Gaussian processes for choosing laser parameters for driven, dissipative Rydberg aggregates

To facilitate quantum simulation of open quantum systems at finite temperatures, an important ingredient is to achieve thermalization on a given time-scale. We consider a Rydberg aggregate (an arrangement of Rydberg atoms that interact via long-range interactions) embedded in a laser-driven atomic environment. For the smallest aggregate (two atoms), suitable laser parameters can be found by brute force scanning of the four tunable laser parameters. For more atoms, however, such parameter scans are too computationally costly. Here we apply Gaussian processes to predict the thermalization performance as a function of the laser parameters for two-atom and four-atom aggregates. These predictions perform remarkably well using just 1000 simulations, demonstrating the utility of Gaussian processes in an atomic physics setting. Using this approach, we find and present effective laser parameters for generating thermalization, the robustness of these parameters to variation, as well as different thermalization dynamics

Flexible scheme to truncate the hierarchy of pure states

The hierarchy of pure states (HOPS) is a wavefunction-based method which can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a 'good' truncation method, where by 'good' we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work we demonstrate the application of the '$n$-particle approximation' ($n$PA) to HOPS. We also introduce a new approximation, which we call the '$n$-mode approximation' ($n$MA). We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy. We show that truncation approximations can be used in combination to achieve convergence in two exemplary problems: absorption and energy transfer of molecular aggregates.Comment: 8 pages, 3 figure

Fast gates for ion traps by splitting laser pulses

We present a fast phase gate scheme that is experimentally achievable and has an operation time more than two orders of magnitude faster than current experimental schemes for low numbers of pulses. The gate time improves with the number of pulses following an inverse power law. Unlike implemented schemes which excite precise motional sidebands, thus limiting the gate timescale, our scheme excites multiple motional states using discrete ultra-fast pulses.We use beam-splitters to divide pulses into smaller components to overcome limitations due to the finite laser pulse repetition rate. This provides gate times faster than proposed theoretical schemes when we optimize a practical setup

Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi

Objectives This study aimed to define the molecular basis of co-trimoxazole resistance in Malawian pneumococci under the dual selective pressure of widespread co-trimoxazole and sulfadoxine/pyrimethamine use. Methods We measured the trimethoprim and sulfamethoxazole MICs and analysed folA and folP nucleotide and translated amino acid sequences for 143 pneumococci isolated from carriage and invasive disease in Malawi (2002–08). Results Pneumococci were highly resistant to both trimethoprim and sulfamethoxazole (96%, 137/143). Sulfamethoxazole-resistant isolates showed a 3 or 6 bp insertion in the sulphonamide-binding site of folP. The trimethoprim-resistant isolates fell into three genotypic groups based on dihydrofolate reductase (encoded by folA) mutations: Ile-100-Leu (10%), the Ile-100-Leu substitution together with a residue 92 substitution (56%) and those with a novel uncharacterized resistance genotype (34%). The nucleotide sequence divergence and dN/dS of folA and folP remained stable from 2004 onwards. Conclusions S. pneumoniae exhibit almost universal co-trimoxazole resistance in vitro and in silico that we believe is driven by extensive co-trimoxazole and sulfadoxine/pyrimethamine use. More than one-third of pneumococci employ a novel mechanism of co-trimoxazole resistance. Resistance has now reached a point of stabilizing evolution. The use of co-trimoxazole to prevent pneumococcal infection in HIV/AIDS patients in sub-Saharan Africa should be re-evaluated

Flare energetics

In this investigation of flare energetics, researchers sought to establish a comprehensive and self-consistent picture of the sources and transport of energy within a flare. To achieve this goal, they chose five flares in 1980 that were well observed with instruments on the Solar Maximum Mission, and with other space-borne and ground-based instruments. The events were chosen to represent various types of flares. Details of the observations available for them and the corresponding physical parameters derived from these data are presented. The flares were studied from two perspectives, the impulsive and gradual phases, and then the results were compared to obtain the overall picture of the energics of these flares. The role that modeling can play in estimating the total energy of a flare when the observationally determined parameters are used as the input to a numerical model is discussed. Finally, a critique of the current understanding of flare energetics and the methods used to determine various energetics terms is outlined, and possible future directions of research in this area are suggested

Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process

Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then 'unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. The process has parallels with paper folding sequences that arise when a piece of paper is folded several times and then unfolded. Here we adapt such methods to study the breakage-fusion-bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are 2^(n(n-1)/2) qualitatively distinct evolutions involving n breakage-fusion-bridge cycles. Secondly we consider the stochastic nature of the fold positions, to determine evolution likelihoods, and also describe how amplicons become localised. Finally we highlight these methods by inferring the evolution of breakage-fusion-bridge cycles with data from primary tissue cancer samples

Telemedicine and cystic fibrosis:Do we still need face-to-face clinics?

There has been growing interest in telemedicine for cystic fibrosis over recent years based largely on convenience for patients and/or increasing the frequency of surveillance and early detection which, it is assumed, could improve treatment outcomes. During 2020, the covid-19 pandemic catalysed the pace of development of this field, as CF patients were presumed to be at high risk of infection. Most clinics adapted to digital platforms with provision of lung function monitoring and sample collection systems. Here, we present the views of multidisciplinary team members at a large paediatric CF centre on what has worked well and what requires further optimisation in the future. In response to the question posed, ‘Do we still need face to face clinics?’ our answer is ‘Yes, but not every time, and not for everyone’.</p

A well-separated pairs decomposition algorithm for k-d trees implemented on multi-core architectures

Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.Variations of k-d trees represent a fundamental data structure used in Computational Geometry with numerous applications in science. For example particle track tting in the software of the LHC experiments, and in simulations of N-body systems in the study of dynamics of interacting galaxies, particle beam physics, and molecular dynamics in biochemistry. The many-body tree methods devised by Barnes and Hutt in the 1980s and the Fast Multipole Method introduced in 1987 by Greengard and Rokhlin use variants of k-d trees to reduce the computation time upper bounds to O(n log n) and even O(n) from O(n2). We present an algorithm that uses the principle of well-separated pairs decomposition to always produce compressed trees in O(n log n) work. We present and evaluate parallel implementations for the algorithm that can take advantage of multi-core architectures.The Science and Technology Facilities Council, UK