| 1. |
- Aurell, Erik, et al.
(författare)
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Diffusion of a Brownian ellipsoid in a force field
- 2016
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Ingår i: Europhysics letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 114:3
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Tidskriftsartikel (refereegranskat)abstract
- We calculate the effective long-term convective velocity and dispersive motion of an ellipsoidal Brownian particle in three dimensions when it is subjected to a constant external force. This long-term motion results as a "net" average behavior from the particle rotation and translation on short time scales. Accordingly, we apply a systematic multi-scale technique to derive the effective equations of motion valid on long times. We verify our theoretical results by comparing them to numerical simulations.
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| 2. |
- Hernández, Carlos S., et al.
(författare)
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Impact of Switchbacks on Turbulent Cascade and Energy Transfer Rate in the Inner Heliosphere
- 2021
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 922:1
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Tidskriftsartikel (refereegranskat)abstract
- Recent Parker Solar Probe (PSP) observations of inner heliospheric plasma have shown an abundant presence of Alfvénic polarity reversal of the magnetic field, known as "switchbacks." While their origin is still debated, their role in driving the solar wind turbulence has been suggested through analysis of the spectral properties of magnetic fluctuations. Here, we provide a complementary assessment of their role in the turbulent cascade. The validation of the third-order linear scaling of velocity and magnetic fluctuations in intervals characterized by a high occurrence of switchbacks suggests that, irrespective of their local or remote origin, these structures are actively embedded in the turbulent cascade, at least at the radial distances sampled by PSP during its first perihelion. The stronger positive energy transfer rate observed in periods with a predominance of switchbacks indicates that they act as a mechanism injecting additional energy in the turbulence cascade.
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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Marino, Raffaele, et al.
(författare)
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Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry
- 2016
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Ingår i: Physical Review E. - 2470-0045. ; 93:6
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Tidskriftsartikel (refereegranskat)abstract
- We consider coupled diffusions in n-dimensional space and on a compact manifold and the resulting effective advective-diffusive motion on large scales in space. The effective drift (advection) and effective diffusion are determined as a solvability conditions in a multiscale analysis. As an example, we consider coupled diffusions in three-dimensional space and on the group manifold SO(3) of proper rotations, generalizing results obtained by H. Brenner [J. Colloid Interface Sci. 80, 548 (1981)]. We show in detail how the analysis can be conveniently carried out using local charts and invariance arguments. As a further example, we consider coupled diffusions in two-dimensional complex space and on the group manifold SU(2). We show that although the local operators may be the same as for SO(3), due to the global nature of the solvability conditions the resulting diffusion will differ and generally be more isotropic.
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| 5. |
- Marino, Raffaele, 1987-, et al.
(författare)
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Brownian motion of an ellipsoidal particle in a tilted periodic potential: long-term velocity and diffusion
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We consider the overdamped diffusive motion of an ellipsoidal Brownian particle in a tilted periodic potential. Exact analytical expressions for the net drift and diffusion of the ellipsoid are derived for the cases that it is much smaller, comparable in size and much larger than the periodicity of the potential. Known results for spherical particles are recovered as special cases.
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| 6. |
- Marino, Raffaele, 1987-
(författare)
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Dynamics and Thermodynamics of Translational and Rotational Diffusion Processes Driven out of Equilibrium
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Diffusion processes play an important role in describing systems in many fields of science, as in physics, biology, finance and social science. One of the most famous examples of the diffusion process is the Brownian motion. At mesoscopic scale, the Brownian theory describes the very irregular and animated motion of a particle suspended in a fluid. In this thesis, the dynamics and thermodynamics of diffusion processes driven out of equilibrium, at mesoscopic scale, are investigated. For dynamics, the theory of Brownian motion for a particle which is able to rotate and translate in three dimensions is presented. Moreover, it is presented how to treat diffusion process on n-dimensional Riemann manifolds defining the Kolmogorov forward equation on such manifold. For thermodynamics, this thesis describes how to define thermodynamics quantities at mesoscopic scale using the tools of Brownian theory. The theoryof stochastic energetics and how to compute entropy production along a trajectory are presented introducing the new field of stochastic thermodynamics.Moreover, the "anomalous entropy production" is introduced. This anomaly in the entropy production arises when diffusion processes are driven out of equilibrium by space dependent temperature field. The presence of this term expresses the fallacy of the overdamped approximation in computing thermodynamic quantities. In the first part of the thesis the translational and rotational motion of an ellipsoidal particle in a heterogeneous thermal environment, with a space-dependent temperature field, is analyzed from the point of view of stochastic thermodynamics. In the final part of the thesis, the motion of a Brownian rigid body three-dimensional space in a homogeneous thermal environment under the presence of an external force field is analyzed, using multiscale method and homogenization.
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| 7. |
- Marino, Raffaele, 1987-, et al.
(författare)
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Entropy production of a Brownian ellipsoid in the overdamped limit
- 2016
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1063-651X .- 1095-3787. ; 93:1
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Tidskriftsartikel (refereegranskat)abstract
- We analyze the translational and rotational motion of an ellipsoidal Brownian particle from the viewpoint of stochastic thermodynamics. The particle's Brownian motion is driven by external forces and torques and takes place in an heterogeneous thermal environment where friction coefficients and (local) temperature depend on space and time. Our analysis of the particle's stochastic thermodynamics is based on the entropy production associated with single particle trajectories. It is motivated by the recent discovery that the overdamped limit of vanishing inertia effects (as compared to viscous fricion) produces a so-called “anomalous” contribution to the entropy production, which has no counterpart in the overdamped approximation, when inertia effects are simply discarded. Here we show that rotational Brownian motion in the overdamped limit generates an additional contribution to the “anomalous” entropy. We calculate its specific form by performing a systematic singular perturbation analysis for the generating function of the entropy production. As a side result, we also obtain the (well-known) equations of motion in the overdamped limit. We furthermore investigate the effects of particle shape and give explicit expressions of the “anomalous entropy” for prolate and oblate spheroids and for near-spherical Brownian particles.We analyze the translational and rotational motion of an ellipsoidal Brownian particle from the viewpoint of stochastic thermodynamics. The particle's Brownian motion is driven by external forces and torques and takes place in an heterogeneous thermal environment where friction coefficients and (local) temperature depend on space and time. Our analysis of the particle's stochastic thermodynamics is based on the entropy production associated with single particle trajectories. It is motivated by the recent discovery that the overdamped limit of vanishing inertia effects (as compared to viscous fricion) produces a so-called “anomalous” contribution to the entropy production, which has no counterpart in the overdamped approximation, when inertia effects are simply discarded. Here we show that rotational Brownian motion in the overdamped limit generates an additional contribution to the “anomalous” entropy. We calculate its specific form by performing a systematic singular perturbation analysis for the generating function of the entropy production. As a side result, we also obtain the (well-known) equations of motion in the overdamped limit. We furthermore investigate the effects of particle shape and give explicit expressions of the “anomalous entropy” for prolate and oblate spheroids and for near-spherical Brownian particles.
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| 8. |
- Marino, Raffaele, et al.
(författare)
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Scaling laws for the energy transfer in space plasma turbulence
- 2023
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Ingår i: Physics reports. - : Elsevier. - 0370-1573 .- 1873-6270. ; 1006, s. 1-144
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Forskningsöversikt (refereegranskat)abstract
- One characteristic trait of space plasmas is the multi-scale dynamics resulting from non-linear transfers and conversions of various forms of energy. Routinely evidenced in a range from the large-scale solar structures down to the characteristic scales of ions and electrons, turbulence is a major cross-scale energy transfer mechanism in space plasmas. At intermediate scales, the fate of the energy in the outer space is mainly determined by the interplay of turbulent motions and propagating waves. More mechanisms are advocated to account for the transfer and conversion of energy, including magnetic reconnection, emission of radiation and particle energization, all contributing to make the dynamical state of solar and heliospheric plasmas difficult to predict. The characterization of the energy transfer in space plasmas benefited from numerous robotic missions. However, together with breakthrough technologies, novel theoretical developments and methodologies for the analysis of data played a crucial role in advancing our understanding of how energy is transferred across the scales in the space. In recent decades, several scaling laws were obtained providing effective ways to model the energy flux in turbulent plasmas. Under certain assumptions, these relations enabled to utilize reduced knowledge (in terms of degrees of freedom) of the fields from spacecraft observations to obtain direct estimates of the energy transfer rates (and not only) in the interplanetary space, also in the proximity of the Sun and planets. Starting from the first third-order exact law for the magnetohydrodynamics by Politano and Pouquet (1998), we present a detailed review of the main scaling laws for the energy transfer in plasma turbulence and their application, presenting theoretical, numerical and observational milestones of what has become one of the main approaches for the characterization of turbulent dynamics and energetics in space plasmas.
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| 9. |
- Marino, Raffaele, et al.
(författare)
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The backtracking survey propagation algorithm for solving random K-SAT problems
- 2016
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Discrete combinatorial optimization has a central role in many scientific disciplines, however, for hard problems we lack linear time algorithms that would allow us to solve very large instances. Moreover, it is still unclear what are the key features that make a discrete combinatorial optimization problem hard to solve. Here we study random K-satisfiability problems with K=3,4, which are known to be very hard close to the SAT-UNSAT threshold, where problems stop having solutions. We show that the backtracking survey propagation algorithm, in a time practically linear in the problem size, is able to find solutions very close to the threshold, in a region unreachable by any other algorithm. All solutions found have no frozen variables, thus supporting the conjecture that only unfrozen solutions can be found in linear time, and that a problem becomes impossible to solve in linear time when all solutions contain frozen variables.
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| 10. |
- Nguyen, Thanh N, et al.
(författare)
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Global Impact of the COVID-19 Pandemic on Stroke Volumes and Cerebrovascular Events: A 1-Year Follow-up.
- 2023
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Ingår i: Neurology. - 1526-632X. ; 100:4
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Tidskriftsartikel (refereegranskat)abstract
- Declines in stroke admission, IV thrombolysis (IVT), and mechanical thrombectomy volumes were reported during the first wave of the COVID-19 pandemic. There is a paucity of data on the longer-term effect of the pandemic on stroke volumes over the course of a year and through the second wave of the pandemic. We sought to measure the effect of the COVID-19 pandemic on the volumes of stroke admissions, intracranial hemorrhage (ICH), IVT, and mechanical thrombectomy over a 1-year period at the onset of the pandemic (March 1, 2020, to February 28, 2021) compared with the immediately preceding year (March 1, 2019, to February 29, 2020).We conducted a longitudinal retrospective study across 6 continents, 56 countries, and 275 stroke centers. We collected volume data for COVID-19 admissions and 4 stroke metrics: ischemic stroke admissions, ICH admissions, IVT treatments, and mechanical thrombectomy procedures. Diagnoses were identified by their ICD-10 codes or classifications in stroke databases.There were 148,895 stroke admissions in the 1 year immediately before compared with 138,453 admissions during the 1-year pandemic, representing a 7% decline (95% CI [95% CI 7.1-6.9]; p < 0.0001). ICH volumes declined from 29,585 to 28,156 (4.8% [5.1-4.6]; p < 0.0001) and IVT volume from 24,584 to 23,077 (6.1% [6.4-5.8]; p < 0.0001). Larger declines were observed at high-volume compared with low-volume centers (all p < 0.0001). There was no significant change in mechanical thrombectomy volumes (0.7% [0.6-0.9]; p = 0.49). Stroke was diagnosed in 1.3% [1.31-1.38] of 406,792 COVID-19 hospitalizations. SARS-CoV-2 infection was present in 2.9% ([2.82-2.97], 5,656/195,539) of all stroke hospitalizations.There was a global decline and shift to lower-volume centers of stroke admission volumes, ICH volumes, and IVT volumes during the 1st year of the COVID-19 pandemic compared with the prior year. Mechanical thrombectomy volumes were preserved. These results suggest preservation in the stroke care of higher severity of disease through the first pandemic year.This study is registered under NCT04934020.
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