221 research outputs found
Network coarsening dynamics in a plasmodial slime mould: Modelling and experiments
The giant unicellular slime mould Physarum polycephalum forms an extended network of stands (veins) that provide for an effective intracellular transportation system, which coarsens in time. The network coarsening was investigated numerically using an agent-based model and the results were compared to experimental observations. The coarsening process of both numerical and experimental networks was characterised by analyses of the kinetics of coarsening, of the distributions of geometric network parameters (as, for instance, the lengths and widths of vein segments) and of network topologies
Recommended from our members
Fundamentals of Liquid Phase Sintering During Selective Laser Sintering
One of the advantages of the Selective Laser Sintering (SLS) process is that a variety of materials
can be processed. However, the goal of being able to produce fully dense metal parts with no post
processing has been elusive. Using Selective Laser Sintering to produce metal parts with full
density without post processing poses a challenge since both the processing conditions and the
metal system must be controlled. This article describes two metallurgical mechanisms by which
loose metal powder beds could be sintered to nearly full density using a scanning laser beam. The
mechanisms are particle rearrangement during liquid phase sintering (LPS) and in-situ infiltration.
Some of the particles, when heated by the laser radiation, melt and form a liquid. Ifthis liquid has
certain physical properties (e.g., low viscosity and high surface tension) and wets the other solid
particles, then the SLS process can in theory produce dense layers by either mechanism. The
purpose of this study is to determine the process and material selection parameters required to
achieve fully dense parts during direct Selective Laser Sintering of metal.Mechanical Engineerin
Robust Inference of Trees
This paper is concerned with the reliable inference of optimal
tree-approximations to the dependency structure of an unknown distribution
generating data. The traditional approach to the problem measures the
dependency strength between random variables by the index called mutual
information. In this paper reliability is achieved by Walley's imprecise
Dirichlet model, which generalizes Bayesian learning with Dirichlet priors.
Adopting the imprecise Dirichlet model results in posterior interval
expectation for mutual information, and in a set of plausible trees consistent
with the data. Reliable inference about the actual tree is achieved by focusing
on the substructure common to all the plausible trees. We develop an exact
algorithm that infers the substructure in time O(m^4), m being the number of
random variables. The new algorithm is applied to a set of data sampled from a
known distribution. The method is shown to reliably infer edges of the actual
tree even when the data are very scarce, unlike the traditional approach.
Finally, we provide lower and upper credibility limits for mutual information
under the imprecise Dirichlet model. These enable the previous developments to
be extended to a full inferential method for trees.Comment: 26 pages, 7 figure
Universal features of the order-parameter fluctuations : reversible and irreversible aggregation
We discuss the universal scaling laws of order parameter fluctuations in any
system in which the second-order critical behaviour can be identified. These
scaling laws can be derived rigorously for equilibrium systems when combined
with the finite-size scaling analysis. The relation between order parameter,
criticality and scaling law of fluctuations has been established and the
connexion between the scaling function and the critical exponents has been
found. We give examples in out-of-equilibrium aggregation models such as the
Smoluchowski kinetic equations, or of at-equilibrium Ising and percolation
models.Comment: 19 pages, 10 figure
Kob-Andersen model: a non-standard mechanism for the glassy transition
We present new results reflecting the analogies between the Kob-Andersen
model and other glassy systems. Studying the stability of the blocked
configurations above and below the transition we also give arguments that
supports their relevance for the glassy behaviour of the model.
However we find, surprisingly, that the organization of the phase space of
the system is different from the well known organization of other mean-field
spin glasses and structural glasses.Comment: New reference added and one update
Ab initio Quantum and ab initio Molecular Dynamics of the Dissociative Adsorption of Hydrogen on Pd(100)
The dissociative adsorption of hydrogen on Pd(100) has been studied by ab
initio quantum dynamics and ab initio molecular dynamics calculations. Treating
all hydrogen degrees of freedom as dynamical coordinates implies a high
dimensionality and requires statistical averages over thousands of
trajectories. An efficient and accurate treatment of such extensive statistics
is achieved in two steps: In a first step we evaluate the ab initio potential
energy surface (PES) and determine an analytical representation. Then, in an
independent second step dynamical calculations are performed on the analytical
representation of the PES. Thus the dissociation dynamics is investigated
without any crucial assumption except for the Born-Oppenheimer approximation
which is anyhow employed when density-functional theory calculations are
performed. The ab initio molecular dynamics is compared to detailed quantum
dynamical calculations on exactly the same ab initio PES. The occurence of
quantum oscillations in the sticking probability as a function of kinetic
energy is addressed. They turn out to be very sensitive to the symmetry of the
initial conditions. At low kinetic energies sticking is dominated by the
steering effect which is illustrated using classical trajectories. The steering
effects depends on the kinetic energy, but not on the mass of the molecules.
Zero-point effects lead to strong differences between quantum and classical
calculations of the sticking probability. The dependence of the sticking
probability on the angle of incidence is analysed; it is found to be in good
agreement with experimental data. The results show that the determination of
the potential energy surface combined with high-dimensional dynamical
calculations, in which all relevant degrees of freedon are taken into account,
leads to a detailed understanding of the dissociation dynamics of hydrogen at a
transition metal surface.Comment: 15 pages, 9 figures, subm. to Phys. Rev.
Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein
Publisher Copyright: © 2022 National Academy of Sciences. All rights reserved.Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available coronavirus disease 2019 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors, which block formation of the so-called heptad repeat 1 and 2 (HR1HR2) six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. We performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based and virus-based assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ∼100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a prehairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the prehairpin intermediate of the S protein.Peer reviewe
- …