggested that the most effective way to establish a just system of global governance is to equalize effective communicative freedom among nation-states.

Tenant Right and Agrarian Society in Ulster 1600-1870

The book has been described by various Irish historians as "the definitive treatment of that most peculiar institution--the Ulster Custom--and its tangled relationship with irish land and politics" (Liam Kennedy), "a brilliantly reconceptualised sketch of the Irish land question" (David Miller). "All previous discussion," according to another reviewer, "must take second place to Dowling's exhaustive survey, which draws on the whole range of surviving estate records to examine the theory and practice of tenant right across three centuries" (Sean Connolly).

Information-flux approach to multiple-spin dynamics

We introduce and formalize the concept of information flux in a many-body register as the influence that the dynamics of a specific element receive from any other element of the register. By quantifying the information flux in a protocol, we can design the most appropriate initial state of the system and, noticeably, the distribution of coupling strengths among the parts of the register itself. The intuitive nature of this tool and its flexibility, which allow for easily manageable numerical approaches when analytic expressions are not straightforward, are greatly useful in interacting many-body systems such as quantum spin chains. We illustrate the use of this concept in quantum cloning and quantum state transfer and we also sketch its extension to nonunitary dynamics.

Introduction

The scholarly interest in norm implementation in the area of minority rights protection emerged during the period of the European accession of post-communist societies, which were characterised by persistent cleavage along ethnic lines. These studies have analysed democratic transition of ethnically segmented societies and developed into a broad field that focuses its attention on inter-ethnic relations, the role of history, interstate cooperation and the impact of international organisations on post-communist states' treatment of domestic minorities. All these are usually conducted from a vantage point of the European conditionality research. In our introduction to the special issue we sketch a number of reasons why it is encouraging and indeed, desirable to move beyond the perusal of conditionality into the domain of implementation research.

Through the lens of the hospital magazine - Downshire and Holywell psychiatric hospitals in the 1960s and 1970s

An exploration of the pages of two psychiatric hospital magazines, Speedwell from Holywell Hospital, Antrim, and The Sketch from Downshire Hospital, Downpatrick, reveals the activity filled lives of patients and staff during the 1960s and 1970s. This was a time of great change in mental health care. It was also a time of political turbulence in Northern Ireland. With large in-patient populations, both hospitals had a range of occupational and sporting activities available to patients and staff. The magazines formed part of the effort to promote the ethos of a therapeutic community. While hospital magazines may be viewed as one aspect of an institutional system that allowed people to cut themselves from the wider society, they also provided opportunities for budding writers to express their views on life in a hospital from the service user perspective. As such they offer some valuable insights into the lives of psychiatric patients.

An efficient unbounded lock-free queue for multi-core systems

The use of efficient synchronization mechanisms is crucial for implementing fine grained parallel programs on modern shared cache multi-core architectures. In this paper we study this problem by considering Single-Producer/Single- Consumer (SPSC) coordination using unbounded queues. A novel unbounded SPSC algorithm capable of reducing the row synchronization latency and speeding up Producer-Consumer coordination is presented. The algorithm has been extensively tested on a shared-cache multi-core platform and a sketch proof of correctness is presented. The queues proposed have been used as basic building blocks to implement the FastFlow parallel framework, which has been demonstrated to offer very good performance for fine-grain parallel applications. © 2012 Springer-Verlag.

Tomographic characterisation of correlations in a photonic tripartite state

Starting from a four-partite photonic hyper-entangled Dicke resource, we report the full tomographic characterization of three-, two-, and one-qubit states obtained by projecting out part of the computational register. The reduced states thus obtained correspond to fidelities with the expected states larger than 87%, therefore certifying the faithfulness of the entanglement-sharing structure within the original four-qubit resource. The high quality of the reduced three-qubit state allows for the experimental verification of the Koashi-Winter relation for the monogamy of correlations within a tripartite state. We show that, by exploiting the symmetries of the three-qubit state obtained upon projection over the four-qubit Dicke resource, such relation can be experimentally fully characterized using only 5 measurement settings. We highlight the limitations of such approach and sketch an experimentally-oriented way to overcome them.

Beyond the National Resource Privilege: towards an International Court of the Environment

The national resource privilege, which holds that states are allowed to control all the natural resources found in their territory, is a cornerstone of international politics. Supporters of the national resource privilege claim that without the privilege states would fail to be sovereign and self-determining entities which provide for the needs of their citizens. However, as this paper shows the case is not as simple as that. In fact, control over resources must be carefully unpacked. Doing so shows that states do not require full control over all resources found in their territory in order to be sovereign. Moreover, sovereignty and self-determination come with a set of responsibilities and duties attached. Based on these observations the paper will sketch the contours of an alternative resource governance scheme built around the idea of an International Court of the Environment.

Preface Writers Are Consistent

The preface paradox does not show that it can be rational to have inconsistent beliefs, because preface writers do not have inconsistent beliefs. I argue, first, that a fully satisfactory solution to the preface paradox would have it that the preface writer's beliefs are consistent. The case here is on basic intuitive grounds, not the consequence of a theory of rationality or of belief. Second, I point out that there is an independently motivated theory of belief--sensitivism--which allows such a solution. I sketch a sensitivist account of the preface writer's (consistent) doxastic state.