Particle Dynamics Research Articles

Transferable local density-dependent friction in tert-butanol/water mixtures.

Coarse-grained (CG) models informed from molecular dynamics simulations provide a way to represent the structure of an underlying all-atom (AA) model by deriving an effective interaction potential. However, this leads to a speed-up in dynamics due to the lost friction, which is especially pronounced in CG implicit solvent models. Applying a thermostat based on the Langevin equation (LE) provides a way to represent the long-time dynamics of CG particles by reintroducing friction to the system. To improve the representability CG models of heterogeneous molecular mixtures and their transferability over the mixture compositions, we parameterize an LE thermostat in which the friction coefficient depends on the local particle density (LD). The thermostat friction was iteratively optimized with a Markovian variant of the recently introduced Iterative Optimization of Memory Kernels (IOMK) method. We simulated tert-butanol/water mixtures over a range of compositions, which show a distinct clustering behavior. Our model with LD-dependent friction reproduces the AA diffusion coefficients well over the full range of mixtures and is, therefore, transferable with respect to dynamics.

Numerical simulation of neutral gas dynamics in the W7-X sub-divertor

Abstract The present work presents a 2D and 3D modelling of the neutral gas flow in the sub-divertor region of the W7-X. The investigations have been done using the DIVGAS code. The complex 2D and 3D geometries of the divertor components in the sub-divertor region have been considered and the Standard and High-Iota magnetic configurations have been numerically simulated. The main objective of this study is to investigate the dynamics of neutral particles in the sub-divertor region including the effects due to geometry and toroidal and poloidal leakages located at the divertor targets and baffles on the achieved pumping efficiency. A sensitivity analysis has been performed for the effect of various geometrical and flow parameters on the pumping performance, under different plasma scenarios. The considered incoming fluxes in the sub-divertor range between 1020 to 1022 (H2/s). The main conclusions, which can be extracted from the present numerical analysis could be summarized as follows; a large fraction of incoming neutral particle flux i.e. > 70% on the low iota side and > 40% for the high iota side is leaked back to the main divertor region, while higher incoming neutral fluxes facilitate the increase of the pumped flux as well as the decrease of the outflux. It has been estimated that a small fraction ~3-4% of the incoming neutral flux is being pumped via the turbo-molecular pumps. The closure of the toroidal leakages as well as the inclination of the pumping gap panel by 9 o facilitate the increase of the pumped flux, but considering the all the engineering constraints, the latter option seems to be more easy to be implemented. For low incoming neutral fluxes (~1020 H2/s) and for the case of AEH section, free molecular flow conditions are estimated and therefore neutral-neutral collisions could be neglected. For higher incoming neutral fluxes and for both AEH and AEP sections neutral-neutral collisions play a significant role in the flow establishment. A comparison with available experimental measurements of the neutral pressure in the sub-divertor has been performed for Standard and High-Iota plasma discharges. The 3D DIVGAS simulations predict qualitatively the experimental data with relative deviation between 25 and 63%. All the above numerical findings will actively support the optimization of the W7-X particle exhaust, in view of the experimental campaign OP2.

DPD simulation to reproduce lipid membrane microdomains based on fragment molecular orbital calculations

Abstract Lipid domains play a critical role in signal transduction and transport across cell 
membranes. The formation of domains in "HLC" ternary lipid bilayers composed of high 
transition temperature (high-Tm) lipids, low-Tm lipids, and cholesterol (Chol) has been 
extensively studied as a raft-like system. Recently, experiments were performed to control 
the formation of submicron domains in LLC lipid bilayers containing low-Tm
phosphatidylethanolamine (PE), low-Tm phosphatidylcholine (PC), and Chol by 
manipulating the presence or absence of Chol. The formation of microdomains in this LLC 
mixture was replicated by dissipative particle dynamics (DPD) simulation. The results show 
that domain formation can be replicated.

Reduced Variance Random Batch Methods for Nonlocal PDEs

Random Batch Methods (RBM) for mean-field interacting particle systems enable the reduction of the quadratic computational cost associated with particle interactions to a near-linear cost. The essence of these algorithms lies in the random partitioning of the particle ensemble into smaller batches at each time step. The interaction of each particle within these batches is then evolved until the subsequent time step. This approach effectively decreases the computational cost by an order of magnitude while increasing the amount of fluctuations due to the random partitioning. In this work, we propose a variance reduction technique for RBM applied to nonlocal PDEs of Fokker-Planck type based on a control variate strategy. The core idea is to construct a surrogate model that can be computed on the full set of particles at a linear cost while maintaining enough correlations with the original particle dynamics. Examples from models of collective behavior in opinion spreading and swarming dynamics demonstrate the great potential of the present approach.

Escape from textured adsorbing surfaces.

The escape dynamics of sticky particles from textured surfaces is poorly understood despite importance to various scientific and technological domains. In this work, we address this challenge by investigating the escape time of adsorbates from prevalent surface topographies, including holes/pits, pillars, and grooves. Analytical expressions for the probability density function and the mean of the escape time are derived. A particularly interesting scenario is that of very deep and narrow confining spaces within the surface. In this case, the joint effect of the entrapment and stickiness prolongs the escape time, resulting in an effective desorption rate that is dramatically lower than that of the untextured surface. This rate is shown to abide a universal scaling law, which couples the equilibrium constants of adsorption with the relevant confining length scales. While our results are analytical and exact, we also present an approximation for deep and narrow cavities based on an effective description of one-dimensional diffusion that is punctuated by motionless adsorption events. This simple and physically motivated approximation provides high-accuracy predictions within its range of validity and works relatively well even for cavities of intermediate depth. All theoretical results are corroborated with extensive Monte Carlo simulations.

Diffusion, viscosity, and linear rheology of valence-limited disordered fluids.

We numerically investigate the dynamics and linear rheology of disordered systems made of patchy particles, focusing on the role of valence, temperature, and bonding mechanism. We demonstrate that the dynamics is enslaved to bonding, giving rise to an activated behavior at low temperatures. By independently computing the diffusion constant and the viscosity from the simulations, we also confirm the validity of the Stokes-Einstein relation in valence-limited systems, with two caveats: (i) the diffusion constant requires a finite-size correction, at least at the intermediate density we investigate, and (ii) there is the onset of a breakdown that appears at the lowest temperatures considered. Finally, our results show that the storage and loss moduli of mixtures of divalent and M-valent particles exhibit an apparent power-law dependence on frequency, hinting at the possibility of using the composition to finely tune the rheological response of these materials. Our results compare well with literature experimental data on valence-limited DNA nanostars. In addition, the wealth of data we present and analyze here will help develop and test theoretical frameworks aimed at describing the dynamics of flexible limited-valence particles that self-assemble into disordered networks.

Particle dynamics in a pseudo-2D spouted bed: Experiments and Euler–Lagrange simulations

This study is dedicated to a comprehensive examination of particle dynamics within a pseudo-2D spouted bed, employing a combination of experimental analysis and numerical simulations conducted with the Euler-Lagrange approach. To develop a robust CFD-DEM model for predicting particle dynamics in a pseudo-2D spouted bed, our proposed methodology includes the measurement of DEM parameters based on experimental data, a grid size independence test assessment, and an analysis of appropriate turbulent models and wall boundary conditions for the fluid phase. The effect of different operating conditions, e.g., particle mass and inlet air velocity, on the complex turbulent multiphase flow behavior is assessed. Additionally, we numerically investigated the frequency of collisions between particles and the temporal changes in collisional forces across various conditions. The experiments and numerical simulations provide valuable insights into the intricacies of particle dynamics within a pseudo-2D spouted bed, offering essential knowledge for the optimization of processes employing this equipment.

Development of 6-way CFD-DEM-FEM momentum coupling interface using partitioned coupling approach

Fluid-particle-structure interactions (FPSI) govern a wide range of natural and engineering phenomena, from landslides to erosion in abrasive water jet cutting nozzles. Despite the importance of studying FPSI, existing numerical frameworks often simplify or neglect certain physics, limiting their applicability. This work introduces a novel 6-way CFD-DEM-FEM momentum coupling for FPSI using a partitioned coupling approach, providing a flexible and adaptable solution.Our prototype uses the preCICE coupling library to couple three numerical solvers: OpenFOAM for fluid dynamics, eXtended Discrete Element Method (XDEM) for particle motion, and CalculiX for structural mechanics. The coupling approach extends existing adapters and introduces a novel XDEM preCICE adapter, allowing data exchange over surface and volumetric meshes.Numerical experiments successfully demonstrate the 6-way coupling, showcasing fluid-structure interactions and particle dynamics. The versatility of the partitioned coupling approach is highlighted, allowing the interchangeability of different single-physics solvers and facilitating the study of complex FPSI phenomena.This article offers a thorough description of the methodology, coupling strategies, and detailed results, offering insights into the advantages and disadvantages of the proposed approach. This work lays the groundwork for a scalable and customizable FPSI simulation framework with a wide range of applications.

Dissipative particle dynamics for coarse-grained models

We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully off-lattice method that allows straightforward incorporation of hydrodynamics at desired solvent viscosity, compressibility, and solute diffusivity with any particle-based solute model. Solutes interact with the solvent only through the DPD thermostat, which ensures that the equilibrium properties of the solute system are not affected by the introduction of the DPD solvent, while the thermostat coupling strength sets the desired solute diffusivity. Thus, DPDS can be used as a replacement for traditional molecular dynamics thermostats such as Nosé–Hoover and Langevin. We demonstrate the applicability of DPDS in the case of polymer dynamics and electroosmotic flow through a nanopore. The method should be broadly useful as a means to introduce hydrodynamic interactions to existing coarse-grained models of solutes and soft materials.

Particle dynamic behaviors in bubble curtain barriers blocking the diffusion of sediment

Bubble curtains are linear multiphase plumes that are used in industry and engineering to reduce diffusive flows between two zones. The circulating shear flow generated by the bubble plume can effectively create a particle barrier in the water; thus, it is also widely used to suppress the diffusion of suspended particles during dredging operations. To clarify the interaction mechanism between the bubble curtain and suspended particles under pressure-driven flow, experimental studies and numerical simulations were conducted to investigate the particle dynamics in the flow field around the bubble curtain. In this study, we established a formal analogy between a bubble curtain and an air curtain and qualitatively identified four typical distribution zones of the particles in the flow field. Based on the quantitative measurements and theoretical considerations, the optimal operating conditions and the upper limit of effectiveness of the bubble curtain were determined. In addition, the blocking behavior and efficiency of bubble plumes on particles with different ReU and FrUgnumbers and different particle properties were simulated via the computational fluid dynamicsdiscrete element method (CFDDEM) numerical simulation method.

Excitation signal optimization for minimizing fluctuations in knock out slow extraction

The synchrotron is a circular particle accelerator used for high energy physics experiments, material and life science, as well as hadron cancer therapy. After acceleration to the desired energies, particle beams are commonly extracted from the synchrotron using the method of resonant slow extraction. The goal is to deliver a steady particle flux—referred to as spill—to experiments and treatment facilities over the course of seconds while slowly emptying the storage ring. Any uncontrolled intensity fluctuations in the spill are detrimental to the efficiency of beam usage, as they lead to detector pileups or detector interlocks, hindering experiments and cancer treatment. Among the most widely used extraction scheme in medical facilities is the Radio Frequency Knock Out (RF-KO) driven resonant slow extraction, where the stored beam is transversely excited with a radio frequency (RF) field and the spill intensity is controlled by the excitation signal strength. This article presents particle dynamics simulations of the RF-KO system with the focus on finding effective mechanism for minimizing the intensity fluctuations while maintaining a good extraction efficiency and other advantages of KO extraction. An improved beam excitation signal which optimizes these main objectives is found, and is rigorously compared experimentally with other commonly applied techniques.

Dual targeting total saponins of Pulsatilla of natural polymer crosslinked gel beads with multiple therapeutic effects for ulcerative colitis

Oral colon targeted drug delivery system (OCTDDS) is desirable for the treatment of ulcerative colitis (UC). In this study, we designed a partially oxidized sodium alginate-chitosan crosslinked microsphere for UC treatment. Dissipative particle dynamics (DPD) was used to study the formation and enzyme response of gel beads from a molecular perspective. The formed gel beads have a narrow particle size distribution, a compact structure, low cytotoxicity and great colon targeting in vitro and in vivo. Animal experiments demonstrated that gel beads promoted colonic epithelial barrier integrity, decreased the level of pro-inflammatory factors, accelerated the recovery of intestinal microbial homeostasis in UC rats and restored the intestinal metabolic disorders. In conclusion, our gel bead is a promising approach for the treatment of UC and significant for the researches on the pathogenesis and treatment mechanism of UC.

Quasi-periodic oscillations and particle motion around charged black hole surrounded by a cloud of strings and quintessence field in Rastall gravity

This work mainly focuses on unveiling the particle dynamics features of black holes. For this objective, we utilize the charged black hole geometry consisting of the cloud strings and quintessence under the ansatz of Rastall gravity. We have calculated and analyzed the effective potential, angular momentum, particle energy, horizon radius, inner stable circular orbit, photon sphere radius, quasi-periodic oscillations, and effective force to reveal the dynamical features. We in detail discussed the effects of charge in black hole, Rastall parameter, strings of cloud parameter, and quintessential parameter on the calculated results. To ensure the scenario of accelerated expansion, ω q lies in the range −1 < ω q < −1/3. From this specific range, we choose ω q = −2/3.

A new dynamic Monte Carlo method satisfying n-particle diffusion equation with position-dependent diffusion coefficient, free energy, and intermolecular interactions

A dynamic Monte Carlo (MC) method recently proposed by us [Nagai et al., J. Chem. Phys. 156, 154506 (2022)] to describe single-particle diffusion of a molecule in a heterogeneous space with position-dependent diffusion coefficient and free energy is generalized here to n-particle dynamics, where n molecules diffuse in heterogeneous media interacting via their intermolecular potential. Starting from the master equation, we give an algebraic proof that the dynamic MC transition probabilities proposed here produce particle trajectories that satisfy the n-particle diffusion equation with position-dependent diffusion coefficient D0i(ri), free energy F1i(ri), and intermolecular interactions Vij(ri, rj). The MC calculations based on this method are compared to molecular dynamics (MD) calculations for two-dimensional heterogeneous Lennard-Jones test systems, showing excellent agreement of the long-distance global diffusion coefficient between the two cases. Thus, the particle trajectories produced by the present MC transition probabilities satisfy the n-particle diffusion equation, and the diffusion equation well describes the long-distance trajectories produced by the MD calculations. The method is also an extension of the conventional equilibrium Metropolis MC calculation for homogeneous systems with a constant diffusion coefficient to the dynamics in heterogeneous systems with a position-dependent diffusion coefficient and potential. In the present method, interactions and dynamics of the real systems are coarse-grained such that the calculation cost is drastically reduced. This provides an approach for the investigation of particle dynamics in very complex and large systems, where the diffusing length is of sub-micrometer order and the diffusion time is of the order of milliseconds or more.

Advanced fuel fusion, phase space engineering, and structure-preserving geometric algorithms

Non-thermal advanced fuel fusion trades the requirement of a large amount of recirculating tritium in the system for that of large recirculating power. Phase space engineering technologies utilizing externally injected electromagnetic fields can be applied to meet the challenge of maintaining non-thermal particle distributions at a reasonable cost. The physical processes of the phase space engineering are studied from a theoretical and algorithmic perspective. It is emphasized that the operational space of phase space engineering is limited by the underpinning symplectic dynamics of charged particles. The phase space incompressibility according to the Liouville theorem is just one of many constraints, and Gromov's non-squeezing theorem determines the minimum footprint of the charged particles on every conjugate phase space plane. In this sense and level of sophistication, the mathematical abstraction of phase space engineering is symplectic topology. To simulate the processes of phase space engineering, such as the Maxwell demon and electromagnetic energy extraction, and to accurately calculate the minimum footprints of charged particles, recently developed structure-preserving geometric algorithms can be used. The family of algorithms conserves exactly, on discretized spacetime, symplecticity and thus incompressibility, non-squeezability, and symplectic capacities. The algorithms apply to the dynamics of charged particles under the influence of external electromagnetic fields as well as the charged particle–electromagnetic field system governed by the Vlasov–Maxwell equations.

From primary HPV infection to carcinoma in situ: A mathematical approach to cervical intraepithelial neoplasia

AbstractCervical intraepithelial neoplasia (CIN) is the development of abnormal cells on the surface of the cervix, caused by a human papillomavirus (HPV) infection. Although in most of the cases it is resolved by the immune system, a small percentage of people might develop a more serious CIN which, if left untreated, can develop into cervical cancer. Cervical cancer is the fourth most common cancer in women globally, for which the World Health Organization (WHO) recently adopted the Global Strategy for cervical cancer elimination by 2030. With this research topic being more imperative than ever, in this paper, we develop a nonlinear mathematical model describing the CIN progression. The model consists of partial differential equations describing the dynamics of epithelial, dysplastic, and immune cells, as well as the dynamics of viral particles. We use our model to explore numerically three important factors of dysplasia progression, namely, the geometry of the cervix, the strength of the immune response, and the frequency of viral exposure.

Dynamics of the surface growth resulted from sedimentation of spheres in a Hele–Shaw cell containing a low-viscosity fluid

In this paper, we investigate the dynamics of surface growth resulting from sedimentation of spherical granular particles in a fluid environment, using experiments and simulations. In the experimental part, spherical polystyrene particles are poured down from the top of a vertical Hele–Shaw cell and form a 1 + 1-dimensional growing surface. The surface roughness is obtained from the images, and the growth and roughness exponents are measured. In the numerical simulation part, the surface growth process is simulated using the discrete element method, considering the interactions between the grains, and the exponents are calculated. In this method, unlike conventional simulation models, instead of a discrete deposition law, the dynamics of the individual particles throughout the process are obtained, considering different forces acting on the particles. Finally, the simulation results are compared with the experiment, and we see a very good agreement between them. We find different values for the exponents using different methods, indicating that the system is multi-affine and does not obey the scaling laws of affine models.

Investigation of morphology and structure of drug-loaded PLA-b-PEO-b-PLA polymeric micelle: A dissipative particle dynamics simulations study.

The dissipative particle dynamics (DPD) simulation was used to study the morphologies and structures of the paclitaxel-loaded PLA-b-PEO-b-PLA polymeric micelle. We focused on the influences of PLA block length, PLA-b-PEO-b-PLA copolymer concentration, paclitaxel drug content on morphologies and structures of the micelle. Our simulations show that: (i) with the PLA block length increase, the self-assemble structure of PLA-b-PEO-b-PLA copolymers with paclitaxel vary between onion-like structure (core-middle layer-shell) to spherical core-shell structure. The PEO shell thins and the size of the PLA core increases. The onionlike structures are comprised of the PEO hydrophilic core, the PLA hydrophobic middle layer, and the PEO hydrophilic shell, the distribution of the paclitaxel drug predominantly occurs within the hydrophobic intermediate layer; (ii) The system forms a spherical core-shell structure when a small amount of the drug is added, and within a certain range, the size of the spherical structure increases as the drug amount increases. When the drug contents (volume fraction) cdrug = 10%, it can be observed that the PLA4-b-PEO19-b-PLA4 spherical structures connect to form rod-shaped structures. With the length of PLA block NPLA = 8, as the paclitaxel drug concentrations cdrug = 4%, PEO has been insufficient to completely encapsulate the PLA and paclitaxel drug beads. To enhance drug loading capacity while maintaining stability of the system in aqueous solution, the optimal composition for loading paclitaxel is PLA4-b-PEO19-b-PLA4; the drug content is not higher than 4%; (iii) The paclitaxel-loaded PLA4-b-PEO19-b-PLA4 micelle undergo the transition from onionlike (core-middle layer-shell) to spherical (core-shell) to rod-shaped and lamellar structure as the PLA4-b-PEO19-b-PLA4 copolymer concentration increases from ccp = 10% to 40%.

Understanding self-assembly mechanisms in supramolecular fiber materials through multiscale simulation

Supramolecular materials, assembled through non-covalent interactions, have emerged as a versatile and tunable platform for the development of advanced functional materials with tailored properties and applications. However, comprehending the interactions between self-assembled monomers at the molecular level, particularly when organized into fibrous structures, remains a considerable challenge. In this study, we discovered that solely relying on all-atomistic molecular dynamics simulations is insufficient to reproduce the self-assembly process and the formation of fibrous supramolecular structures. Thus, we combined dissipative particle dynamics (DPD) and all-atomistic molecular dynamic simulations to accurately simulate the fibrous supramolecular structures previously observed in experiments. These structures consist of benzene-1,3,5-tricarboxamide (BTA-EG4), 2-ureido-4 [1H]-pyrimidinone-ethylene glycol molecules (UPy-EG), and glycyrrhizic acid (GA) molecules, each exhibiting varying degrees of topology and planarity. Our analyses focused on elucidating the stability mechanism of these fibrous structures. Notably, we found that hydrogen bonds, π-π interactions and nonbonded interactions, especially Coulomb interaction between monomers and water molecules, play pivotal roles in stabilizing these fibrous structures. This study significantly contributes to our understanding of self-assembly mechanism in supramolecular fiber materials and opens avenues for extending this knowledge to other fibrous supramolecular architectures.

Multi-wavelength pulse profiles from the force-free neutron star magnetosphere

The last two decades have witnessed dramatic progress in our understanding of neutron star magnetospheres thanks to force-free and particle-in-cell simulations. However, the associated particle dynamics and its emission mechanisms and locations have not been fully constrained, notably in X-rays. In this paper, we compute a full atlas of radio, X-ray, and gamma -ray pulse profiles, relying on the force-free magnetosphere model. Our goal is to use such a data bank of multi-wavelength profiles to fit a substantial number of radio-loud gamma -ray pulsars that have also been detected in non-thermal X-rays to decipher the X-ray radiation mechanism and sites. Using results from the third gamma -ray pulsar catalogue (3PC), we investigate the statistical properties of this population. We assume that radio emission emanates from field lines rooted to the polar caps, at varying height above the surface, close to the surface, at an altitude about 5-10&lt;!PCT!&gt; of the light cylinder radius, rlight . The X-ray photons are produced in the separatrix region within the magnetosphere; that is, the current sheet formed by the jump from closed to open magnetic field lines. We allow for substantial variations in emission height. The gamma -rays are produced within the current sheet of the striped wind, outside the light cylinder. A comprehensive set of radio, X-ray, and gamma -ray light curves was computed. Based on only geometric considerations about magnetic obliquity, line-of-sight inclination, and the radio beam cone opening angle, pulsars can be classified as radio-loud or quiet and as gamma -ray-loud or quiet. We found that the 3PC sample is compatible with an isotropic distribution of obliquity and line of sight. The atlases constructed in this work are the fundamental tools with which to explore individual pulsars and fit their multi-wavelength pulse profiles in order to constrain their magnetic topology, the emission sites, and the observer's line of sight.