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.

The Analogical Peacock Hypothesis: The Sexual Selection of Mind-Reading and Relational Cognition in Human Communication

This integrative review presents a novel hypothesis as a basis for integrating two evolutionary viewpoints on the origins of human cognition and communication, the sexual selection of human mental capacities, and the social brain hypothesis. This new account suggests that mind-reading social skills increased reproductive success and consequently became targets for sexual selection. The hypothesis proposes that human communication has three purposes: displaying mind-reading abilities, aligning and maintaining representational parity between individuals to enable displays, and the exchange of propositional information. Intelligence, creativity, language, and humor are mental fitness indicators that signal an individual’s quality to potential mates, rivals, and allies. Five features central to the proposed display mechanism unify these indicators, the relational combination of concepts, large conceptual knowledge networks, processing speed, contextualization, and receiver knowledge. Sufficient between-mind alignment of conceptual networks allows displays based upon within-mind conceptual mappings. Creative displays communicate previously unnoticed relational connections and novel conceptual combinations demonstrating an ability to read a receiver’s mind. Displays are costly signals of mate quality with costs incurred in the developmental production of the neural apparatus required to engage in complex displays and opportunity costs incurred through time spent acquiring cultural knowledge. Displays that are fast, novel, spontaneous, contextual, topical, and relevant are hard-to-fake for lower quality individuals. Successful displays result in elevated social status and increased mating options. The review addresses literatures on costly signaling, sexual selection, mental fitness indicators, and the social brain hypothesis; drawing implications for nonverbal and verbal communication.

Invariant Information Local Sub-map Filter (IILSF) for Efficient Simultaneous Localisation and Mapping of Large Environments

This paper presents an Invariant Information Local Sub-map Filter (IILSF) as a technique for consistent Simultaneous Localisation and Mapping (SLAM) in a large environment. It harnesses the benefits of sub-map technique to improve the consistency and efficiency of Extended Kalman Filter (EKF) based SLAM. The IILSF makes use of invariant information obtained from estimated locations of features in independent sub-maps, instead of incorporating every observation directly into the global map. Then the global map is updated at regular intervals. Applying this technique to the EKF based SLAM algorithm: (a) reduces the computational complexity of maintaining the global map estimates and (b) simplifies transformation complexities and data association ambiguities usually experienced in fusing sub-maps together. Simulation results show that the method was able to accurately fuse local map observations to generate an efficient and consistent global map, in addition to significantly reducing computational cost and data association ambiguities.

When our thoughts are not our own: Investigating agency misattributions using the Mind-to-Mind paradigm

At the core ofthe sense ofagency for self-produced action is the sense that I, and not some other agent, am producing and directing those actions. While there is an ever-expanding body of empirical research investigating the sense of agency for bodily action, there has, to date, been little empirical investigation of the sense ofagency for thought.The present study uses the novel Mind-to-Mind paradigm, in which the agentive source of a target thought is ambiguous, to measure misattributions of agency. Seventy-two percent of participants made at least one misattribution of agency during a 5-min trial. Misattributions were significantly more frequent when the target thought was an arousing negative thought as compared to a neutral control.The findings establish a novel protocol for measuring the sense of agency for thought, and suggest that both contextual factors and emotional experience play a role in its generation.

Peer effects in UK adolescent substance use: Never mind the classmates?

This article estimates peer influences on the alcohol, tobacco and cannabis use of UK adolescents. We present evidence of large, positive and statistically significant peer effects in all three behaviours when classmates are taken as the reference group. We also find large, positive and statistically significant associations between own substance use and friends' substance use. When both reference groups are considered simultaneously, the influence of classmates either disappears or is much reduced, whereas the association between own and friends' behaviours does not change. The suggestion is that classmate behaviour is primarily relevant only inasmuch as it proxies for friends' behaviour.

The Map Defines the Territory: Remodelling NGO Partnerships for Knowledge Translation in Transition Contexts

The initial impetus for a theoretical exploration of organisational relationships is based on case study research on a Bulgarian NGO's implementation of values and goals into practices under a guiding relationship from a very experienced UK organisation in the same field. Findings diverged from conventional accounts of developing NGOs' dependence on more developed counterparts and that case study findings characterised the inter- dependency between the two organisations as more alike to a collaborative knowledge ...

The Map of Watchful Architecture

The international border between Northern Ireland and the South (the Republic of Ireland) came into being in 1922, but there are many important historical antecedents to the notion and expression of spatial separation in this borderland. The author identifies historical precedents and links them to recent defensive features in order to generate a 'map of watchful architecture' that includes recent and much older elements.

Fictional Ulster:A map of places created by writers

Ballybeg, the fictitious setting for Brian Friel’s plays, is more famous than most real villages in Ulster. Despite not existing, the village has a kind of cultural and geographic life. This is part of what this map is about. It locates and charts Ulster’s fictional places — places invented by writers down through the years. These places have meaning too, they are part of how Ulster pictures itself and how others picture Ulster.

The Map of Connections 3.1: Unofficial and previously unmapped Irish border crossings

I charted unofficial border-crossings along Ireland's border, those not found on any other map.

During many surveys of Ireland's border I discovered that it is often perforated. Gates are set in hedgerows for the convenience of farmers, stepping stones and community-built bridges span rivers, walkers’ routes and muddy by-ways go wherever they please. These kinds of connections have always been there, although I think it is fair to say that their numbers have increased during the Peace Process. Roads blocked or cratered during the Troubles are being re-connected at a rate too fast for the Ordnance Survey to keep up with. On the local level cross-border movement is quietly happening, unchecked and often unmapped, until now.

This map attempts to throw the borderline in perpendicular, showing it as a place of connection rather than division.

The Map of Watchful Architecture 2.0:Defensive forms along Ireland's border

For The Map of Watchful Architecture I only concerned myself with defensive architecture along the Border. As the map followed a border it came out as a wavy line of points. This was largely artificial, I only charted architecture within the Border corridor, but was not entirely artificial. That linear landscape has long been staked-out by the regularity of certain kinds of architecture. The 1st/2nd century Black Pig’s Dyke and Dorsey correspond with today’s Border. The concentration of souterrains in north Louth indicate that it may have been a volatile interface zone in later centuries. In 1618 Londonderry and its walls were built. Further north and two centuries later, Martello Towers were constructed to watch over Lough Foyle. During the Second World War pillboxes and observation posts were manned along the Border, close to what was now an international frontier. Then came the Operation Banner installations built during The Troubles. All this adds up to be one of the longest unbroken traditions of defensive architecture anywhere in Western Europe, a tradition some thought finally broken as the last of the Operation Banner towers were de-installed in 2007. But, take a bus south across the Border and you will often be pulled over by the Garda Síochána. They ID check the passengers in an attempt to stop illegal immigration via the UK. What about illegal immigrants who walk through the fields or along quiet lanes? They will have understood the Border is not really how it seems on most maps. It is not a solid line, it is a row of points.

Integrated Earth Resistivity Tomography (ERT) and Multilevel Gas Sampling: A Tool to Map Geogenic and Anthropogenic Methane Accumulation on Brownfield Sites

Soil gas emissions of methane and carbon dioxide on brownfield sites are usually attributed to anthropogenic activities; however geogenic sources of soil gas are often not considered during site investigation and risk management strategies. This paper presents a field study at a redeveloped brownfield site on a flood plain to identify accumulations of methane biogas trapped in underlying sediments. The investigation is based on a multidisciplinary approach using direct multi-level sampling measurements and Earth resistivity tomography . Resistivity imaging was applied to evaluate the feasibility of identifying the size and spatial continuity of soil gas accumulations in anthropogenic and naturally occurring deposits. As a result, biogas accumulations are described within both anthropogenic deposits and pristine organic sediments. This result is important to identify the correct approaches to identify and manage risks associated with soil gas emissions on brownfield and pristine sites. The organic-rich sediments in Quaternary fluvial environments of São Paulo Basin in particular the Tietê River, biogas reservoirs can be generated and trapped beneath geogenic and anthropogenic layers, potentially requiring the management of brownfield developments across this region.