Constant Number Of Particles Research Articles

Single cell-inductively coupled plasma-mass spectrometry (SC-ICP-MS) reveals metallic heterogeneity in a macrophage model of infectious diseases.

Single cell-inductively coupled plasma-mass spectrometry (SC-ICP-MS) offers an attractive option for rapidly measuring trace metal heterogeneity at the single cell level. Chemical fixation has been previously applied to mammalian cells prior to sample introduction so that they can be resuspended in a solution suitable for SC-ICP-MS. However, the effect of fixation on the elemental composition of suspended cells is unknown, and robust methodologies are urgently needed so that the community can measure the effects of intracellular pathogens on elemental composition of their host cells. We demonstrate that different fixatives impact measured cell elemental composition. We have compared suspensions treated using different fixatives (methanol 60-100% in H2O and 4% paraformaldehyde in phosphate-buffered saline solution), and the number of distinguishable single cell events, keeping a constant particle number concentration. Significantly more single cell events (n = 3, P ≤ 0.05) were observed for Ca and Mg when cells were fixed in 4% paraformaldehyde than for the methanol-based fixatives, confirming the hypothesis that methanol fixatives cause leaching of these elements from the cells. The impact of fixation on Mn and Zn was less pronounced. Microbial and viral infection of eukaryotic cells can have profound effects on their elemental composition, but chemical fixation is necessary to render infected cells safe before analysis. We have successfully applied our methodology to a macrophage model of tuberculosis demonstrating utility in understanding metal homeostasis during microbial infection of mammalian cells.

Behavioral swarms: A mathematical theory toward swarm intelligence

This paper presents a mathematical theory of behavioral swarms, where the state of interacting entities, which are called active particles, includes in addition to position and velocity, an internal variable, called activity, which has the ability to interact with mechanical variables thus affecting the interaction rules. In turn, the mechanical variables can modify the dynamics of activity variable. This approach is useful for describing the dynamics of living systems with a finite number of interacting entities. This paper provides a general conceptual framework that extends the pioneering work [N. Bellomo, S.-Y. Ha and N. Outada, Towards a mathematical theory of behavioral swarms, ESAIM: Control Theory Var. Calculus 26 (2020) 125, https://doi.org/10.1051/cocv/2020071 ]. The theory is firstly developed for the constant number of active particles. Then, it is considered for the case of particles tending to infinity. This theory is useful for describing the dynamics of living systems. Therefore, it provides the conceptual basis for developing a mathematical theory of behavioral swarms, which naturally lead to the study of a theory of swarm intelligence. A study of the dynamics of swarms shows how the theory can be applied to real world collective dynamics.

Research on AGV composition algorithm based on variable and complex environment

Aiming at the traditional Gmapping algorithm with constant number of particles, which lead to the failure of composition in variable and complex environments, based on SLAM mapping technology, this paper proposed an Adaptive Sampling (AS) algorithm, which increased the number of sampling particles when the fluctuation of the 2D laser point cloud is larger than a certain threshold, and the experimental results shown that the algorithm was able to reasonably utilize the system resources, and effectively enhanced the algorithm’s ability to compose maps in a variable and complex environment. In addition, in order to make the system have a better effect of building maps in complex environments, this paper also integrated the firefly algorithm (AF) with it, and utilized AF’s high aggregation ability to improve the distribution of sampling particles, which then improved the estimation ability of the filter. Verified by offline real environment experiments, the results shown that the optimized algorithm significantly improves the map building ability of the system.

THRESHOLD EFFECT IN DUSTY CLUSTERS IN A MAGNETIC FIELD

The process of occurrence of rotational motion of dusty plasma in a longitudinal magnetic field was investigated. It was experimentally found that the occurrence of rotation depends on the number of dust particles in the direction perpendicular to the magnetic induction vector, as well as on their vertical position in the dust trap (i.e., the magnitude of the electric field). The value of the threshold for the appearance of rotation in the magnetic field at a constant number of particles depends on the particle size and discharge conditions. The parameters of the experiment are selected, at which the effect manifests itself in detail. It has been established that for stationary rotation, a stable position of dust particles in the cross section is required, which corresponds to the filling of the shells of a rotating dust structure.

Stability and mechanical, thermodynamic and optical properties of WC polytypes and the TiC-WC solid solutions: A first-principles study

First-principles calculations and molecular dynamics (FPMD) simulations in the constant number of particles – pressure – temperature (NPT) ensemble were used to investigate the phase stability, phase diagram, electronic and phonon structures, chemical bonding, mechanical, thermodynamical and optical properties of various tungsten carbide polytypes as well as the hexagonal (α) and cubic (β) Ti1-xWxCy solid solutions. The known α-WC (P-6m2) and β-WCy (Fm-3m) polytypes and eight hypothetical ones were studied. Gibbs free energy calculations predicted the α-WC → β-WCy and α-WC → tP4-129 (P4/nmm) phase transitions. The P-6m2 → Fm-3m → I41md, Fm-3m → P4/nmm and P-6m2 → Pm-3m phase transformations were revealed during FPMD simulations of: α-WC at T = 2500 K, β-WC at T = 100 K, and α-WC at T = 2500 K and P = 500 GPa, respectively. It is found that the known α-polytype and new tI8-109 (I41md), oP12-25 (Pmm2), hP4-194 (P63/mmc), hP8-194 (P63/mmc), cP2-221 polytypes are ultraincompressible and ultrastiff materials, and exhibit the highest hardness (29–38 GPa), fracture toughness (4.7–7.2 MPa m1/2) and Debye temperature (615–663 GPa). Other characteristics of the WC polytypes, namely, the stress-shear strain curves, dielectric function, reflectivity spectra, heat capacity and spatial distribution of the elastic moduli, were calculated and discussed. The stability, mechanical properties and lattice parameter of β-WCy and Ti1-xWxCy as functions of composition were studied. The binodal and spinodal for Ti1-xWxC were calculated. The calculated characteristics are compared with available experimental data and used for their interpretation.

Electrodynamic suspension of particles with finite electrical conductivity

The electrodynamic suspension of micrometric inertialess particles with finite electrical conductivity in the gap between two parallel horizontal electrodes subjected to a DC potential difference is analyzed in a collision-dominated regime in which the mean free path between particle collisions is small compared with the interelectrode distance. Operation with a constant number of suspended particles and with an excess of particles deposited on the lower electrode are modelled. Stationary solutions in a laterally unbounded gap are computed and their linear stability is analyzed. In both cases, these solutions become unstable when the number of suspended particles increases, and they transition to time dependent solutions. Numerical computations show that particle and charge accumulations develop at the lower electrode and eventually become electrohydrodynamic plumes rising across the gap. The electric current carried by the suspended particles from the lower to the upper electrode is a rapidly increasing function of the particle conductivity.

Synthesis and characterization of rutin-loaded micelles for glioblastoma multiforme treatment: A computational and experimental study

The current experiments aimed to develop an anti-glioblastoma multiforme (GBM) formulation based on rutin-loaded nanomicelles. First, the molecular structure of water, and ethanol was constructed using Material Studio software. Then, the structure of the molecules was optimized through the Forcite module in the software. In sequence, to set the temperature of the system the MD simulations were run under the NVT ensemble (constant number of particles, volume, and temperature) with velocity scale as a thermostat and total simulation time equal to 100 ps as the initialization step. We applied the hydrophobic-hydrophobic interactions and micellization process method to encapsulate rutin into micellar nanoparticles. The computational studies showed that in the first 30 ps of the simulation the system is unstable, but after that, the system reached a stable condition. Moreover, we observed that the density of the system rapidly decreased from 0.98 g/cm3 to a stable mean value equal to 0.95 g/cm3. The characterizations using DLS and SEM imaging showed that the synthesized NPs have a size lower than 100 nm. The hemolysis evaluation showed that the Rut-micelles are hemocompatible and induced lower than 10% hemolysis in all tested groups. The highest cell lethality was observed in the group treated with the synthesized Rut-micelles with a concentration of 400 μM, which was statistically significant (p < 0.05) to the control and other test groups. The anti-metastatic effect of the Rut-micelles was confirmed via the cell monolayer wound scratch assay. These results illustrated that the synthesized rutin-loaded nanomicelles could be applied as a GBM treatment option to improve the treatment efficiency of glioblastoma multiforme.

Estimation of bubble cavitation rates in a symmetrical Lennard-Jones mixture by NVT seeding simulations.

The liquid-vapor transition starts with the formation of a sufficiently large bubble in the metastable liquid to trigger the phase transition. Understanding this process is of fundamental and practical interest, but its study is challenging because it occurs over timescales that are too short for experiments but too long for simulations. The seeding method estimates cavitation rates by simulating a liquid in which a bubble is inserted, thus avoiding the long times needed for its formation. In one-component systems, in the NpT ensemble, the bubble grows or redissolves depending on whether its size is larger or smaller than the critical size, whereas in the NVT ensemble (i.e., at constant number of particles, volume, and temperature), the critical bubble can remain in equilibrium. Provided that a good criterion is used to determine the bubble size, this method, combined with the Classical Nucleation Theory (CNT), gives cavitation rates consistent with those obtained by methods independent of the CNT. In this work, the applicability of NVT seeding to homogeneous cavitation in mixtures is demonstrated, focusing on a partially miscible symmetrical binary Lennard-Jones (LJ) liquid at a temperature within the mixing regime. At the same stretching pressure, cavitation rates are higher in the binary mixture than in the pure liquid due to the lower interfacial free energy of the mixture. Curiously, the cost of creating a bubble is similar in the pure and binary LJ liquids at the same metastability, Δμ/Δμspin, with Δμ being the difference in chemical potential between the metastable liquid and coexistence, and Δμspin between the spinodal and coexistence.

Thermodynamics of stationary states of the ideal gas in a heat flow.

There is a long-standing question as to whether and to what extent it is possible to describe nonequilibrium systems in stationary states in terms of global thermodynamic functions. The positive answers have been obtained only for isothermal systems or systems with small temperature differences. We formulate thermodynamics of the stationary states of the ideal gas subjected to heat flow in the form of the zeroth, first, and second law. Surprisingly, the formal structure of steady state thermodynamics is the same as in equilibrium thermodynamics. We rigorously show that U satisfies the following equation dU = T*dS* - pdV for a constant number of particles, irrespective of the shape of the container, boundary conditions, the size of the system, or the mode of heat transfer into the system. We calculate S* and T* explicitly. The theory selects stable nonequilibrium steady states in a multistable system of ideal gas subjected to volumetric heating. It reduces to equilibrium thermodynamics when heat flux goes to zero.

Quantitative Analysis of Core Lipid Production in Methanothermobacter marburgensis at Different Scales.

Archaeal lipids have a high biotechnological potential, caused by their high resistance to oxidative stress, extreme pH values and temperatures, as well as their ability to withstand phospholipases. Further, methanogens, a specific group of archaea, are already well-established in the field of biotechnology because of their ability to use carbon dioxide and molecular hydrogen or organic substrates. In this study, we show the potential of the model organism Methanothermobacter marburgensis to act both as a carbon dioxide based biological methane producer and as a potential supplier of archaeal lipids. Different cultivation settings were tested to gain an insight into the optimal conditions to produce specific core lipids. The study shows that up-scaling at a constant particle number (n/n = const.) seems to be a promising approach. Further optimizations regarding the length and number of the incubation periods and the ratio of the interaction area to the total liquid volume are necessary for scaling these settings for industrial purposes.

On the thermodynamics of curved interfaces and the nucleation of hard spheres in a finite system.

We determine, for hard spheres, the Helmholtz free energy of a liquid that contains a solid cluster as a function of the size of the solid cluster by means of the formalism of the thermodynamics of curved interfaces. This is done at the constant total number of particles, volume, and temperature. We show that under certain conditions, one may have several local minima in the free energy profile, one for the homogeneous liquid and others for the spherical, cylindrical, and planar solid clusters surrounded by liquid. The variation of the interfacial free energy with the radius of the solid cluster and the distance between equimolar and tension surfaces are inputs from simulation results of nucleation studies. This is possible because stable solid clusters in the canonical ensemble become critical in the isothermal-isobaric ensemble. At each local minimum, we find no difference in chemical potential between the phases. At local maxima, we also find equal chemical potential, albeit in this case the nucleus is unstable. Moreover, the theory allows us to describe the stable solid clusters found in simulations. Therefore, we can use it for any combination of the total number of particles, volume, and global density as long as a minimum in the Helmholtz free energy occurs. We also study under which conditions the absolute minimum in the free energy corresponds to a homogeneous liquid or to a heterogeneous system having either spherical, cylindrical, or planar geometry. This work shows that the thermodynamics of curved interfaces at equilibrium can be used to describe nucleation.

Fluctuations of a swarm of Brownian bees.

The "Brownian bees" model describes an ensemble of N independent branching Brownian particles. When a particle branches into two particles, the particle farthest from the origin is eliminated so as to keep the number of particles constant. In the limit of N→∞, the spatial density of the particles is governed by the solution of a free boundary problem for a reaction-diffusion equation. At long times the particle density approaches a spherically symmetric steady-state solution with a compact support. Here, we study fluctuations of the "swarm of bees" due to the random character of the branching Brownian motion in the limit of large but finite N. We consider a one-dimensional setting and focus on two fluctuating quantities: the swarm center of mass X(t) and the swarm radius ℓ(t). Linearizing a pertinent Langevin equation around the deterministic steady-state solution, we calculate the two-time covariances of X(t) and ℓ(t). The variance of X(t) directly follows from the covariance of X(t), and it scales as 1/N as to be expected from the law of large numbers. The variance of ℓ(t) behaves differently: It exhibits an anomalous scaling (1/N)lnN. This anomaly appears because all spatial scales, including a narrow region near the edges of the swarm where only a few particles are present, give a significant contribution to the variance. We argue that the variance of ℓ(t) can be obtained from the covariance of ℓ(t) by introducing a cutoff at the microscopic time 1/N where the continuum Langevin description breaks down. Our theoretical predictions are in good agreement with Monte Carlo simulations of the microscopic model. Generalizations to higher dimensions are briefly discussed.

Anionic Tuning of Zeolite Crystallization

Zeolites are of great industrial relevance as catalysts, adsorbents, and ion-exchangers and typically synthesized under hydrothermal conditions. Rational regulation of their crystallization process...

Effect of Material and Population on the Delivery of Nanoparticles to an Atherosclerotic Plaque: A Patient-specific In Silico Study.

Coronary artery disease (CAD) is the prevalent reason of mortality all around the world. Targeting CAD, specifically atherosclerosis, with controlled delivery of micro and nanoparticles, as drug carriers, is a very proficient approach. In this work, a patient-specific and realistic model of an atherosclerotic plaque in the left anterior descending (LAD) artery was created by image-processing of CT-scan images and implementing a finite-element mesh. Next, a fluid-solid interaction simulation considering the physiological boundary conditions was conducted. By considering the simulated force fields and particle-particle interactions, the correlation between injected particles at each cardiac cycle and the surface density of adhered particles over the atherosclerotic plaque (SDP) were examined. For large particles (800 and 1000 nm) the amount of SDP on the plaque increased significantly when the number of the injected particles became higher. However, by increasing the number of the injected particles, for the larger particles (800 and 1000 nm) the increase in SDP was about 50% greater than that of the smaller ones (400 and 600 nm). Furthermore, for constant number of particles, depending on their size, different trends in SDP were observed. Subsequently, the distribution and adhesion of metal-based nanoparticles including SiO2, Fe3O4, NiO2, silver and gold with different properties were simulated. The injection of metal particles with medium density among the considered particles resulted in the highest SDP. Remarkably, the affinity, the geometrical features, and the biophysical factors involved in the adhesion outweighed the effect of difference in the density of particles on the SDP. Finally, the consideration of the lift force in the simulations significantly reduced the SDP and consistently decreased the particle residence time in the studied domain.

EXPERIMENTAL STUDY OF THE TRANSFER OF MICROPARTICLES IN A THIN LIQUID LAYER UNDER THE INFLUENCE OF A TEMPERATURE GRADIENT

This article studies the main regularities of polyethylene microparticles transfer process in a layer of volatile and non-volatile fluid by thermocapillary currents under local heating and cooling. The authors show the possibility of creating circular and ring-shaped patterns by inducing positive and negative radial-directional temperature gradients. A methodology and computer program have been developed to quantify the transfer process, consisting in measuring the area of the particle pattern (assembly) formed during heating and the area freed from the particles (cleaning area) during cooling on a sequence of video recording frames obtained with an optical microscope. This technique is based on comparing the intensity of image pixels with respect to a threshold value and counting the total area of pixels occupied or not occupied by particles. The influence of such experiment parameters as the volume of the carrier fluid (layer thickness), at a constant number of particles, fluid evaporation and the ratio of particle and fluid densities on the size of the resulting pattern and the time of reaching the steady state has been established. The results show that the area of the final pattern during local heating and the clearing area, during local cooling, tends to decrease with increasing layer thickness, while the time of reaching the steady state does not depend on the layer thickness, but depends on the properties of the liquid and the ratio of particle and liquid densities.

A Notable Quasi-Relativistic Wave Equation and Its Relation to the Schr&amp;amp;ouml;dinger, Klein-Gordon, and Dirac Equations

An intriguing quasi-relativistic wave equation, which is useful between the range of applications of the Schrödinger and the Klein-Gordon equations, is discussed. This equation allows for a quantum description of a constant number of spin-0 particles moving at quasi-relativistic energies. It is shown how to obtain a Pauli-like version of this equation from the Dirac equation. This Pauli-like quasi-relativistic wave equation allows for a quantum description of a constant number of spin-1/2 particles moving at quasi-relativistic energies and interacting with an external electromagnetic field. In addition, it was found an excellent agreement between the energies of the electron in heavy Hydrogen-like atoms obtained using the Dirac equation, and the energies calculated using a perturbation approach based on the quasi-relativistic wave equation. Finally, it is argued that the notable quasi-relativistic wave equation discussed in this work provides interesting pedagogical opportunities for a fresh approach to the introduction to relativistic effects in introductory quantum mechanics courses.

The influence of binary mixtures' structuring on the calculation of Kirkwood-Buff integrals: A molecular dynamics study

The Kirkwood-Buff integrals (KBIs) provide a link between structuring on an atomic scale accessed by simulations and thermodynamics, which makes it a powerful tool for bridging the gap between microscopic and macroscopic quantities. Here we present the simulation study of the concentration dependence of KBIs for various types of binary ethanol mixtures which range from simple to complex. The thermodynamically ideal but extensively clustered methanol-ethanol mixture shows linearity in KBIs. The non-ideal mixtures, ethanol-water and ethanol-benzene, have the extrema in KBIs which are linked to the formation of the domains due to the association of molecules of the same species. We also explore some of the issues in KBI calculation, as KBI, a property of an open ensemble, is usually obtained by using the running integrals of a pair correlation function, calculated from the simulation of constant number of particles placed in a finite simulation box. The study includes a multifaceted analysis of the LP shift (J. Mol. Liq. 159, 52, 2011) and Ganguly and van der Vegt correction (J. Chem. Theory Comput. 9(3), 1347, 2013) of the radial distribution function, and compares different approaches in the computation of running KBI (J. Phys. Chem. Lett. 4(2), 235, 2013), both of which compensate for finite-size and ensemble effects. The results show how the best approach to the KBI calculation varies depending on the structural complexity of the simulated system.

Molecular Dynamics Simulations of Channelrhodopsin Chimera, C1C2.

Molecular dynamics (MD) simulations have been successfully used for modeling dynamic behavior of biologically relevant systems, such as ion channels in representative environments to decode protein structure-function relationships. Protocol presented here describes steps for generating input files and modeling a monomer of transmembrane cation channel, channelrhodopsin chimera (C1C2), in representative environment of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) planar lipid bilayer, TIP3P water and ions (Na+ and Cl-) using molecular dynamics package NAMD, molecular graphics/analysis tool VMD, and other relevant tools. MD simulations of C1C2 were performed at 303.15K and in constant particle number, isothermal-isobaric (NpT) ensemble. The results of modeling have helped understand how key interactions in the center of the C1C2 channel contribute to channel gating and subsequent solvent transport across the membrane.

Insight into structural properties of polyethylene glycol monolaurate in water and alcohols from molecular dynamics studies.

By means of molecular dynamics (MD) simulations, we explored the structural properties of polyethylene glycol monolaurate (PEGML) in water and in various aliphatic alcohols (methanol, ethanol, 2-propanol, 2-butanol, tert-butanol, and 1-pentanol). The PEGML and the alcohols were simulated using the optimized potentials for liquid simulations, all-atom (OPLS-AA) force field and water using the extended simple point charge (SPC/E) model. From the isothermal-isobaric (NPT, constant number of particles, constant pressure, and constant temperature) ensemble, we extracted the densities from the simulations and compared them with those from experimental results in order to confirm the validity of the selected force fields. The densities from MD simulations are in good agreement with the experimental values. To gain more insight into the nature of interactions between the PEGML and the solvent molecules, we analyzed the hydrogen-bonds, the electrostatic (Coulomb) interactions, and the van der Waals (Lennard-Jones) interaction energies extracted from MD simulations. The results were further strengthened by computing the solvation free energy by employing the free energy perturbation (FEP) approach. In this method, the free energy difference was computed by using the Bennet Acceptance Ratio (BAR) method. Moreover, the radial distribution functions were analyzed in order to gain more understanding of the solution behavior at the molecular level.

"Dense diffusion" in colloidal glasses: short-ranged long-time self-diffusion as a mechanistic model for relaxation dynamics.

Despite decades of exploration of the colloidal glass transition, mechanistic explanation of glassy relaxation processes has remained murky. State-of-the-art theoretical models of the colloidal glass transition such as random first order transition theory, active barrier hopping theory, and non-equilibrium self-consistent generalized Langevin theory assert that relaxation reported at volume fractions above the ideal mode coupling theory prediction φg,MCT requires some sort of activated process, and that cooperative motion plays a central role. However, discrepancies between predicted and measured values of φg and ambiguity in the role of cooperative dynamics persist. Underlying both issues is the challenge of conducting deep concentration quenches without flow and the difficulty in accessing particle-scale dynamics. These two challenges have led to widespread use of fitting methods to identify divergence, but most a priori assume divergent behavior; and without access to detailed particle dynamics, it is challenging to produce evidence of collective dynamics. We address these limitations by conducting dynamic simulations accompanied by experiments to quench a colloidal liquid into the putative glass by triggering an increase in particle size, and thus volume fraction, at constant particle number density. Quenches are performed from the liquid to final volume fractions 0.56 ≤ φ ≤ 0.63. The glass is allowed to age for long times, and relaxation dynamics are monitored throughout the simulation. Overall, correlated motion acts to release dynamics from the glassy plateau - but only over length scales much smaller than a particle size - allowing self-diffusion to re-emerge; self-diffusion then relaxes the glass into an intransient diffusive state, which persists for φ < 0.60. We observe similar relaxation dynamics up to φ = 0.63 before achieving the intransient state. We find that this long-time self-diffusion is short-ranged: analysis of mean-square displacement reveals a glassy cage size a fraction of a particle size that shrinks with quench depth, i.e. increasing volume fraction. Thus the equivalence between cage size and particle size found in the liquid breaks down in the glass, which we confirm by examining the self-intermediate scattering function over a range of wave numbers. The colloidal glass transition can hence be viewed mechanistically as a shift in the long-time self-diffusion from long-ranged to short-ranged exploration of configurations. This shift takes place without diverging dynamics: there is a smooth transition as particle mobility decreases dramatically with concomitant emergence of a dense local configuration space that permits sampling of many configurations via local particle motion.