1,900 research outputs found
Topological thermal instability and length of proteins
We present an analysis of the effects of global topology on the structural
stability of folded proteins in thermal equilibrium with a heat bath. For a
large class of single domain proteins, we computed the harmonic spectrum within
the Gaussian Network Model (GNM) and determined the spectral dimension, a
parameter describing the low frequency behaviour of the density of modes. We
find a surprisingly strong correlation between the spectral dimension and the
number of amino acids of the protein. Considering that larger spectral
dimension value relate to more topologically compact folded state, our results
indicate that for a given temperature and length of the protein, the folded
structure corresponds to the less compact folding compatible with thermodynamic
stability.Comment: 15 pages, 6 eps figures, 2 table
Anomalous mobility of a driven active particle in a steady laminar flow
We study, via extensive numerical simulations, the force-velocity curve of an
active particle advected by a steady laminar flow, in the nonlinear response
regime. Our model for an active particle relies on a colored noise term that
mimics its persistent motion over a time scale . We find that the
active particle dynamics shows non-trivial effects, such as negative
differential and absolute mobility (NDM and ANM, respectively). We explore the
space of the model parameters and compare the observed behaviors with those
obtained for a passive particle () advected by the same laminar flow.
Our results show that the phenomena of NDM and ANM are quite robust with
respect to the details of the considered noise: in particular for finite
a more complex force-velocity relation can be observed.Comment: 12 pages, 9 figures, paper submitted for the Special Issue of Journal
of Physics: Condensed Matter, "Transport in Narrow Channels", Guest Editors
P. Malgaretti, G. Oshanin, J. Talbo
Anomalous force-velocity relation of driven inertial tracers in steady laminar flows
We study the nonlinear response to an external force of an inertial tracer
advected by a two-dimensional incompressible laminar flow and subject to
thermal noise. In addition to the driving external field , the main
parameters in the system are the noise amplitude and the characteristic
Stokes time of the tracer. The relation velocity vs force shows
interesting effects, such as negative differential mobility (NDM), namely a
non-monotonic behavior of the tracer velocity as a function of the applied
force, and absolute negative mobility (ANM), i.e. a net motion against the
bias. By extensive numerical simulations, we investigate the phase chart in the
parameter space of the model, , identifying the regions where NDM,
ANM and more common monotonic behaviors of the force-velocity curve are
observed.Comment: 5 pages, 13 figures. Contribution to the Topical Issue "Fluids and
Structures: Multi-scale coupling and modeling", edited by Luca Biferale,
Stefano Guido, Andrea Scagliarini, Federico Toschi. The final publication is
available at Springer via http://dx.doi.org/10.1140/epje/i2017-11571-
Nonlinear Response of Inertial Tracers in Steady Laminar Flows: Differential and Absolute Negative Mobility
We study the mobility and the diffusion coefficient of an inertial tracer advected by a two-dimensional incompressible laminar flow, in the presence ofthermal noise and under the actionof an external force. We show, with extensive numerical simulations, that the force-velocity rela-tion for the tracer, in the nonlinear regime, displays complex and rich behaviors, including negativedifferential and absolute mobility. These effects rely upon asubtle coupling between inertia andapplied force which induce the tracer to persist in particular regions of phase space with a velocityopposite to the force. The relevance of this coupling is revisited in the framework of non-equilibriumresponse theory, applying a generalized Einstein relationto our system. The possibility of experi-mental observation of these results is also discussed
Understanding the dependence on the pulling speed of the unfolding pathway of proteins
The dependence of the unfolding pathway of proteins on the pulling speed is
investigated. This is done by introducing a simple one-dimensional chain
comprising units, with different characteristic bistable free energies.
These units represent either each of the modules in a modular protein or each
of the intermediate "unfoldons" in a protein domain, which can be either folded
or unfolded. The system is pulled by applying a force to the last unit of the
chain, and the units unravel following a preferred sequence. We show that the
unfolding sequence strongly depends on the pulling velocity . In the
simplest situation, there appears a critical pulling speed : for pulling
speeds
it is the pulled unit that unfolds first. By means of a perturbative expansion,
we find quite an accurate expression for this critical velocity.Comment: accepted for publication in JSTA
Thermally induced directed currents in hard rod systems
We study the non equilibrium statistical properties of a one dimensional
hard-rod fluid undergoing collisions and subject to a spatially non uniform
Gaussian heat-bath and periodic potential. The system is able to sustain finite
currents when the spatially inhomogeneous heat-bath and the periodic potential
profile display an appropriate relative phase shift, . By comparison with
the collisionless limit, we determine the conditions for the most efficient
transport among inelastic, elastic and non interacting rods. We show that the
situation is complex as, depending on shape of the temperature profile, the
current of one system may outperform the others.Comment: 5 pages, 2 figure
Data-Driven Process Mining Framework for Risk Management in Construction Projects
Construction Projects are exposed to numerous risks due to their complex and uncertain nature, threatening the realization of the project objectives. However, Risk Management (RM) is a less efficient realm in the industry than other knowledge areas given the manual and time-consuming nature of its processes and reliance on experience-based subjective judgments. This research proposes a Process Mining-based framework for detecting, monitoring, and analysing risks, improving the RM processes using evidence-based event logs, such as Risk Registers and Change-Logs within previous projects' documents. Process Mining (PM) is a data- driven methodology, well established in other industries, that benefits from Artificial Intelligence(AI) to identify trends and complex patterns among event logs. It performs well while intaking large amounts of data and predicting future outputs based on historical data. Therefore, this research proposes a Bayesian Network (BN)-based Process Mining framework for graphical representation of the RM processes, intaking the conditional dependence structure between Risk variables, and continuous and automated risk identification and management. A systematic literature review on RM, PM, and AI forms the framework theoretical basis and delineates the integration areas for practical implementation. The proposed framework is applied to a small database of 20 projects as the case study, the scope of which can be tailored to the enterprise requirements. It contributes to creating a holistic theoretical foundation and practical workflow applicable to construction projects and filling the knowledge gap in inefficient and discrete conventional RM methods, which ignore the interdependencies between risk variables and assess each risk isolated
Left ventricular systolic function evaluated by strain echocardiography and relationship with mortality in patients with severe sepsis or septic shock. a systematic review and meta-analysis
Sepsis-induced myocardial dysfunction is associated with poor outcomes, but traditional measurements of systolic function such as left ventricular ejection fraction (LVEF) do not directly correlate with prognosis. Global longitudinal strain (GLS) utilizing speckle-tracking echocardiography (STE) could be a better marker of intrinsic left ventricular (LV) function, reflecting myocardial deformation rather than displacement and volume changes. We sought to investigate the prognostic value of GLS in patients with sepsis and/or septic shock
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