Interacting with the biomolecular solvent accessible surface via a haptic feedback device

Background: From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results: A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion: By using the software, named HaptiMol ISAS (available from http://​www.​haptimol.​co.​uk), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software

Energy of gravitational radiation in plane-symmetric space-times

Gravitational radiation in plane-symmetric space-times can be encoded in a complex potential, satisfying a non-linear wave equation. An effective energy tensor for the radiation is given, taking a scalar-field form in terms of the potential, entering the field equations in the same way as the matter energy tensor. It reduces to the Isaacson energy tensor in the linearized, high-frequency approximation. An energy conservation equation is derived for a quasi-local energy, essentially the Hawking energy. A transverse pressure exerted by interacting low-frequency gravitational radiation is predicted.Comment: 7 REVTeX4 page

Unified first law of black-hole dynamics and relativistic thermodynamics

A unified first law of black-hole dynamics and relativistic thermodynamics is derived in spherically symmetric general relativity. This equation expresses the gradient of the active gravitational energy E according to the Einstein equation, divided into energy-supply and work terms. Projecting the equation along the flow of thermodynamic matter and along the trapping horizon of a blackhole yield, respectively, first laws of relativistic thermodynamics and black-hole dynamics. In the black-hole case, this first law has the same form as the first law of black-hole statics, with static perturbations replaced by the derivative along the horizon. There is the expected term involving the area and surface gravity, where the dynamic surface gravity is defined as in the static case but using the Kodama vector and trapping horizon. This surface gravity vanishes for degenerate trapping horizons and satisfies certain expected inequalities involving the area and energy. In the thermodynamic case, the quasi-local first law has the same form, apart from a relativistic factor, as the classical first law of thermodynamics, involving heat supply and hydrodynamic work, but with E replacing the internal energy. Expanding E in the Newtonian limit shows that it incorporates the Newtonian mass, kinetic energy, gravitational potential energy and thermal energy. There is also a weak type of unified zeroth law: a Gibbs-like definition of thermal equilibrium requires constancy of an effective temperature, generalising the Tolman condition and the particular case of Hawking radiation, while gravithermal equilibrium further requires constancy of surface gravity. Finally, it is suggested that the energy operator of spherically symmetric quantum gravity is determined by the Kodama vector, which encodes a dynamic time related to E.Comment: 18 pages, TeX, expanded somewhat, to appear in Class. Quantum Gra

The bias of the submillimetre galaxy population: SMGs are poor tracers of the most massive structures in the z ~ 2 Universe

It is often claimed that overdensities of (or even individual bright) submillimetre-selected galaxies (SMGs) trace the assembly of the most-massive dark matter structures in the Universe. We test this claim by performing a counts-in-cells analysis of mock SMG catalogues derived from the Bolshoi cosmological simulation to investigate how well SMG associations trace the underlying dark matter structure. We find that SMGs exhibit a relatively complex bias: some regions of high SMG overdensity are underdense in terms of dark matter mass, and some regions of high dark matter overdensity contain no SMGs. Because of their rarity, Poisson noise causes scatter in the SMG overdensity at fixed dark matter overdensity. Consequently, rich associations of less-luminous, more-abundant galaxies (i.e. Lyman-break galaxy analogues) trace the highest dark matter overdensities much better than SMGs. Even on average, SMG associations are relatively poor tracers of the most significant dark matter overdensities because of 'downsizing': at z < ~2.5, the most-massive galaxies that reside in the highest dark matter overdensities have already had their star formation quenched and are thus no longer SMGs. At a given redshift, of the 10 per cent most-massive overdensities, only ~25 per cent contain at least one SMG, and less than a few per cent contain more than one SMG.Comment: 6 pages, 3 figures, 1 table; accepted for publication in MNRAS; minor revisions from previous version, conclusions unchange

A complete distribution of redshifts for sub-millimetre galaxies in the SCUBA-2 Cosmology Legacy Survey UDS field

This is a pre-copyedited, author-produced PDF of an article accepted for publication in Monthly Notices of the Royal Astronomical Society following peer review. Available online at https://doi.org/10.1093/mnras/stx1689. © 2017 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Sub-milllimetre galaxies (SMGs) are some of the most luminous star-forming galaxies in the Universe, however their properties remain hard to determine due to the difficulty of identifying their optical\slash near-infrared counterparts. One of the key steps to determining the nature of SMGs is measuring a redshift distribution representative of the whole population. We do this by applying statistical techniques to a sample of 761 850$\mu$m sources from the SCUBA-2 Cosmology Legacy Survey observations of the UKIDSS Ultra-Deep Survey (UDS) Field. We detect excess galaxies around $> 98.4$ per cent of the 850$\mu$m positions in the deep UDS catalogue, giving us the first 850$\mu$m selected sample to have virtually complete optical\slash near-infrared redshift information. Under the reasonable assumption that the redshifts of the excess galaxies are representative of the SMGs themselves, we derive a median SMG redshift of $z = 2.05 \pm 0.03$, with 68 per cent of SMGs residing between $1.07Peer reviewedFinal Accepted Versio

A Systematic Review and Thematic Synthesis of Qualitative Literature on Personal Recovery and Voice Hearing.

Personal recovery literature has been influential in the conceptualisation of emotional distress and service provision. While personal recovery in psychosis has been well-studied, voice hearing literature has not been reviewed to elucidate recovery processes. Five databases were systematically searched to identify relevant qualitative recovery literature. 12 eligible studies were included in this review and an appraisal tool was applied to assess quality. Thematic synthesis was used to examine results. Three superordinate themes were found relating to 'Recovery Phases', 'Recovery Facilitators' and 'Barriers to Recovery'. Papers included descriptions of finding voices distressing initially yet moving toward integrating and accepting voices. Searching for meaning versus seeking distance from voices were pivotal processes to recovery pathways. Enabling and disrupting recovery experiences are discussed within a proposed model. Recovery in voice hearing is an individual and potentially ongoing process. Future research should seek to examine recovery factors in voice hearing longitudinally and add further evidence to the supportive role services can play in recovery and voice hearing. [Abstract copyright: This article is protected by copyright. All rights reserved.

A Cosmological Constant Limits the Size of Black Holes

In a space-time with cosmological constant $\Lambda>0$ and matter satisfying the dominant energy condition, the area of a black or white hole cannot exceed $4\pi/\Lambda$. This applies to event horizons where defined, i.e. in an asymptotically deSitter space-time, and to outer trapping horizons (cf. apparent horizons) in any space-time. The bound is attained if and only if the horizon is identical to that of the degenerate `Schwarzschild-deSitter' solution. This yields a topological restriction on the event horizon, namely that components whose total area exceeds $4\pi/\Lambda$ cannot merge. We discuss the conjectured isoperimetric inequality and implications for the cosmic censorship conjecture.Comment: 10 page

A Reverse Hex Solver

We present Solrex,an automated solver for the game of Reverse Hex.Reverse Hex, also known as Rex, or Misere Hex, is the variant of the game of Hex in which the player who joins her two sides loses the game. Solrex performs a mini-max search of the state space using Scalable Parallel Depth First Proof Number Search, enhanced by the pruning of inferior moves and the early detection of certain winning strategies. Solrex is implemented on the same code base as the Hex program Solver, and can solve arbitrary positions on board sizes up to 6x6, with the hardest position taking less than four hours on four threads.Comment: Presented at Computers and Games 2016 Leiden, International Conference on Computers and Games. Springer International Publishing, 201