A
bstract
Of the J/
ψ
mesons (inclusively) produced in pp collisions, a big fraction results from B decays, increasing with transverse momentum and exceeding 50% for
p
T
>
20 GeV. These events must ...be subtracted in measurements of the polarization of prompt J/
ψ
mesons. While several studies have addressed the
ψ
(2S) and
χ
c
impact on the determination of the polarization of the directly-produced J/
ψ
mesons, the theoretical and experimental knowledge of the non-prompt polarization is very poor. Furthermore, non-prompt J/
ψ
polarization measurements can provide interesting information on quarkonium hadroproduction, complementing the studies of prompt production. We review the method of measuring the polarization of non-prompt J/
ψ
mesons (produced in decays of unreconstructed B mesons and detected in the dilepton channel), in conditions typical of LHC experiments studying J/
ψ
production. Realistic model-independent scenarios are validated with data from experiments studying
e
+
e
−
→ Υ(4S) interactions, converted to the high-momentum regime using B differential cross sections measured at the LHC. The non-prompt J/
ψ
polarization measurements are seen to remain dependent on the event selection criteria, even after correcting for the dilepton acceptance and efficiencies. This implies that reproducible definitions of all relevant analysis choices must be reported with the polarization result, for rigorous comparisons with other measurements and/or theoretical calculations. We also discuss how the non-prompt J/
ψ
polarization significantly depends on the relative importance of two complementary B → J
/ψ
decay topologies, two-body (reasonably dominated by singlet production) and multi-body (including octet contributions), providing, hence, valuable information for studies of the charmonium formation mechanisms.
While the prompt
J
/
ψ
cross section and polarization have been measured with good precision as a function of transverse momentum,
p
T
, those of the directly produced
J
/
ψ
are practically unknown, ...given that the cross sections and polarizations of the
χ
c
1
and
χ
c
2
mesons, large indirect contributors to
J
/
ψ
production, are only known with rather poor accuracy. The lack of precise measurements of the
χ
cJ
polarizations induces large uncertainties in the level of their feed-down contributions to the prompt
J
/
ψ
yield, because of the polarization-dependent acceptance corrections. The experimental panorama of charmonium production can be significantly improved through a consistent and model-independent global analysis of existing measurements of
J
/
ψ
,
ψ
(
2
S
)
and
χ
c
cross sections and polarizations, faithfully respecting all the correlations and uncertainties. In particular, it is seen that the
χ
cJ
polarizations and feed-down fractions to
J
/
ψ
production have a negligible dependence on the
J
/
ψ
p
T
, with average values
λ
ϑ
χ
c
1
=
0.55
±
0.23
,
λ
ϑ
χ
c
2
=
-
0.39
±
0.22
,
R
χ
c
1
=
(
18.8
±
1.4
)
%
and
R
χ
c
2
=
(
6.5
±
0.5
)
%
. The analysis also shows that
(
67.2
±
1.9
)
% of the prompt
J
/
ψ
yield is due to directly-produced mesons, of polarization constrained to remarkably small values,
λ
ϑ
J
/
ψ
=
0.04
±
0.06
.
Abstract
Structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, Molecular Dynamics (MD) simulations enable us to investigate ...these thermally activated processes with an atomic level of resolution. In practice, an exponentially large fraction of computational resources must be invested to simulate thermal fluctuations in metastable states. Path sampling methods focus the computational power on sampling the rare transitions between states. One of their outstanding limitations is to efficiently generate paths that visit significantly different regions of the conformational space. To overcome this issue, we introduce a new algorithm for MD simulations that integrates machine learning and quantum computing. First, using functional integral methods, we derive a rigorous low-resolution spatially coarse-grained representation of the system’s dynamics, based on a small set of molecular configurations explored with machine learning. Then, we use a quantum annealer to sample the transition paths of this low-resolution theory. We provide a proof-of-concept application by simulating a benchmark conformational transition with all-atom resolution on the D-Wave quantum computer. By exploiting the unique features of quantum annealing, we generate uncorrelated trajectories at every iteration, thus addressing one of the challenges of path sampling. Once larger quantum machines will be available, the interplay between quantum and classical resources may emerge as a new paradigm of high-performance scientific computing. In this work, we provide a platform to implement this integrated scheme in the field of molecular simulations.
We present a comprehensive approach to the dynamics of heavy quarks in a quark–gluon plasma, including the possibility of bound state formation and dissociation. In this exploratory paper, we ...restrict ourselves to the case of an Abelian plasma, but the extension of the techniques used to the non-Abelian case is doable. A chain of well defined approximations leads eventually to a generalized Langevin equation, where the force and the noise terms are determined from a correlation function of the equilibrium plasma, and depend explicitly on the configuration of the heavy quarks. We solve the Langevin equation for various initial conditions, numbers of heavy quark–antiquark pairs and temperatures of the plasma. Results of simulations illustrate several expected phenomena: dissociation of bound states as a result of combined effects of screening of the potential and collisions with the plasma constituent, formation of bound pairs (recombination) that occurs when enough heavy quarks are present in the system.
Several fixed-target experiments reported J/ψ and ϒ polarizations, as functions of Feynman x (xF) and transverse momentum (pT), in three different frames, using different combinations of beam ...particles, target nuclei, and collision energies. Despite the diverse and heterogeneous picture formed by these measurements, a detailed look allows us to discern qualitative physical patterns that inspire a simple empirical model. This data-driven scenario offers a good quantitative description of the J/ψ and ϒ(1S) polarizations measured in proton- and pion-nucleus collisions, in the xF≲0.5 domain: more than 80 data points (not statistically independent) are well reproduced with only one free parameter. This study sets the context for future low-pT quarkonium polarization measurements in proton- and pion-nucleus collisions, such as those to be made by the AMBER experiment, and shows that such measurements provide significant constraints on the poorly-known parton distribution functions of the pion.
The observation of unpolarized quarkonium production in high energy pp collisions, at mid rapidity, implies a significant violation of the non-relativistic QCD (NRQCD) velocity scaling rules. A ...precise experimental confirmation of this picture could definitely rule out the current formulation of the factorization expansion. This conclusion relies on current perturbative determinations of the short-distance kinematic factors and may be reverted if improved calculations would modify, in a very specific way, their transverse momentum dependences. That solution would result, however, in a full degeneracy in the presently assumed basis of
2
S
+
1
L
J
Fock states. Therefore, whatever the outcome, improved polarization measurements will challenge and improve our fundamental understanding of quarkonium production.
Measurements made at the LHC have shown that the production of the
J
/
ψ
,
ψ
(
2
S
)
,
Υ
(
1
S
)
and
Υ
(
2
S
)
quarkonia is suppressed in Pb–Pb collisions, with respect to the extrapolation of the pp ...production yields. The
ψ
(
2
S
)
and
Υ
(
2
S
)
states are more strongly suppressed than the ground states and the level of the suppression changes with the centrality of the collision. We show that the measured patterns can be reproduced by a simple model, where all quarkonia are treated in a unified way, starting from the recent realisation that, in pp collisions, the probability of quarkonium formation has a universal dependence on the binding-energy of the bound state. The hot-medium suppression effect is parametrized by a penalty factor in the binding energy, identical for all (S- and P-wave) charmonium and bottomonium states, including those that indirectly contribute to the measured results through feed-down decays. This single parameter, computed through a global fit of all available suppression patterns, fully determines the hierarchy of nuclear effects, for all states and centrality bins. The resulting faithful description of the data provides convincing evidence in favour of the conjecture of sequential quarkonium suppression induced by QGP formation.
Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical ...properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.
A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop offers an insightful overview of the understanding of the mechanistic foundations of allostery, gained from computational and experimental analyses of real protein systems and model systems. Various practical applications are illustrated.
Prions are unusual protein assemblies that propagate their conformationally-encoded information in absence of nucleic acids. The first prion identified, the scrapie isoform (PrPSc) of the cellular ...prion protein (PrPC), caused epidemic and epizootic episodes 1. Most aggregates of other misfolding-prone proteins are amyloids, often arranged in a Parallel-In-Register-β-Sheet (PIRIBS) 2 or β-solenoid conformations 3. Similar folding models have also been proposed for PrPSc, although none of these have been confirmed experimentally. Recent cryo-electron microscopy (cryo-EM) and X-ray fiber-diffraction studies provided evidence that PrPSc is structured as a 4-rung β-solenoid (4RβS) 4, 5. Here, we combined different experimental data and computational techniques to build the first physically-plausible, atomic resolution model of mouse PrPSc, based on the 4RβS architecture. The stability of this new PrPSc model, as assessed by Molecular Dynamics (MD) simulations, was found to be comparable to that of the prion forming domain of Het-s, a naturally-occurring β-solenoid. Importantly, the 4RβS arrangement allowed the first simulation of the sequence of events underlying PrPC conversion into PrPSc. This study provides the most updated, experimentally-driven and physically-coherent model of PrPSc, together with an unprecedented reconstruction of the mechanism underlying the self-catalytic propagation of prions.
Polarization measurements are usually considered as the most difficult challenge for the QCD description of quarkonium production. In fact, global data fits for the determination of the ...non-perturbative parameters of bound-state formation traditionally exclude polarization observables and use them as a posteriori verifications of the predictions, with perplexing results. With a change of perspective, we move polarization data to the centre of the study, advocating that they actually provide the strongest fundamental indications about the production mechanisms, even before we explicitly consider perturbative calculations.
Considering ψ(2S) and ϒ(3S) measurements from LHC experiments and state-of-the-art next-to-leading order cross sections for the short-distance production of heavy quark–antiquark pairs of relevant colour and angular momentum configurations, we perform a search for a kinematic domain where quarkonium polarizations can be correctly reproduced together with the respective cross sections, by systematically scanning the phase space and accurately treating the experimental uncertainties. This strategy provides a straightforward solution to the “quarkonium polarization puzzle” and reassuring signs that the factorization of short- and long-distance effects works, at least in the high-transverse-momentum region, least affected by limitations in the current fixed-order calculations. The results expose unexpected hierarchies in the phenomenological long-distance parameters that open new paths towards the understanding of bound-state formation in QCD.
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