Nonadiabatic approach to dimerization gap and optical absorption coefficient of the Su-Schrieffer-Heeger model

An analytical nonadiabatic approach has been developed to study the dimerization gap and the optical absorption coefficient of the Su-Schrieffer-Heeger model where the electrons interact with dispersive quantum phonons. By investigating quantitatively the effects of quantum phonon fluctuations on the gap order and the optical responses in this system, we show that the dimerization gap is much more reduced by the quantum lattice fluctuations than the optical absorption coefficient is. The calculated optical absorption coefficient and the density of states do not have the inverse-square-root singularity, but have a peak above the gap edge and there exist a significant tail below the peak. The peak of optical absorption spectrum is not directly corresponding to the dimerized gap. Our results of the optical absorption coefficient agree well with those of the experiments in both the shape and the peak position of the optical absorption spectrum.Comment: 14 pages, 7 figures. to be published in PR

Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins

Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we describe computer simulations of a few related model systems. The dynamics of collapse of eicosane shows that upon expulsion of water the linear hydrocarbon chain adopts an ordered helical hairpin structure with 1.5 turns. The structure of dimer of eicosane molecules has two well ordered helical hairpins that are stacked perpendicular to each other. As a prelude to studying folding in confined spaces we used simulations to understand changes in hydrophobic and ionic interactions in nano droplets. Solvation of hydrophobic and charged species change drastically in nano water droplets. Hydrophobic species are localized at the boundary. The tendency of ions to be at the boundary where water density is low increases as the charge density decreases. Interaction between hydrophobic, polar, and charged residue are also profoundly altered in confined spaces. Using the results of computer simulations and accounting for loss of chain entropy upon confinement we argue and then demonstrate, using simulations in explicit water, that ordered states of generic amphiphilic peptide sequences should be stabilized in cylindrical nanopores

Against all odds? Forming the planet of the HD196885 binary

HD196885Ab is the most "extreme" planet-in-a-binary discovered to date, whose orbit places it at the limit for orbital stability. The presence of a planet in such a highly perturbed region poses a clear challenge to planet-formation scenarios. We investigate this issue by focusing on the planet-formation stage that is arguably the most sensitive to binary perturbations: the mutual accretion of kilometre-sized planetesimals. To this effect we numerically estimate the impact velocities $dv$ amongst a population of circumprimary planetesimals. We find that most of the circumprimary disc is strongly hostile to planetesimal accretion, especially the region around 2.6AU (the planet's location) where binary perturbations induce planetesimal-shattering $dv$ of more than 1km/s. Possible solutions to the paradox of having a planet in such accretion-hostile regions are 1) that initial planetesimals were very big, at least 250km, 2) that the binary had an initial orbit at least twice the present one, and was later compacted due to early stellar encounters, 3) that planetesimals did not grow by mutual impacts but by sweeping of dust (the "snowball" growth mode identified by Xie et al., 2010b), or 4) that HD196885Ab was formed not by core-accretion but by the concurent disc instability mechanism. All of these 4 scenarios remain however highly conjectural.Comment: accepted for publication by Celestial Mechanics and Dynamical Astronomy (Special issue on EXOPLANETS

Distinct clinical symptom patterns in patients hospitalised with COVID-19 in an analysis of 59,011 patients in the ISARIC-4C study

COVID-19 is clinically characterised by fever, cough, and dyspnoea. Symptoms affecting other organ systems have been reported. However, it is the clinical associations of different patterns of symptoms which influence diagnostic and therapeutic decision-making. In this study, we applied clustering techniques to a large prospective cohort of hospitalised patients with COVID-19 to identify clinically meaningful sub-phenotypes. We obtained structured clinical data on 59,011 patients in the UK (the ISARIC Coronavirus Clinical Characterisation Consortium, 4C) and used a principled, unsupervised clustering approach to partition the first 25,477 cases according to symptoms reported at recruitment. We validated our findings in a second group of 33,534 cases recruited to ISARIC-4C, and in 4,445 cases recruited to a separate study of community cases. Unsupervised clustering identified distinct sub-phenotypes. First, a core symptom set of fever, cough, and dyspnoea, which co-occurred with additional symptoms in three further patterns: fatigue and confusion, diarrhoea and vomiting, or productive cough. Presentations with a single reported symptom of dyspnoea or confusion were also identified, alongside a sub-phenotype of patients reporting few or no symptoms. Patients presenting with gastrointestinal symptoms were more commonly female, had a longer duration of symptoms before presentation, and had lower 30-day mortality. Patients presenting with confusion, with or without core symptoms, were older and had a higher unadjusted mortality. Symptom sub-phenotypes were highly consistent in replication analysis within the ISARIC-4C study. Similar patterns were externally verified in patients from a study of self-reported symptoms of mild disease. The large scale of the ISARIC-4C study enabled robust, granular discovery and replication. Clinical interpretation is necessary to determine which of these observations have practical utility. We propose that four sub-phenotypes are usefully distinct from the core symptom group: gastro-intestinal disease, productive cough, confusion, and pauci-symptomatic presentations. Importantly, each is associated with an in-hospital mortality which differs from that of patients with core symptoms

Delayed mucosal antiviral responses despite robust peripheral inflammation in fatal COVID-19

Background While inflammatory and immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in peripheral blood are extensively described, responses at the upper respiratory mucosal site of initial infection are relatively poorly defined. We sought to identify mucosal cytokine/chemokine signatures that distinguished coronavirus disease 2019 (COVID-19) severity categories, and relate these to disease progression and peripheral inflammation. Methods We measured 35 cytokines and chemokines in nasal samples from 274 patients hospitalized with COVID-19. Analysis considered the timing of sampling during disease, as either the early (0–5 days after symptom onset) or late (6–20 days after symptom onset) phase. Results Patients that survived severe COVID-19 showed interferon (IFN)-dominated mucosal immune responses (IFN-γ, CXCL10, and CXCL13) early in infection. These early mucosal responses were absent in patients who would progress to fatal disease despite equivalent SARS-CoV-2 viral load. Mucosal inflammation in later disease was dominated by interleukin 2 (IL-2), IL-10, IFN-γ, and IL-12p70, which scaled with severity but did not differentiate patients who would survive or succumb to disease. Cytokines and chemokines in the mucosa showed distinctions from responses evident in the peripheral blood, particularly during fatal disease. Conclusions Defective early mucosal antiviral responses anticipate fatal COVID-19 but are not associated with viral load. Early mucosal immune responses may define the trajectory of severe COVID-19