Effect Of System Size Research Articles

Heavy flavor dynamics across system size at the LHC

One of the fundamental signatures of the Quark Gluon Plasma has been the suppression of heavy flavor (specifically D mesons), which has been measured via the nuclear modification factor, RAA and azimuthal anisotropies, vn , in large systems. However, multiple competing models can reproduce the same data for RAA to vn . In this talk we break down the competing effects that conspire together to successfully reproduce RAA and vn in experimental data using Trento+v-USPhydro+DAB-MOD. Then using our best fit model we make predictions for RAA and vn across system size for 208PbPb, 129XeXe, 40ArAr, and 16OO collisions. We find that 0–10% centrality has a non-trivial interplay between the system size and eccentricities such that system size effects are masked in v2 whereas in 30–50% centrality the eccentricities are approximately constant across system size and, therefore, is a better centrality class to study D meson dynamics across system size.

The Effect of KcsA Channel on Lipid Bilayer Electroporation Induced by Picosecond Pulse Trains.

Membrane proteins are the major component of plasma membranes, and they play crucial roles in all organisms. To understand the influence of the presence of KcsA channel on cell membrane electroporation induced by picosecond pulse trains (psPT), in this paper, the electroporation of KcsA membrane protein system and bare lipid bilayer system (POPC) with the applied psPT are simulated using molecular dynamics (MD) method. First, we find that the average pore formation time of the KcsA system is longer than the bare system with the applied psPT. In the KcsA system, water protrusions appear more slowly. Then, the system size effects of psPT in the MD simulations are investigated. When the system size decreases, the average pore formation time of small KcsA membrane protein system is shorter than the bare system with the applied psPT. It is found that the psPT makes the protein fluctuation of small system increase greatly; meanwhile the instability of protein disturbs the water and then affects the water protrusion appearance time. Furthermore, it shows that the protein fluctuation of constant electric field is smaller than that of psPT and no field, and protein fluctuation increases with the psPT repetition frequency increasing.

Relation between the convective field and the stationary probability distribution of chemical reaction networks

We investigate the relation between the stationary probability distribution of chemical reaction systems and the convective field derived from the chemical Fokker–Planck equation (CFPE) by comparing predictions of the convective field to the results of stochastic simulations based on Gillespie’s algorithm. The convective field takes into account the drift term of the CFPE and the reaction bias introduced by the diffusion term. For one-dimensional systems, fixed points and bifurcations of the convective field correspond to extrema and phenomenological bifurcations of the stationary probability distribution whenever the CFPE is a good approximation to the stochastic dynamics. This provides an efficient way to calculate the effect of system size on the number and location of probability maxima and their phenomenological bifurcations in parameter space. For two-dimensional systems, we study models that have saddle-node and Hopf bifurcations in the macroscopic limit. Here, the existence of two stable fixed points of the convective field correlates either with two peaks of the stationary probability distribution, or with a peak and a shoulder. In contrast, a Hopf bifurcation that occurs in the convective field for decreasing system size is not accompanied by the onset of a crater-shaped probability distribution; decreasing system size rather destroys craters and replaces them by local maxima.

System-size effect on the friction at liquid-solid interfaces

The friction at the liquid-solid interfaces is widely involved in various phenomena ranging from nanometer to micrometer scales. By the molecular dynamic (MD) simulation, the friction properties of liquid-solid interfaces at the molecular level are calculated via the Green-Kubo relation. It is found that the system size will influence the value of the friction coefficient, especially for the solid surfaces with the larger polar charge. The value of the friction coefficient decreases with the increase in the system size and converges at large system sizes. The large polar charge will lead to a significant friction coefficient. However, the diffusion of water molecules on this surface is almost a constant, indicating that the diffusion coefficient seems to be independent of the system size and polar charge. This work provides insights for the selection of the system size in modeling the frictional properties of hydrophobic/hydrophilic surfaces.

Dynamical versus statistical production of Intermediate Mass Fragments at Fermi Energies

The emission probability of Intermediate Mass Fragments (IMFs) in non-central reactions has been investigated in collisions of heavy $$^{124}\hbox {Xe}$$ projectiles with the two different medium-mass targets of $$^{64}\hbox {Ni}$$ and $$^{64}\hbox {Zn}$$ at the laboratory energy of 35 A MeV. The two colliding systems differ only for the target atomic number Z and, consequently, for the isospin N/Z ratio. The probability of IMFs emission from the projectile-like fragment has been measured, showing an enhancement of the IMFs emission for the neutron rich $$^{64}\hbox {Ni}$$ target. Most of the observed projectile break-up yield is associated with the production of only one IMF, that is, a quasi-binary splitting of projectile in two fragments in a broad range of charge asymmetry. For the events with one IMF, the relative contributions of the dynamical and statistical emissions have been evaluated. We find an enhancement of dynamical break-up probability for the neutron rich target with respect to the neutron poor one. The analysis suggests influence of the target isospin in inducing the dynamical break-up of projectile-like fragments. The new data have been also compared with previous published results of $$^{112,124}\hbox {Sn}$$ + $$^{58,64}\hbox {Ni}$$ systems, in order to disentangle between isospin effects against system-size effects on the emission probability. The comparisons between previous and new data suggest that the dynamical break-up is determined by the N/Z content of both projectile and target; for the cases here investigated, the influence of the system size on the dynamical emission probability can be excluded.

Anisotropic mechanical behavior of two dimensional silicon carbide: effect of temperature and vacancy defects

Mechanical stability, which is featured by high tensile strength, is one of the most critical concerns for the reliability of next-generation nanoelectromechanical systems (NEMS). Presently, sp2 hybridized two-dimensional silicon carbide (2D-SiC) is supposed to be a novel nanomaterial to apply in nanocomposites, NEMS, and nano-energy harvesting applications because of its amazing electronic, mechanical and thermal properties. This paper explores the mechanical behavior, including fracture stress, fracture strain, and elastic modulus of both pristine and vacancy defected 2D-SiC at temperatures 300–700 K using molecular dynamics simulation. Two types of vacancy defects such as point and bi-vacancies with concentration 0.1%–1.0% are considered. Moreover, the effect of system size and strain rate on the mechanical behavior of 2D-SiC is also analyzed. A highly anisotropic mechanical behavior is found at all temperature and defect conditions. At 300 K, a fracture stress and an elastic modulus of 71.02 GPa and 637.26 GPa, respectively is obtained along the armchair direction, which is ∼24.42% and ∼14.38% higher compared to the zigzag directed fracture stress and elastic modulus. A reduction of fracture stress, fracture strain, and elastic modulus with the increase of temperature and defect concentration is also perceived in both armchair and zigzag directions. Moreover, due to the large symmetry breakdown by the point vacancy, a comparatively larger drastic reduction is noticed in the fracture behavior than the bi-vacancy at all temperatures and loading directions. These results would provide a new insight for solving the mechanical instability problem of SiC-based NEMS and nanodevices in the near future.

Two-channel totally asymmetric simple exclusion process with site-wise dynamic disorder

Being inspired by the biological process of gene transcription, we investigate the phenomenology of transport on two-channel TASEP in the presence of dynamical defects under symmetric coupling conditions. The continuum mean-field equations are derived and then solved numerically to obtain steady-state phase diagrams. The role of various parameters namely defect (un-)binding constants, lane-changing rates has been thoroughly examined. The defect (un-)binding rates are found to affect the phase boundaries in the phase plane. The effect of system size on the steady-state dynamics of the system has also been analyzed. The theoretical results are validated by performing extensive Monte Carlo simulations.

System size effect on crystal nuclei morphology in supercooled metallic melt

We present a molecular dynamics (MD) study of size effect on the crystal nuclei geometry, formation and growth in supercooled tantalum film. The process is studied in a set of MD trajectories that are obtained by ultrafast cooling from the stable liquid phase to the temperature below the glass transition temperature. We describe the nucleation process by two morphological parameters. Along with the nucleus size, we analyze the asphericity that is a measure of deviation of crystal nuclei from idealized spherical form. This method allows to demonstrate that there are two paths for crystal nucleus shape and size evolution. The first path is crystal growth through high asphericity values. We show that this is caused by coalescence of the crystals. This mechanism is not affected by the size of the system. The second path is formation of long-lived crystal clusters that do not lead to the crystallization of the whole system on the MD simulation timescale. We demonstrate that such clusters have common geometric features which strongly depend on the system size.

Electrocrystallization of Supercooled Water Confined between Graphene Layer

A key feature of the crystallization of supercooled water confined in an applied static electric field is that the structural order here is determined not only by usual thermodynamic and kinematic factors (degree of supercooling, difference between chemical potentials for a liquid and a crystal, and viscosity) but also by the strength and direction of the applied electric field, size of a system (size effects), and the geometry of bounding surfaces. In this work, the electrocrystallization of supercooled water confined between ideally flat parallel graphene sheets at a temperature of $T=268$~K has been considered in this work. It has been established that structural order is determined by two characteristic modes. The initial mode correlates with the orientation of dipolar water molecules by the applied electric field. The subsequent mode is characterized by the relaxation of a metastable system to a crystalline phase. The uniform electric field applied perpendicularly to the graphene sheets suppresses structural ordering, whereas the field applied in the lateral direction promotes cubic ice $I_c$.

Density-dependent finite system-size effects in equilibrium molecular dynamics estimation of shear viscosity: Hydrodynamic and configurational study.

We study the intrinsic nature of the finite system-size effect in estimating shear viscosity of dilute and dense fluids within the framework of the Green-Kubo approach. From extensive molecular dynamics simulations, we observe that the size effect on shear viscosity is characterized by an oscillatory behavior with respect to system size L at high density and by a scaling behavior with an L-1 correction term at low density. Analysis of the potential contribution in the shear-stress autocorrelation function reveals that the former is configurational and is attributed to the inaccurate description of the long-range spatial correlations in finite systems. Observation of the long-time inverse-power decay in the kinetic contribution confirms its hydrodynamic nature. The L-1 correction term of shear viscosity is explained by the sensitive change in the long-time tail obtained from a finite system.

Viscosity calculations from hadron resonance gas model: Finite size effect

We have attempted to review on microscopic calculation of transport coefficients like shear and bulk viscosities in the framework of hadron resonance gas (HRG) model, where a special attention is explored on the effect of finite system size. The standard expressions of transport coefficients, obtained from relaxation time approximation of kinetic theory or diagrammatic Kubo-type formalism, carry mainly two temperature-dependent components — thermodynamical phase space and relaxation time of medium constituent. Owing to the quantum effect of finite system size, thermodynamical phase space can be reduced as its momentum distribution will be started from some finite lower momentum cut-off instead of zero momentum. On the other hand, relaxation time of hadrons can also face finite size effect by considering only those relaxation scales, which are lower than the system size. Owing to these phenomenological issues, we have proposed a system size-dependent upper bound of transport coefficients for ideal HRG model, whose qualitative technique may also be applicable in other models. This finite size-prescription may guide to shorten the broad numerical band, within which earlier estimated values of transport coefficients for hadronic matter are located. It is also suspected that the hadronic matter may not be far from the (nearly) perfect fluid nature like the quark gluon plasma.

Relaxation dynamics in supercooled oligomer liquids: From shear-stress fluctuations to shear modulus and structural correlations

Static and dynamical properties of a model glass-forming oligomer liquid are analyzed using molecular dynamics simulations. The temperature and system size effects are assessed for the affine shear modulus μA, the quasistatic shear modulus μsf (obtained using the stress-fluctuation relation), and the shear relaxation modulus G(t). It is found that while both μA and μsf are nearly independent of the system size, their variances show significant system size dependence, in particular, below the glass transition temperature Tg. It is also shown that the standard deviation of the shear modulus, δμsf(T), exhibits a pronounced peak at T ≈ Tg whose position is nearly independent of the system volume V. Moreover, the whole function δμsf(T) is nearly the same for different system sizes above the glass transition. We propose a theory which quantitatively predicts δμsf(T) at T ≳ Tg and explains both its independence of V and its peak near Tg. It is also established that below Tg the variance of the affine modulus follows the standard power law, δμA2∝1/V, while δμsf shows anomalously a slow decrease with V as δμsf2∝1/Vα with α < 1. On this basis, it is argued that the studied glass-forming systems must show long-range structural correlations in the amorphous state.

Fick diffusion coefficients of binary fluid mixtures consisting of methane, carbon dioxide, and propane via molecular dynamics simulations based on simplified pair-specific ab initio-derived force fields

For the calculation of thermophysical properties of fluids with molecular dynamics (MD) simulations, effective force fields (FFs) which are optimized against experimental vapor-liquid equilibria are often used. Examples for this FF category are TraPPE, OPLS, and AMBER. An alternative are simplified pair-specific, ab initio-based FFs (AI-FFs), which are derived from quantum-chemical calculations in the limit of zero-density in combination with the kinetic theory of gases, and, thus, feature a predictive character. In the present study, we show with the help of selected binary fluid mixtures that the predictive power of MD simulations in calculating Fick diffusion coefficients can be improved using simplified pair-specific AI-FFs based on corresponding FFs for the pure substances. To evaluate the performance of the new AI-FFs in comparison with the TraPPE FFs, binary mixtures consisting of methane, carbon dioxide, and propane were investigated from the superheated vapor to the gas state and supercritical region up to the compressed liquid state. For the determination of the Fick diffusion coefficient at pressures between (0.1 and 12) MPa, temperatures between (293 and 355) K, and mole fractions between 0.05 and 0.95, separate simulations for the analysis of the Maxwell–Stefan diffusion coefficient and the thermodynamic factor were performed considering system size effects. With the exception of the compressed liquid state and regions in vicinity of the two-phase boundary, where the TraPPE FFs are generally superior, the AI-FFs show improved predictions for the Fick diffusion coefficient with average expanded statistical uncertainties of 12%. This could be demonstrated by comparison of the simulation results with the theoretical ab initio calculations and the available experimental data, resulting in average absolute deviations of 7% and 13% for the AI-FFs and TraPPE FFs.

Effect of alkyl chain length on the wetting behavior of imidazolium based ionic liquids: A molecular dynamics study

Molecular dynamics (MD) simulations are performed to investigate the wetting behavior of imidazolium-based ionic liquids (ILs), which mainly consist of an imidazolium ring with a flexible alkyl chain attachment. The length of the alkyl chain can be easily manipulated to modulate the wetting properties of the ILs. To understand the role of the alkyl chain, we investigate the wetting behavior of two room-temperature ionic liquids (RTILs), 1,3-dimethylimidazolium tetra-fluoroborate [DMIM][BF4] and 1-propyl-3-methylimidazolium tetra-fluoroborate [PrMIM][BF4], on a graphite surface. Furthermore, the effects of the droplet size and temperature on the contact angle of the IL droplets are investigated. The wetting behaviors of both IL droplets are characterized using a density profile and orientation order parameter profile along the axis normal to the surface. The length of the alkyl chain is found to be crucial for modulating the wetting properties of the ILs. With an increase in the length of the alkyl chain, the contact angle of the droplet decreases, which is also in line with experimental results [1,2]. The wetting of the IL droplets strongly depends on the temperature and the relative fluid-fluid and fluid-substrate interactions. With the increase in temperature, the contact angle of the IL droplet decreases, resulting in the formation of a single layer film at a high temperature. In addition, the behavior of the contact angle of the IL droplet is analyzed through the surface tension as well as the graphite-IL interfacial tension. Furthermore, considering the anisotropic properties of the imidazolium-based ILs, we calculate the contact angles for cylindrical filaments (2D) on the graphite surface and compare the obtained values with the contact angle obtained from the spherical droplet (3D). The contact angle of the cylindrical droplet is found to have a negligible system size effect as compared to the case with the spherical droplet.

Heavy Ion Results from ATLAS and CMS

The heavy-ion programmes in the ATLAS and CMS experiments at the Large Hadron Collider aim to probe and characterise properties of the quark-gluon plasma created in relativistic nuclear collisions. This work presents selected results of collective effects, system size effects, and quarkonia production in p-p, p-Pb, Pb-Pb, and Xe-Xe collisions.

Machine Learning Enabled Prediction of Mechanical Properties of Tungsten Disulfide Monolayer.

One of two-dimensional transition metal dichalcogenide materials, tungsten disulfide (WS2), has aroused much research interest, and its mechanical properties play an important role in a practical application. Here the mechanical properties of h-WS2 and t-WS2 monolayers in the armchair and zigzag directions are evaluated by utilizing the molecular dynamics (MD) simulations and machine learning (ML) technique. We mainly focus on the effects of chirality, system size, temperature, strain rate, and random vacancy defect on mechanical properties, including fracture strain, fracture strength, and Young’s modulus. We find that the mechanical properties of h-WS2 surpass those of t-WS2 due to the different coordination spheres of the transition metal atoms. It can also be observed that the fracture strain, fracture strength, and Young’s modulus decrease when temperature and vacancy defect ratio are enhanced. The random forest (RF) supervised ML algorithm is employed to model the correlations between different impact factors and target outputs. A total number of 3600 MD simulations are performed to generate the training and testing dataset for the ML model. The mechanical properties of WS2 (i.e., target outputs) can be predicted using the trained model with the knowledge of different input features, such as WS2 type, chirality, temperature, strain rate, and defect ratio. The mean square errors of ML predictions for the mechanical properties are orders of magnitude smaller than the actual values of each property, indicating good training results of the RF model.

Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations.

We investigate system-size effects on the rotational diffusion of membrane proteins and other membrane-embedded molecules in molecular dynamics simulations. We find that the rotational diffusion coefficient slows down relative to the infinite-system value by a factor of one minus the ratio of protein and box areas. This correction factor follows from the hydrodynamics of rotational flows under periodic boundary conditions and is rationalized in terms of Taylor–Couette flow. For membrane proteins like transporters, channels, or receptors in typical simulation setups, the protein-covered area tends to be relatively large, requiring a significant finite-size correction. Molecular dynamics simulations of the protein adenine nucleotide translocase (ANT1) and of a carbon nanotube porin in lipid membranes show that the hydrodynamic finite-size correction for rotational diffusion is accurate in standard-use cases. The dependence of the rotational diffusion on box size can be used to determine the membrane viscosity.

Two-stage stochastic approximation for dynamic rebalancing of shared mobility systems

Mobility systems featuring shared vehicles are often unable to serve all potential customers, as the distribution of demand does not coincide with the positions of vehicles at any given time. System operators often choose to reposition these shared vehicles (such as bikes, cars, or scooters) actively during the course of the day to improve service rate. They face a complex dynamic optimization problem in which many integer-valued decisions must be made, using real-time state and forecast information, and within the tight computation time constraints inherent to real-time decision-making. We first present a novel nested-flow formulation of the problem, and demonstrate that its linear relaxation is significantly tighter than one from existing literature. We then adapt a two-stage stochastic approximation scheme from the generic SPAR algorithm due to Powell et al., in which rebalancing plans are optimized against a value function representing the expected cost (in terms of fulfilled and unfulfilled customer demand) of the future evolution of the system. The true value function is approximated by a separable function of contributions due to the rebalancing actions carried out at each station and each time step of the planning horizon. The new algorithm requires surprisingly few iterations to yield high-quality solutions, and is suited to real-time use as it can be terminated early if required. We provide insight into this good performance by examining the mathematical properties of our new flow formulation, and perform rigorous tests on standardized benchmark networks to explore the effect of system size. We then use data from Philadelphia’s public bike sharing scheme to demonstrate that the approach also yields performance gains for real systems.

Plant root growth affects FDR soil moisture sensor calibration

To acquire accurate volumetric water content (VWC) measurements from horticultural substrates using dielectric sensors, a substrate-specific calibration is critical. Calibrations typically are conducted with a substrate without plants, but water in the root system may affect soil moisture sensor readings. We investigated the effect of root growth on the measured VWC. Lettuce seedlings (Lactuca sativa L. ‘Joek Chi Ma’) were grown in 10 cm round containers (440 mL) filled with soilless substrate. Four EC-5 soil moisture sensors (Decagon Devices Inc., Pullman, WA, USA) were used to determine the effect of root system size on sensor calibration over an eight week period. Both calibration coefficients (slope and intercept) decreased (P < 0.001) with increasing root system size. The actual VWC at 8 weeks after transplanting (WAT) was 9% lower at 65% VWC compared to the estimated VWC from the substrate-only calibration. Multiple regression models indicated that various root size indicators (WAT, root fresh weight, root dry weight, and root water content) all had a negative effect on the estimation of VWC. The effect of root system size on estimated VWC may be tolerable in production, but should be considered in research applications. Careful interpretation is needed when using FDR soil moisture sensors to monitor substrate VWC in the presence of a growing root system.

OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order- n Algorithm in LAMMPS.

We present a new plugin for LAMMPS for on-the-fly computation of transport properties (OCTP) in equilibrium molecular dynamics. OCTP computes the self- and Maxwell-Stefan diffusivities, bulk and shear viscosities, and thermal conductivities of pure fluids and mixtures in a single simulation. OCTP is the first implementation in LAMMPS that uses the Einstein relations combined with the order- n algorithm for the efficient sampling of dynamic variables. OCTP has low computational requirements and is easy to use because it follows the native input file format of LAMMPS. A tool for calculating the radial distribution function (RDF) of the fluid beyond the cutoff radius, while taking into account the system size effects, is also part of the new plugin. The RDFs computed from OCTP are needed to obtain the thermodynamic factor, which relates Maxwell-Stefan and Fick diffusivities. To demonstrate the efficiency of the new plugin, the transport properties of an equimolar mixture of water-methanol were computed at 298 K and 1 bar.