1,456 research outputs found
Evolutionary Multi-Objective Design of SARS-CoV-2 Protease Inhibitor Candidates
Computational drug design based on artificial intelligence is an emerging
research area. At the time of writing this paper, the world suffers from an
outbreak of the coronavirus SARS-CoV-2. A promising way to stop the virus
replication is via protease inhibition. We propose an evolutionary
multi-objective algorithm (EMOA) to design potential protease inhibitors for
SARS-CoV-2's main protease. Based on the SELFIES representation the EMOA
maximizes the binding of candidate ligands to the protein using the docking
tool QuickVina 2, while at the same time taking into account further objectives
like drug-likeliness or the fulfillment of filter constraints. The experimental
part analyzes the evolutionary process and discusses the inhibitor candidates.Comment: 15 pages, 7 figures, submitted to PPSN 202
Octet-Baryon Form Factors in the Diquark Model
We present an alternative parameterization of the quark-diquark model of
baryons which particularly takes care of the most recent proton electric
form-factor data from the E136 experiment at SLAC. In addition to
electromagnetic form factors of the nucleon, for which good agreement with data
is achieved, we discuss the weak axial vector form factor of the nucleon as
well as electromagnetic form factors of and hyperons.
Technical advance in calculating the pertinent analytic expressions within
perturbative quantum chromodynamics is gained by formulating the wave function
of the quark-diquark system in a covariant way. Finally, we also comment on the
influence of Sudakov corrections within the scope of the diquark model.Comment: 16 pages, WU-B 93-07, latex, uuencoded postscript files of 7 figures
appended at the end of the latex fil
The spin-1/2 XXZ Heisenberg chain, the quantum algebra U_q[sl(2)], and duality transformations for minimal models
The finite-size scaling spectra of the spin-1/2 XXZ Heisenberg chain with
toroidal boundary conditions and an even number of sites provide a projection
mechanism yielding the spectra of models with a central charge c<1 including
the unitary and non-unitary minimal series. Taking into account the
half-integer angular momentum sectors - which correspond to chains with an odd
number of sites - in many cases leads to new spinor operators appearing in the
projected systems. These new sectors in the XXZ chain correspond to a new type
of frustration lines in the projected minimal models. The corresponding new
boundary conditions in the Hamiltonian limit are investigated for the Ising
model and the 3-state Potts model and are shown to be related to duality
transformations which are an additional symmetry at their self-dual critical
point. By different ways of projecting systems we find models with the same
central charge sharing the same operator content and modular invariant
partition function which however differ in the distribution of operators into
sectors and hence in the physical meaning of the operators involved. Related to
the projection mechanism in the continuum there are remarkable symmetry
properties of the finite XXZ chain. The observed degeneracies in the energy and
momentum spectra are shown to be the consequence of intertwining relations
involving U_q[sl(2)] quantum algebra transformations.Comment: This is a preprint version (37 pages, LaTeX) of an article published
back in 1993. It has been made available here because there has been recent
interest in conformal twisted boundary conditions. The "duality-twisted"
boundary conditions discussed in this paper are particular examples of such
boundary conditions for quantum spin chains, so there might be some renewed
interest in these result
A sufficient criterion for integrability of stochastic many-body dynamics and quantum spin chains
We propose a dynamical matrix product ansatz describing the stochastic
dynamics of two species of particles with excluded-volume interaction and the
quantum mechanics of the associated quantum spin chains respectively. Analyzing
consistency of the time-dependent algebra which is obtained from the action of
the corresponding Markov generator, we obtain sufficient conditions on the
hopping rates for identifing the integrable models. From the dynamical algebra
we construct the quadratic algebra of Zamolodchikov type, associativity of
which is a Yang Baxter equation. The Bethe ansatz equations for the spectra are
obtained directly from the dynamical matrix product ansatz.Comment: 19 pages Late
Flux Modulations seen by the Muon Veto of the GERDA Experiment
The GERDA experiment at LNGS of INFN is equipped with an active muon veto.
The main part of the system is a water Cherenkov veto with 66~PMTs in the water
tank surrounding the GERDA cryostat. The muon flux recorded by this veto shows
a seasonal modulation. Two effects have been identified which are caused by
secondary muons from the CNGS neutrino beam (2.2 %) and a temperature
modulation of the atmosphere (1.4 %). A mean cosmic muon rate of /(sm) was found in good agreement with other experiments at
LNGS at a depth of 3500~meter water equivalent.Comment: 7 pages, 6 figure
Limit on the Radiative Neutrinoless Double Electron Capture of Ar from GERDA Phase I
Neutrinoless double electron capture is a process that, if detected, would
give evidence of lepton number violation and the Majorana nature of neutrinos.
A search for neutrinoless double electron capture of Ar has been
performed with germanium detectors installed in liquid argon using data from
Phase I of the GERmanium Detector Array (GERDA) experiment at the Gran Sasso
Laboratory of INFN, Italy. No signal was observed and an experimental lower
limit on the half-life of the radiative neutrinoless double electron capture of
Ar was established: 3.6 10 yr at 90 % C.I.Comment: 7 pages, 3 figure
Multiplicities of charged pions and unidentified charged hadrons from deep-inelastic scattering of muons off an isoscalar target
Multiplicities of charged pions and unidentified hadrons produced in
deep-inelastic scattering were measured in bins of the Bjorken scaling variable
, the relative virtual-photon energy and the relative hadron energy .
Data were obtained by the COMPASS Collaboration using a 160 GeV muon beam and
an isoscalar target (LiD). They cover the kinematic domain in the photon
virtuality > 1(GeV/c, , and . In addition, a leading-order pQCD analysis was performed using the
pion multiplicity results to extract quark fragmentation functions
Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells
B cell responses are critical for antiviral immunity. However, a comprehensive picture of antigen-specific B cell differentiation, clonal proliferation, and dynamics in different organs after infection is lacking. Here, by combining single-cell RNA and B cell receptor (BCR) sequencing of antigen-specific cells in lymph nodes, spleen, and lungs after influenza infection in mice, we identify several germinal center (GC) B cell subpopulations and organ-specific differences that persist over the course of the response. We discover transcriptional differences between memory cells in lungs and lymphoid organs and organ-restricted clonal expansion. Remarkably, we find significant clonal overlap between GC-derived memory and plasma cells. By combining BCR-mutational analyses with monoclonal antibody (mAb) expression and affinity measurements, we find that memory B cells are highly diverse and can be selected from both low- and high-affinity precursors. By linking antigen recognition with transcriptional programming, clonal proliferation, and differentiation, these finding provide important advances in our understanding of antiviral immunity
The Polarised Valence Quark Distribution from semi-inclusive DIS
The semi-inclusive difference asymmetry A^{h^{+}-h^{-}} for hadrons of
opposite charge has been measured by the COMPASS experiment at CERN. The data
were collected in the years 2002-2004 using a 160 GeV polarised muon beam
scattered off a large polarised ^6LiD target and cover the range 0.006 < x <
0.7 and 1 < Q^2 < 100 (GeV/c)^2. In leading order QCD (LO) the asymmetry
A_d^{h^{+}-h^{-}} measures the valence quark polarisation and provides an
evaluation of the first moment of Delta u_v + Delta d_v which is found to be
equal to 0.40 +- 0.07 (stat.) +- 0.05 (syst.) over the measured range of x at
Q^2 = 10 (GeV/c)^2. When combined with the first moment of g_1^d previously
measured on the same data, this result favours a non-symmetric polarisation of
light quarks Delta u-bar = - Delta d-bar at a confidence level of two standard
deviations, in contrast to the often assumed symmetric scenario Delta u-bar =
Delta d-bar = Delta s-bar = Delta s.Comment: 7 pages, 3 figures, COMPASS, revised: details added, author list
update
Investigation of catalysis by bacterial RNase P via LNA and other modifications at the scissile phosphodiester
We analyzed cleavage of precursor tRNAs with an LNA, 2′-OCH3, 2′-H or 2′-F modification at the canonical (c0) site by bacterial RNase P. We infer that the major function of the 2′-substituent at nt −1 during substrate ground state binding is to accept an H-bond. Cleavage of the LNA substrate at the c0 site by Escherichia coli RNase P RNA demonstrated that the transition state for cleavage can in principle be achieved with a locked C3′ -endo ribose and without the H-bond donor function of the 2′-substituent. LNA and 2′-OCH3 suppressed processing at the major aberrant m−1 site; instead, the m+1 (nt +1/+2) site was utilized. For the LNA variant, parallel pathways leading to cleavage at the c0 and m+1 sites had different pH profiles, with a higher Mg2+ requirement for c0 versus m+1 cleavage. The strong catalytic defect for LNA and 2′-OCH3 supports a model where the extra methylene (LNA) or methyl group (2′-OCH3) causes a steric interference with a nearby bound catalytic Mg2+ during its recoordination on the way to the transition state for cleavage. The presence of the protein cofactor suppressed the ground state binding defects, but not the catalytic defects
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