Complete eigenstates of identical qubits arranged in regular polygons

We calculate the energy eigenvalues and eigenstates corresponding to coherent single and multiple excitations of an array of N identical qubits or two-level atoms (TLA's) arranged on the vertices of a regular polygon. We assume only that the coupling occurs via an exchange interaction which depends on the separation between the qubits. We include the interactions between all pairs of qubits, and our results are valid for arbitrary distances relative to the radiation wavelength. To illustrate the usefulness of these states, we plot the distance dependence of the decay rates of the n=2 (biexciton) eigenstates of an array of 4 qubits, and tabulate the biexciton eigenvalues and eigenstates, and absorption frequencies, line widths, and relative intensities for polygons consisting of N=2,...,9 qubits in the long-wavelength limit.Comment: Added a figure showing how these results can be used to compute deviations from "equal collective decoherence" approximation

Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking

Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of interactive molecular dynamics in virtual reality (iMD-VR) as an accurate low-cost strategy for flexible protein-ligand docking. We outline an experimental protocol which enables expert iMD-VR users to guide ligands into and out of the binding pockets of trypsin, neuraminidase, and HIV-1 protease, and recreate their respective crystallographic protein-ligand binding poses within 5 - 10 minutes. Following a brief training phase, our studies shown that iMD-VR novices were able to generate unbinding and rebinding pathways on similar timescales as iMD-VR experts, with the majority able to recover binding poses within 2.15 Angstrom RMSD of the crystallographic binding pose. These results indicate that iMD-VR affords sufficient control for users to carry out the detailed atomic manipulations required to dock flexible ligands into dynamic enzyme active sites and recover crystallographic poses, offering an interesting new approach for simulating drug docking and generating binding hypotheses.Comment: PLOS ON

Sampling molecular conformations and dynamics in a multiuser virtual reality framework

Copyright © 2018 The Authors, some rights reserved. We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic physics simulations with commodity VR hardware, which we have made accessible to readers (see isci.itch.io/nsb-imd). It allows users to visualize and sample, with atomic-level precision, the structures and dynamics of complex molecular structures “on the fly” and to interact with other users in the same virtual environment. A series of controlled studies, in which participants were tasked with a range of molecular manipulation goals (threading methane through a nanotube, changing helical screw sense, and tying a protein knot), quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modeling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically three-dimensional. This framework should accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug development, synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where three-dimensional dynamics matter, spanning research and education

Modelling phosphorus in Lake Simcoe and its subcatchments: scenario analysis to assess alternative management strategies

In Lake Simcoe (Ontario, Canada), anthropogenic phosphorus (P) loads have contributed to increased algal growth, low hypolimnetic dissolved oxygen concentrations, and impaired fish reproduction. Management targets to control eutrophication require an ambitious programme to reduce P loads to the lake. Remediation strategies rely upon an improved understanding of P sources and assessment of the effectiveness of different control options. Here we present an application of the integrated catchment model for phosphorus (INCA-P) to examine P sources across the Lake Simcoe watershed and simulate in-lake P concentrations. This is the first application of INCA-P to a complex watershed of this nature and the first to include a lake component. We evaluated a set of management actions to simulate anticipated effects of P reduction strategies on in-lake total phosphorus (TP) concentrations. The INCA-P scenarios show the difficulty of achieving large-scale reductions from the watershed, given the low rates of P export; however, the study shows that a multifaceted strategy, including fertilizer reduction, addition of buffer strips, more stringent controls on sewage treatment plant effluent, and reduced deposition of P to the lake surface, could achieve a 25% reduction in lake-water TP concentrations and produce TP close to the target of 0.01 mg L−1

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

© 2019 Author(s). As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures

Future-oriented constructs and their role in suicidal ideation and enactment

Despite the heavy focus upon risk factors for suicide, the presence or absence of protective factors are also instrumental in individuals’ vulnerability for developing suicidal ideation and behaviours. Future oriented constructs, including future thinking, future orientation, hope and optimism have been associated with suicidal ideation and behaviour; individuals who are less able to generate positive thoughts about the future, and those are less hopeful and optimistic are more likely to think about or engage in suicidal behaviours. The content and expectations of future thoughts as achievable also play a key role in their protective capacity. Within this chapter we discuss the relationships between future orientated constructs and suicidal ideation and behaviour, as well as potential mediators of these relationships, within the context of the new generation of ideation-to-action frameworks of suicidal behaviour. We also highlight challenges and opportunities for future research and intervention development for suicidal thoughts and behaviours using future oriented constructs