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Pierre de Buyl

Publications and source records attributed to Pierre de Buyl.

At least 19 recordsLinked to original sources
arXiv2024

Satellite-Based Quantification of Contrail Radiative Forcing over Europe: A Two-Week Analysis of Aviation-Induced Climate Effects

Aviation's non-CO$_2$ effects, especially the impact of aviation-induced contrails, drive atmospheric changes and can influence climate dynamics. Although contrails are believed to contribute to global warming through their net warming effect, uncertainties persist due to the challenges in accurately measuring their radiative impacts. This study aims to address this knowledge gap by investigating the relationship between aviation-induced contrails, as observed in Meteosat Second Generation (MSG) satellite imagery, and their impact on radiative forcing (RF) over a two-week study. Results show that while daytime contrails generally have a cooling effect, the higher number of nighttime contrails results in a net warming effect over the entire day. Net RF values for detected contrails range approximately from -8 TW to 2.5 TW during the day and from 0 to 6 TW at night. Our findings also show a 41.03% increase in contrail coverage from January 24-30, 2023, to the same week in 2024, accompanied by a 128.7% rise in contrail radiative forcing (CRF), indicating greater warming from the added contrails. These findings highlight the necessity of considering temporal factors, such as the timing and duration of contrail formation, when assessing their overall warming impact. They also indicate a potential increase in contrail-induced warming from 2023 to 2024, attributable to the rise in contrail coverage. Further investigation into these trends is crucial for the development of effective mitigation strategies.

physics.ao-ph↗
arXiv2022

Brownian motion in a growing population of ballistic particles

We investigate the motility of a growing population of cells in a idealized setting: we consider a system of hard disks in which new particles are added according to prescribed growth kinetics, thereby dynamically changing the number density. As a result, the expected Brownian motion of the hard disks is modified. We compute the density-dependent friction of the hard disks and insert it in an effective Langevin equation to describe the system, assuming that the inter-collision time is smaller than the timescale of the growth. We find that the effective Langevin description captures the changes in motility in agreement with the simulation results. Our framework can be extended to other systems in which the transport coefficient varies with time.

cond-mat.stat-mech↗
arXiv2021

Lees-Edwards boundary conditions for translation invariant shear flow: implementation and transport properties

Molecular dynamics (MD) simulations represent a powerful investigation tool in the field of soft matter. By using shear flows, one can probe the bulk rheology of complex fluids, also beyond the linear response regime, in a way that imitates laboratory experiments. One solution to impose a shear flow in particle-based simulations is the Lees-Edwards technique which ensures that particles experience shear by imposing rules for motion and interactions across the boundary in the direction of the shear plane. Despite their presentation in 1972, a readily available public implementation of Lees-Edwards boundary conditions has been missing from MD simulation codes. In this article, we present our implementation of the Lees-Edwards technique and discuss the relevant technical choices. We used ESPResSo, the extensible simulation package for research on soft matter, for molecular dynamics simulations which can be used as a reference for other implementers. We illustrate our implementation using bulk dissipative particle dynamics fluids, compare different viscosity measurement techniques, and observe the anomalous diffusion in our samples during continuous and oscillatory shear, in good comparison to theoretical estimates.

cond-mat.soft↗
arXiv2018

Mesoscopic simulations of anisotropic chemically-powered nanomotors

Chemically powered self-propelled colloids generate a motor force by converting locally a source of energy into directed motion, a process that has been explored both in experiments and in computational models. The use of active colloids as building blocks for nanotechnology opens the doors to interesting applications, provided we understand the behaviour of these elementary constituents. We build a consistent mesoscopic simulation model for self-propelled colloids of complex shape with the aim of resolving the coupling between their translational and rotational motion. Considering a passive L-shaped colloidal particle, we study its Brownian dynamics and locate its center of hydrodynamics, the tracking point at which translation and rotation decouple. The active L particle displays the same circling trajectories that have been found experimentally, a result which we compare with the Brownian dynamics model. We put forward the role of hydrodynamics by comparing our results with a fluid model in which the particles' velocities are reset randomly. There, the trajectories only display random orientations. We obtain these original simulation results without any parametrization of the algorithm, which makes it a useful method for the preliminary study of active colloids, prior to experimental work.

cond-mat.soft↗
arXiv2017

Sustainable computational science: the ReScience initiative

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests.

cs.DL↗
arXiv2017

Passive and active colloidal chemotaxis in a microfluidic channel: mesoscopic and stochastic models

Chemotaxis is the response of a particle to a gradient in the chemical composition of the environment. While it was originally observed for biological organisms, it is of great interest in the context of synthetic active particles such as nanomotors. Experimental demonstration of chemotaxis for chemically-powered colloidal nanomotor was reported in the literature in the context of chemo-attraction in a still fluid or in a microfluidic channel where the gradient is sustained by a specific inlet geometry. In this work, we use mesoscopic particle-based simulations of the colloid and solvent to demonstrate chemotaxis in a microfluidic channel. On the basis of this particle-based model, we evaluate the chemical concentration profiles in the presence of passive or chemically active colloids, compute the chemotactic force acting upon them and propose a stochastic model that rationalises our findings on colloidal chemotaxis. Our model is also able to explain the results of an earlier simulation work that uses a simpler geometry and to extend its interpretation.

cond-mat.soft↗
arXiv2016

Absence of thermalization for systems with long-range interactions coupled to a thermal bath

We investigate the dynamics of a small long-range interacting system, in contact with a large long-range thermal bath. Our analysis reveals the existence of striking anomalies in the energy flux between the bath and the system. In particular, we find that the evolution of the system is not influenced by the kinetic temperature of the bath, as opposed to what happens for short-range collisional systems. As a consequence, the system may get hotter also when its initial temperature is larger than the bath temperature. This observation is explained quantitatively in the framework of the collisionless Vlasov description of toy models with long-range interactions and shown to be valid whenever the Vlasov picture applies, from cosmology to plasma physics.

cond-mat.stat-mech↗
arXiv2016

RMPCDMD: Simulations of colloids with coarse-grained hydrodynamics, chemical reactions and external fields

The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations, and chemically active solvent particles and catalytic colloids. The main usage of RMPCDMD is the simulation of chemically powered nanomotors, but other setups are considered: colloids in the presence of a thermal gradients or forced flows. RMPCDMD is developed in Fortran 2008 with OpenMP for multithreaded operation and uses the HDF5-based H5MD file format for storing data. RMPCDMD comes with documentation and a tutorial for the simulation of chemically powered nanomotors.

physics.comp-ph↗
arXiv2016

Driving-induced stability with long-range effects

We give a sufficient condition under which an applied rotation on medium particles stabilizes a slow probe in the rotation center. The symmetric part of the stiffness matrix thus gets a positive Lamb shift with respect to equilibrium. For illustration we take diffusive medium particles with a self-potential in the shape of a Mexican hat, high around the origin. There is a short-range attraction between the medium particles and the heavier probe, all immersed in an equilibrium thermal bath. For no or small rotation force on the medium particles, the origin is an unstable fixed point for the probe and the precise shape of the self-potential at large distances from the origin is irrelevant for the statistical force there. Above a certain rotation threshold, while the medium particles are still repelled from the origin, the probe stabilizes there and more details of the medium-density at large distance start to matter. The effect is robust around the quasi-static limit with rotation threshold only weakly depending on the temperature but the stabilization gets stronger at lower temperatures.

cond-mat.stat-mech↗
arXiv2015

Generalized maximum entropy approach to quasi-stationary states in long range systems

Systems with long-range interactions display a short-time relaxation towards Quasi Stationary States (QSS) whose lifetime increases with the system size. In the paradigmatic Hamiltonian Mean-field Model (HMF) out-of-equilibrium phase transitions are predicted and numerically detected which separate homogeneous (zero magnetization) and inhomogeneous (nonzero magnetization) QSS. In the former regime, the velocity distribution presents (at least) two large, symmetric, bumps, which cannot be self-consistently explained by resorting to the conventional Lynden-Bell maximum entropy approach. We propose a generalized maximum entropy scheme which accounts for the pseudo-conservation of additional charges, the even momenta of the single particle distribution. These latter are set to the asymptotic values, as estimated by direct integration of the underlying Vlasov equation, which formally holds in the thermodynamic limit. Methodologically, we operate in the framework of a generalized Gibbs ensemble, as sometimes defined in statistical quantum mechanics, which contains an infinite number of conserved charges. The agreement between theory and simulations is satisfying, both above and below the out of equilibrium transition threshold. A precedently unaccessible feature of the QSS, the multiple bumps in the velocity profile, is resolved by our new approach.

cond-mat.stat-mech↗
arXiv2015

A parallel algorithm for step- and chain-growth polymerization in Molecular Dynamics

Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

cond-mat.soft↗
arXiv2014

The vmf90 program for the numerical resolution of the Vlasov equation for mean-field systems

The numerical resolution of the Vlasov equation provides complementary information with respect to analytical studies and forms an important research tool in domains such as plasma physics. The study of mean-field models for systems with long-range interactions is another field in which the Vlasov equation plays an important role. We present the vmf90 program that performs numerical simulations of the Vlasov equation for this class of mean-field models with the semi-Lagrangian method.

physics.comp-ph↗
arXiv2014

H5MD: a structured, efficient, and portable file format for molecular data

We propose a new file format named "H5MD" for storing molecular simulation data, such as trajectories of particle positions and velocities, along with thermodynamic observables that are monitored during the course of the simulation. H5MD files are HDF5 (Hierarchical Data Format) files with a specific hierarchy and naming scheme. Thus, H5MD inherits many benefits of HDF5, e.g., structured layout of multi-dimensional datasets, data compression, fast and parallel I/O, and portability across many programming languages and hardware platforms. H5MD files are self-contained and foster the reproducibility of scientific data and the interchange of data between researchers using different simulation programs and analysis software. In addition, the H5MD specification can serve for other kinds of data (e.g. experimental data) and is extensible to supplemental data, or may be part of an enclosing file structure.

physics.comp-ph↗
arXiv2014

Self-propulsion through symmetry breaking

In addition to self-propulsion by phoretic mechanisms that arises from an asymmetric distribution of reactive species around a catalytic motor, spherical particles with a uniform distribution of catalytic activity may also propel themselves under suitable conditions. Reactive fluctuation-induced asymmetry can give rise to transient concentration gradients which may persist under certain conditions, giving rise to a bifurcation to self-propulsion. The nature of this phenomenon is analyzed in detail, and particle-level simulations are carried out to demonstrate its existence.

cond-mat.stat-mech↗
arXiv2012

Out-of-equilibrium dynamics in systems with long-range interactions: characterizing quasi-stationary states

Systems with long-range interactions (LRI) display unusual thermodynamical and dynamical properties that stem from the non-additive character of the interaction potential. We focus in this work on the lack of relaxation to thermal equilibrium when a LRI system is started out-of-equilibrium. Several attempts have been made at predicting the so-called quasi-stationary state (QSS) reached by the dynamics and at characterizing the resulting transition between magnetized and non-magnetized states. We review in this work recent theories and interpretations about the QSS. Several theories exist but none of them has provided yet a full account of the dynamics found in numerical simulations.

cond-mat.stat-mech↗
arXiv2012

Phoretic self-propulsion: a mesoscopic description of reaction dynamics that powers motion

The fabrication of synthetic self-propelled particles and the experimental investigations of their dynamics have stimulated interest in self-generated phoretic effects that propel nano- and micron-scale objects. Theoretical modeling of these phenomena is often based on a continuum description of the solvent for different phoretic propulsion mechanisms, including, self-electrophoresis, self-diffusiophoresis and self-thermophoresis. The work in this paper considers various types of catalytic chemical reaction at the motor surface and in the bulk fluid that come into play in mesoscopic descriptions of the dynamics. The formulation is illustrated by developing the mesoscopic reaction dynamics for exothermic and dissociation reactions that are used to power motor motion. The results of simulations of the self-propelled dynamics of composite Janus particles by these mechanisms are presented.

cond-mat.soft↗