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The severity of the COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, calls for the urgent development of a vaccine. The primary immunological target is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface to mediate viral entry into the host cell. To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. We find that the extensive and inherently flexible glycan coat shields a surface area larger than expected from static structures, highlighting the importance of structural dynamics in epitope mapping.
Disordered proteins and nucleic acids can condense into droplets that resemble the membraneless organelles observed in living cells. MD simulations offer a unique tool to characterize the molecular interactions governing the formation of these biomolecular condensates, their physicochemical properties, and the factors controlling their composition and size. However, biopolymer condensation depends sensitively on the balance between different energetic and entropic contributions. Here, we develop a general strategy to fine-tune the potential energy function for molecular dynamics simulations of biopolymer phase separation. We rebalance protein–protein interactions against solvation and entropic contributions to match the excess free energy of transferring proteins between dilute solution and condensate. We illustrate this formalism by simulating liquid droplet formation of the FUS low-complexity domain (LCD) with a rebalanced MARTINI model. By scaling the strength of the nonbonded interactions in the coarse-grained MARTINI potential energy function, we map out a phase diagram in the plane of protein concentration and interaction strength. Above a critical scaling factor of αc ≈ 0.6, FUS-LCD condensation is observed, where α = 1 and 0 correspond to full and repulsive interactions in the MARTINI model. For a scaling factor α = 0.65, we recover experimental densities of the dilute and dense phases, and thus the excess protein transfer free energy into the droplet and the saturation concentration where FUS-LCD condenses. In the region of phase separation, we simulate FUS-LCD droplets of four different sizes in stable equilibrium with the dilute phase and slabs of condensed FUS-LCD for tens of microseconds, and over one millisecond in aggregate. We determine surface tensions in the range of 0.01–0.4 mN/m from the fluctuations of the droplet shape and from the capillary-wave-like broadening of the interface between the two phases. From the dynamics of the protein end-to-end distance, we estimate shear viscosities from 0.001 to 0.02 Pa s for the FUS-LCD droplets with scaling factors α in the range of 0.625–0.75, where we observe liquid droplets. Significant hydration of the interior of the droplets keeps the proteins mobile and the droplets fluid.
The scalar glueball G is the lightest particle of the Yang–Mills sector of QCD, with a lattice predicted mass of about mG≃1.7GeV. It is natural to investigate glueball-glueball scattering and the possible emergence of a bound state, that we call glueballonium. We perform this study in the context of a widely used dilaton potential, that depends on a single dimensionful parameter ΛG. We consider a unitarization prescription that allows us to predict the lowest partial waves in the elastic window. These quantities can be in principle calculated on the lattice, thus offering possibility for testing the validity of the dilaton potential and an independent determination of its parameter. Moreover, we also show that a stable glueballonium exists if ΛG is small enough. In particular, for ΛG compatible with the expectations from the gluon condensate, the glueballonium has a mass of about 3.4GeV.
In physics, the wavefunctions of bosonic particles collapse when the system undergoes a Bose–Einstein condensation. In game theory, the strategy of an agent describes the probability to engage in a certain course of action. Strategies are expected to differ in competitive situations, namely when there is a penalty to do the same as somebody else. We study what happens when agents are interested how they fare not only in absolute terms, but also relative to others. This preference, denoted envy, is shown to induce the emergence of distinct social classes via a collective strategy condensation transition. Members of the lower class pursue identical strategies, in analogy to the Bose–Einstein condensation, with the upper class remaining individualistic.
We present the first very long baseline interferometric (VLBI) observations of the blazar OJ 287 carried out jointly with the Global Millimeter VLBI Array (GMVA) and the phased Atacama Large Millimeter/submillimeter Array (ALMA) at 3.5 mm on 2017 April 2. The participation of phased ALMA has not only improved the GMVA north–south resolution by a factor of ∼3, but has also enabled fringe detections with signal-to-noise ratios up to 300 at baselines longer than 2 Gλ. The high sensitivity has motivated us to image the data with newly developed regularized maximum likelihood imaging methods, revealing the innermost jet structure with unprecedentedly high angular resolution. Our images reveal a compact and twisted jet extending along the northwest direction, with two bends within the inner 200 μas, resembling a precessing jet in projection. The component at the southeastern end shows a compact morphology and high brightness temperature, and is identified as the VLBI core. An extended jet feature that lies at ∼200 μas northwest of the core shows a conical shape, in both total and linearly polarized intensity, and a bimodal distribution of the linear polarization electric vector position angle. We discuss the nature of this feature by comparing our observations with models and simulations of oblique and recollimation shocks with various magnetic field configurations. Our high-fidelity images also enabled us to search for possible jet features from the secondary supermassive black hole (SMBH) and test the SMBH binary hypothesis proposed for this source.
We report the first measurements of the absolute branching fractions of D0 → K0 Lϕ, D0 → K0Lη, D0 → K0Lω, and D0 → K0Lη0, by analyzing 2.93 fb−1 of eþe− collision data taken at a center-of-mass energy of 3.773 GeV with the BESIII detector. Taking the world averages of the branching fractions of D0 → K0Sϕ, D0 → K0Sη, D0 → K0Sω, and D0 → K0Sη0, the K0S − K0L asymmetries RðD0; XÞ in these decay modes are obtained. The CP asymmetries in these decays are also determined. No significant CP violation is observed
In particle collider experiments, elementary particle interactions with large momentum transfer produce quarks and gluons (known as partons) whose evolution is governed by the strong force, as described by the theory of quantum chromodynamics (QCD)1. These partons subsequently emit further partons in a process that can be described as a parton shower2, which culminates in the formation of detectable hadrons. Studying the pattern of the parton shower is one of the key experimental tools for testing QCD. This pattern is expected to depend on the mass of the initiating parton, through a phenomenon known as the dead-cone effect, which predicts a suppression of the gluon spectrum emitted by a heavy quark of mass mQ and energy E, within a cone of angular size mQ/E around the emitter3. Previously, a direct observation of the dead-cone effect in QCD had not been possible, owing to the challenge of reconstructing the cascading quarks and gluons from the experimentally accessible hadrons. We report the direct observation of the QCD dead cone by using new iterative declustering techniques4,5 to reconstruct the parton shower of charm quarks. This result confirms a fundamental feature of QCD. Furthermore, the measurement of a dead-cone angle constitutes a direct experimental observation of the non-zero mass of the charm quark, which is a fundamental constant in the standard model of particle physics.
Modern societies face the challenge that the time scale of opinion formation is continuously accelerating in contrast to the time scale of political decision making. With the latter remaining of the order of the election cycle we examine here the case that the political state of a society is determined by the continuously evolving values of the electorate. Given this assumption we show that the time lags inherent in the election cycle will inevitable lead to political instabilities for advanced democracies characterized both by an accelerating pace of opinion dynamics and by high sensibilities (political correctness) to deviations from mainstream values. Our result is based on the observation that dynamical systems become generically unstable whenever time delays become comparable to the time it takes to adapt to the steady state. The time needed to recover from external shocks grows in addition dramatically close to the transition. Our estimates for the order of magnitude of the involved time scales indicate that socio-political instabilities may develop once the aggregate time scale for the evolution of the political values of the electorate falls below 7–15 months.
We extend the standard solid-state quantum mechanical Hamiltonian containing only Coulomb interactions between the charged particles by inclusion of the (transverse) current-current diamagnetic interaction starting from the non-relativistic QED restricted to the states without photons and neglecting the retardation in the photon propagator. This derivation is supplemented with a derivation of an analogous result along the non-rigorous old classical Darwin-Landau-Lifshitz argumentation within the physical Coulomb gauge.
The rapid spread of the Coronavirus (COVID-19) confronts policy makers with the problem of measuring the effectiveness of containment strategies, balancing public health considerations with the economic costs of social distancing measures. We introduce a modified epidemic model that we name the controlled-SIR model, in which the disease reproduction rate evolves dynamically in response to political and societal reactions. An analytic solution is presented. The model reproduces official COVID-19 cases counts of a large number of regions and countries that surpassed the first peak of the outbreak. A single unbiased feedback parameter is extracted from field data and used to formulate an index that measures the efficiency of containment strategies (the CEI index). CEI values for a range of countries are given. For two variants of the controlled-SIR model, detailed estimates of the total medical and socio-economic costs are evaluated over the entire course of the epidemic. Costs comprise medical care cost, the economic cost of social distancing, as well as the economic value of lives saved. Under plausible parameters, strict measures fare better than a hands-off policy. Strategies based on current case numbers lead to substantially higher total costs than strategies based on the overall history of the epidemic.