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We present a technique for measuring the interactions between pairs of colloidal particles in two optical traps. This method is particularly suitable for measuring strongly attractive potentials, an otherwise challenging task. The interaction energy is calculated from the distribution of inter-particle separations by accounting for the contribution from the optical traps with arbitrary trap profiles. The method is simple to implement and applicable to different types of pair potentials and optical trapping geometries. We apply the method to measure dipolar pair interactions in experiments with paramagnetic colloids in external magnetic fields. We obtain consistent and accurate results in all regimes, from strongly attractive to repulsive potentials. By means of computer simulations, we demonstrate that the proposed method can be successfully applied to systems with complex pair interactions characterized by multiple attractive and repulsive regimes, which are ubiquitous in soft and biological matter. [ABSTRACT FROM AUTHOR]

The celebrated generalized Stokes law predicts that the velocity of a particle pulled through a liquid by an external force, Fex, is directly proportional to the force and inversely proportional to the friction ζ acted by the medium on the particle. We investigate the range of validity of the generalized Stokes law at molecular length scales by employing computer simulations to calculate friction by pulling a tagged particle with a constant force. We thus calculate friction for two model interaction potentials, Lennard-Jones and soft sphere, for several particle sizes, ranging from radius (a) smaller than the solvent particles to three times larger. We next obtain friction from diffusion (D) by using Einstein's relation between diffusion and friction ζ in an unperturbed liquid. We find a quantitative agreement between the two at a small-to-intermediate pulling force regime for all the sizes studied. The law does break down at a large pulling force beyond a threshold value. Importantly, the range of validity of Stokes' scheme to obtain friction increases substantially if we turn off the attractive part of the interaction potential. Additionally, we calculate the viscosity (η) of the unperturbed liquid and find a good agreement with the Stokes–Einstein relation ζ = Cηa for the viscosity dependence with a value of C close to 5 π, which is intermediate between the slip and stick boundary condition. [ABSTRACT FROM AUTHOR]

In this work, the effects of finite size on the determination of the three-phase coexistence temperature (T3) of the carbon dioxide (CO2) hydrate have been studied by molecular dynamic simulations and using the direct coexistence technique. According to this technique, the three phases involved (hydrate–aqueous solution–liquid CO2) are placed together in the same simulation box. By varying the number of molecules of each phase, it is possible to analyze the effect of simulation size and stoichiometry on the T3 determination. In this work, we have determined the T3 value at 8 different pressures (from 100 to 6000 bar) and using 6 different simulation boxes with different numbers of molecules and sizes. In two of these configurations, the ratio of the number of water and CO2 molecules in the aqueous solution and the liquid CO2 phase is the same as in the hydrate (stoichiometric configuration). In both stoichiometric configurations, the formation of a liquid drop of CO2 in the aqueous phase is observed. This drop, which has a cylindrical geometry, increases the amount of CO2 available in the aqueous solution and can in some cases lead to the crystallization of the hydrate at temperatures above T3, overestimating the T3 value obtained from direct coexistence simulations. The simulation results obtained for the CO2 hydrate confirm the sensitivity of T3 depending on the size and composition of the system, explaining the discrepancies observed in the original work by Míguez et al. [J. Chem Phys. 142, 124505 (2015)]. Non-stoichiometric configurations with larger unit cells show a convergence of T3 values, suggesting that finite-size effects for these system sizes, regardless of drop formation, can be safely neglected. The results obtained in this work highlight that the choice of a correct initial configuration is essential to accurately estimate the three-phase coexistence temperature of hydrates by direct coexistence simulations. [ABSTRACT FROM AUTHOR]

In this work, the effect of the range of dispersive interactions in determining the three-phase coexistence line of the CO2 and CH4 hydrates has been studied. In particular, the temperature (T3) at which solid hydrate, water, and liquid CO2/gas CH4 coexist has been determined through molecular dynamics simulations using different cutoff values (from 0.9 to 1.6 nm) for dispersive interactions. The T3 of both hydrates has been determined using the direct coexistence simulation technique. Following this method, the three phases in equilibrium are put together in the same simulation box, the pressure is fixed, and simulations are performed at different temperatures T. If the hydrate melts, then T > T3. Conversely, if the hydrate grows, then T < T3. The effect of the cutoff distance on the dissociation temperature has been analyzed at three different pressures for CO2 hydrate: 100, 400, and 1000 bar. Then, we have changed the guest and studied the effect of the cutoff distance on the dissociation temperature of the CH4 hydrate at 400 bar. Moreover, the effect of long-range corrections for dispersive interactions has been analyzed by running simulations with homo- and inhomogeneous corrections and a cutoff value of 0.9 nm. The results obtained in this work highlight that the cutoff distance for the dispersive interactions affects the stability conditions of these hydrates. This effect is enhanced when the pressure is decreased, displacing the T3 about 2–4 K depending on the system and the pressure. [ABSTRACT FROM AUTHOR]

Clathrate hydrates are vital in energy research and environmental applications. Understanding their stability is crucial for harnessing their potential. In this work, we employ direct coexistence simulations to study finite-size effects in the determination of the three-phase equilibrium temperature (T3) for methane hydrates. Two popular water models, TIP4P/Ice and TIP4P/2005, are employed, exploring various system sizes by varying the number of molecules in the hydrate, liquid, and gas phases. The results reveal that finite-size effects play a crucial role in determining T3. The study includes nine configurations with varying system sizes, demonstrating that smaller systems, particularly those leading to stoichiometric conditions and bubble formation, may yield inaccurate T3 values. The emergence of methane bubbles within the liquid phase, observed in smaller configurations, significantly influences the behavior of the system and can lead to erroneous temperature estimations. Our findings reveal finite-size effects on the calculation of T3 by direct coexistence simulations and clarify the system size convergence for both models, shedding light on discrepancies found in the literature. The results contribute to a deeper understanding of the phase equilibrium of gas hydrates and offer valuable information for future research in this field. [ABSTRACT FROM AUTHOR]

In this work, the univariant two-phase coexistence line of the tetrahydrofuran (THF) hydrate is determined from 100 to 1000 bar by molecular dynamics simulations. This study is carried out by putting in contact a THF hydrate phase with a stoichiometric aqueous solution phase. Following the direct coexistence technique, the pressure is fixed, and the coexistence line is determined by analyzing if the hydrate phase grows or melts at different values of temperature. Water is described using the well-known TIP4P/Ice model. We have used two different models of THF based on the transferable parameters for phase equilibria-united atom approach (TraPPE-UA), the original (flexible) TraPPe-UA model and a rigid and planar version of it. Overall, at high pressures, small differences are observed in the results obtained by both models. However, large differences are observed in the computational efforts required by the simulations performed using both models, being the rigid and planar version much faster than the original one. The effect of the unlike dispersive interactions between the water and THF molecules is also analyzed at 250 bar using the rigid and planar THF model. In particular, we modify the Berthelot combining rule via a parameter ξO-THF that controls the unlike water–THF dispersive interactions. We analyze the effect on the dissociation temperature of the hydrate when ξO-THF is modified from 1.0 (original Berthelot combining rule) to 1.4 (modified Berthelot combining rule). We use the optimized value ξO-THF = 1.4 and the rigid THF model in a transferable way to predict the dissociation temperatures at other pressures. We find excellent agreement between computer simulation predictions and experimental data taken from the literature. [ABSTRACT FROM AUTHOR]

Designing homogeneous networks is considered one typical strategy for solving the problem of strength and toughness conflict of polymer network materials. Experimentalists have proposed the hypothesis of obtaining a structurally homogeneous hydrogel by crosslinking tetra-armed polymers, whose homogeneity was claimed to be verified by scattering characterization and other methods. Nevertheless, it is highly desirable to further evaluate this issue from other perspectives. In this study, a coarse-grained molecular dynamics simulation coupled with a stochastic reaction model is applied to reveal the topological structure of a polymer network synthesized by tetra-armed monomers as precursors. Two different scenarios, distinguished by whether internal cross-linking is allowed, are considered. We introduce the Dijkstra algorithm from graph theory to precisely characterize the network structure. The microscopic features of the network structure, e.g., loop size, dispersity, and size distribution, are obtained via the Dijkstra algorithm. By comparing the two reaction scenarios, Scenario II exhibits an overall more idealized structure. Our results demonstrate the feasibility of the Dijkstra algorithm for precisely characterizing the polymer network structure. We expect this work will provide a new insight for the evaluation and description of gel networks and further help to reveal the dynamic process of network formation. [ABSTRACT FROM AUTHOR]

Computer simulation has long been an essential partner of ultrafast experiments, allowing the assignment of microscopic mechanistic detail to low-dimensional spectroscopic data. However, the ability of theory to make a priori predictions of ultrafast experimental results is relatively untested. Herein, as a part of a community challenge, we attempt to predict the signal of an upcoming ultrafast photochemical experiment using state-of-the-art theory in the context of preexisting experimental data. Specifically, we employ ab initio Ehrenfest with collapse to a block mixed quantum–classical simulations to describe the real-time evolution of the electrons and nuclei of cyclobutanone following excitation to the 3s Rydberg state. The gas-phase ultrafast electron diffraction (GUED) signal is simulated for direct comparison to an upcoming experiment at the Stanford Linear Accelerator Laboratory. Following initial ring-opening, dissociation via two distinct channels is observed: the C3 dissociation channel, producing cyclopropane and CO, and the C2 channel, producing CH2CO and C2H4. Direct calculations of the GUED signal indicate how the ring-opened intermediate, the C2 products, and the C3 products can be discriminated in the GUED signal. We also report an a priori analysis of anticipated errors in our predictions: without knowledge of the experimental result, which features of the spectrum do we feel confident we have predicted correctly, and which might we have wrong? [ABSTRACT FROM AUTHOR]

We investigated the field-dependent Néel relaxation time of magnetic nanoparticles (MNPs) in an AC excitation field. Specifically, a fundamental component of the magnetization for immobilized MNPs was studied by numerical simulation while changing the frequency f and amplitude Hac of the field. From the simulation results, we clarified the Hac dependence of the effective Néel relaxation time τN,e and obtained an empirical expression for τN,e(Hac) for the first time. The expression was obtained for the cases when the angle of the easy axis of magnetization in MNPs is fixed and randomly distributed. Using the Hac dependencies of τN,e and the previously reported Brownian relaxation time τB,e, we showed that the behavior of suspended MNPs changes from Brownian-dominant to Néel-dominant when Hac increases, even when the MNP parameters are fixed, and we obtained an expression for the boundary field between them. Furthermore, we classified several types of responses for the suspended MNPs in the AC field using the magnitude relationship among τN,e(Hac), τB,e(Hac), and 1/(2πf). Finally, we experimentally verified the classification, and reasonable agreement was observed between the experiment and analysis. The results are useful for determining suitable MNP parameters and excitation conditions for various biomedical applications. [ABSTRACT FROM AUTHOR]

Inspired by the emerging field of twistronics, moiré photonic structures have attracted great interest. In this paper, we introduce the concept of the moiré Kagome lattice (MKL), which arises from the overlapping of a Kagome lattice at a commensurable angle of 38.211°. MKL exhibits a significantly broader main photonic bandgap (PBG) when compared to the traditional Kagome lattice. Through numerical simulations, we delved into the adjustable properties of the PBG of MKL by varying lattice parameters, including filling factors and materials. Meanwhile, we also observed the presence of photonic flatbands within the MKL structure. Specifically, the emergence of a super flat isolated flatband aids in achieving single-mode omnidirectional lasers and enhancing the omnidirectional electromagnetic interaction of materials, thereby expanding the applications of moiré photonic crystals. [ABSTRACT FROM AUTHOR]

The impact of successive replacement of K+ by Na+ on the megahertz–gigahertz polarization response of 0.25[fKSCN + (1 − f)NaSCN] + 0.75CH3CONH2 deep eutectic solvents (DESs) was explored via temperature-dependent (303 ≤ T/K ≤ 343) dielectric relaxation (DR) measurements and computer simulations. Both the DR measurements (0.2 ≤ ν/GHz ≤ 50) and the simulations revealed multi-Debye relaxations accompanied by a decrease in the solution static dielectric constant (ɛs) upon the replacement of K+ by Na+. Accurate measurements of the DR response of DESs below 100 MHz were limited by the well-known one-over-frequency divergence for conducting solutions. This problem was tackled in simulations by removing the zero frequency contributions arising from the ion current to the total simulated DR response. The temperature-dependent measurements revealed a much stronger viscosity decoupling of DR times for Na+-containing DES than for the corresponding K+ system. The differential scanning calorimetry measurements indicated a higher glass transition temperature for Na+-DES (∼220 K) than K+-DES (∼200 K), implying more fragility and cooperativity for the former (Na+-DES) than the latter. The computer simulations revealed a gradual decrease in the average number of H bonds (⟨nHB⟩) per acetamide molecule and increased frustrations in the average orientational order upon the replacement of K+ by Na+. Both the measured and simulated ɛs values were found to decrease linearly with ⟨nHB⟩. Decompositions of the simulated DR spectra revealed that the cation-dependent cross interaction (dipole-ion) term contributes negligibly to ɛs and appears in the terahertz regime. Finally, the simulated collective single-particle reorientational relaxations and the structural H-bond fluctuation dynamics revealed the microscopic origin of the cation identity dependence shown by the measured DR relaxation times. [ABSTRACT FROM AUTHOR]

Biological lipid membranes are generally asymmetric, not only with respect to the composition of the two membrane leaflets but also with respect to the state of mechanical stress on the two sides. Computer simulations of such asymmetric membranes pose unique challenges with respect to the choice of boundary conditions and ensemble in which such simulations are to be carried out. Here, we demonstrate an alternative to the usual choice of fully periodic boundary conditions: The membrane is only periodic in one direction, with free edges running parallel to the single direction of periodicity. In order to maintain bilayer asymmetry under these conditions, nanoscale "sticky tapes" are adhered to the membrane edges in order to prevent lipid flip-flop across the otherwise open edge. In such semi-periodic simulations, the bilayer is free to choose both its area and mean curvature, allowing for minimization of the bilayer elastic free energy. We implement these principles in a highly coarse-grained model and show how even the simplest examples of such simulations can reveal useful membrane elastic properties, such as the location of the monolayer neutral surface. [ABSTRACT FROM AUTHOR]

The ice surface is known for presenting a very small kinetic friction coefficient, but the origin of this property remains highly controversial to date. In this work, we revisit recent computer simulations of ice sliding on atomically smooth substrates, using newly calculated bulk viscosities for the TIP4P/ice water model. The results show that spontaneously formed premelting films in static conditions exhibit an effective viscosity that is about twice the bulk viscosity. However, upon approaching sliding speeds in the order of m/s, the shear rate becomes very large, and the viscosities decrease by several orders of magnitude. This shows that premelting films can act as an efficient lubrication layer despite their small thickness and illustrates an interesting interplay between confinement enhanced viscosities and shear thinning. Our results suggest that the strongly thinned viscosities that operate under the high speed skating regime could largely reduce the amount of frictional heating. [ABSTRACT FROM AUTHOR]

The operations of current quantum computers are still significantly affected by decoherence caused by interaction with the environment. In this work, we employ the non-perturbative hierarchical equations of motion (HEOM) method to simulate the operation of model quantum computers and reveal the effects of dissipation on the entangled quantum states and on the performance of well-known quantum algorithms. Multi-qubit entangled states in Shor's factorizing algorithm are first generated and propagated using the HEOM. It is found that the failure of factorization is accompanied by a loss of fidelity and mutual information. An important challenge in using the HEOM to simulate quantum computers in a dissipative environment is how to efficiently treat systems with many qubits. We propose a two-dimensional tensor network scheme for this problem and demonstrate its capability by simulating a one-dimensional random circuit model with 21 qubits. [ABSTRACT FROM AUTHOR]

A numerical model for a spin wave delay-line active ring resonator is presented. Spin wave dynamics along a one-dimensional strip of magnetic material are modeled using the nonlinear Schrödinger equation. The equation is solved numerically in Fourier space using the fourth-order Runge–Kutta method and yields qualitative agreement with experimental measurements of spin wave dynamics in two different regimes. The model provides a useful tool for performing experiments based on neuromorphic computing and logic gates in traveling spin wave devices. [ABSTRACT FROM AUTHOR]

Polymer blends are critical in many commercial products and industrial processes and their phase behavior is therefore of paramount importance. In most circumstances, such blends are formulated with samples of high dispersity, which have generally only been studied at the mean-field level. Here, we extend the renormalized one-loop theory of concentration fluctuations to account for blends of disperse polymers. Analyzing the short and long length-scale fluctuations in a consistent manner, various measures of polymer molecular weight and dispersity arise naturally in the free energy. Thermodynamic analysis in terms of moments of the molecular weight distribution(s) provides exact results for the inverse susceptibility and demonstrates that the theory is not formally renormalizable. However, physically motivated approximations allow for an "effective" renormalization, yielding (1) an effective interaction parameter, χe, which depends directly on the sample dispersities (i.e., Mw/Mn) and leaves the form of the mean-field spinodal unchanged, and (2) an apparent interaction parameter χa that depends on higher-order dispersity indices, for instance Mz/Mw, and characterizes the true limits of blend stability accounting for long-range off-critical fluctuations. We demonstrate the importance of dispersity on several example systems, including both "toy" models that may be realized in computer simulation and more realistic industrially relevant blends. We find that the effects of long-range fluctuations are particularly prominent in blends where the component dispersities are mismatched, especially when there is a small quantity of the high-dispersity species. This can be understood as a consequence of the shift in the critical concentration(s) from the monodisperse value(s). [ABSTRACT FROM AUTHOR]

Polyrotaxanes, which consist of mechanically interlocked bonds with rings threaded onto soft polymer chains, exhibit unique mechanical properties and find applications in diverse fields. In this study, we investigate the anomalous segmental dynamics of supercooled polyrotaxane melts using coarse-grained molecular dynamics simulations. Our simulations reveal that the presence of rings effectively reduces the packing efficiency, resulting in well-contained local motion even below the glass transition temperature. We also observe variations in dynamical free volume, characterized by the Debye–Waller factor, which shows a minimum at a ring coverage of 0.1 on threading chains. Such a non-monotonic dependence on coverage shows great consistency in structural relaxation time and dynamic heterogeneity. Specifically, the high segmental mobility of threading linear chains at large coverage can be attributed to the increased dynamical free volume due to supported rigid rings. However, such anomalous segmental dynamics is limited to length scales smaller than one ring size. Beyond this characteristic length scale, the diffusion is dominated by topological constraints, which significantly reduce the mobility of polyrotaxanes and enhance the dynamic heterogeneity. These findings offer microscopic insights into the unique packing structures and anomalous segmental dynamics of supercooled polyrotaxane melts, facilitating the design of advanced materials based on mechanical interlocking polymers for various applications. [ABSTRACT FROM AUTHOR]

In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. We use the solubility method proposed recently by some of us to evaluate the dissociation temperature of the hydrate at different pressures, from 500 to 1500 bar. Particularly, we calculate the solubility of N2 in the aqueous solution when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase via planar interfaces as functions of temperature. Since the solubility of N2 decreases with temperature in the first case and increases with temperature in the second case, both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We find a good agreement between the predictions obtained in this work and the experimental data taken from the literature in the range of pressures considered in this work. From our knowledge of the solubility curves of N2 in the aqueous solution, we also determine the driving force for nucleation of the hydrate, as a function of temperature, at different pressures. In particular, we use two different thermodynamic routes to evaluate the change in chemical potential for hydrate formation. Although the driving force for nucleation slightly decreases (in absolute value) when the pressure is increased, our results indicate that the effect of pressure can be considered negligible in the range of pressures studied in this work. To the best of our knowledge, this is the first time the driving force for nucleation of a hydrate that exhibits crystallographic structure sII, along its dissociation line, is studied from computer simulation. [ABSTRACT FROM AUTHOR]

Solid-state reactions proceeding from an initial microstructure enable the synthesis of complex materials in a wide variety of applications. However, despite the importance of such reactions in materials' processing, the connection between an initial, reactant microstructure and the ensuing transformation kinetics has been relatively little studied. In this work, we employ computer simulation of a reaction–diffusion model and a quantitative analysis of the associated kinetic equations to examine the propagation and interaction of evolving fronts in a prototypical system transforming via a solid-state reaction. It is found that the interaction between fronts dictates transformation kinetics. We then use our results to describe the kinetics of phase formation in the Co–Ti–O system, which contains the entropy-stabilized line compound cobalt dititanate, CoTi 2 O 5. This system is of particular interest as it has been shown that the solid-state synthesis may be exploited to produce single-crystal cobalt dititanate. [ABSTRACT FROM AUTHOR]

Chatbots are "computer agents that can interact with the user" in a way that feels like human-to-human conversation.1 While the use of chatbots for reference service in academic libraries is a topic of interest for both library professionals and researchers, little is known about how they are used in library reference service, especially in academic libraries in Canada. This article aims to fill this gap by conducting a web-based survey of 106 academic library websites in Canada and analyzing the prevalence and characteristics of chatbot and live chat services offered by these libraries. The authors found that only two libraries were using chatbots for reference service. For live chat services, the authors found that 78 libraries provided this service. The article discusses possible reasons for the low adoption of chatbots in academic libraries, such as accessibility, privacy, cost, and professional identity issues. The article also provides a case study of the authors' institution, the University of Calgary, which integrated a chatbot service in 2021. The article concludes with suggestions for future research on chatbot use in libraries. [ABSTRACT FROM AUTHOR]

Thermodynamics of far-from-equilibrium systems often require measurement of effective parameters such as temperature. Whether such approach is valid for the general case of resetting protocols, active systems, or of confined systems under time-varying fields is still under investigation. We report on the effect of switching ON-OFF of an asymmetric bistable potential to the mean first passage time (MFPT) of a probed particle to go from one potential minima to the other. Experimental results coupled with numerical simulations shows the potential becoming more symmetric at slow switching. Moreover, the MFPT deviates from equilibrium condition with an effective temperature, Teff < T, at slow switching but approaches room temperature, T, at fast switching. For each switching rate, we quantify how far the system is from equilibrium by measuring deviation from a detailed balance like relation and the net circulation of flux present in phase-space. Both analysis suggest equilibrium condition are met at high switching. [ABSTRACT FROM AUTHOR]

Alternating current (ac) losses in conductor-on-rounded-core (CORC) cables of YBCO high-temperature superconducting (HTS) tapes are a significant challenge in HTS power applications. This study employs two finite element analysis (FEA) models to investigate the contributions from different ac loss components and provide approaches for reducing ac losses in cables. An FEA model based on the T-A formulation treats the cross section of thin superconducting layers as 1D lines and, therefore, only can predict the ac loss generated by the perpendicular magnetic field. In contrast, the model based on H-formulation can be performed on the actual 2D rectangular cross section HTS tapes to provide the total ac losses generated by magnetic fluxes penetrating from both the edges and surfaces of HTS tapes, although this model requires more computing time and memory. The 1D and 2D simulation models were validated by cross comparing the results from both models and by comparing sub-section and full cross section models. Subsequently, two models relate cable design and operational parameters to the surface and edge losses of a two-layer CORC cable by considering the (1) relative contributions of edge and surface losses to the overall ac losses; (2) effect of the current distribution between inner and outer HTS layers on ac losses; (3) impact of the tape alignment on ac losses in each HTS layer; (4) influence of the thickness of HTS layers on ac losses; (5) effect of size and number of inter-tape gaps on ac losses; and (6) contribution frequency on the ac losses. The research results given in this paper are therefore not only valuable to suggest strategies for reducing ac loss in multi-layer cables but also for developing more accurate and effective methods to calculate ac loss in CORC HTS cables. [ABSTRACT FROM AUTHOR]

The functionality of many polymeric materials depends on their glass transition temperatures (Tg). In computer simulations, Tg is often calculated from the gradual change in macroscopic properties. Precise determination of this change depends on the fitting protocols. We previously proposed a robust data-driven approach to determine Tg from the molecular dynamics simulation data of a coarse-grained semiflexible polymer model. In contrast to the global macroscopic properties, our method relies on high-resolution microscopic details. Here, we demonstrate the generality of our approach by using various dimensionality reduction and clustering methods and apply it to an atomistic model of acrylic polymers. Our study reveals the explicit contribution of the side chain and backbone residues in influencing the determination of the glass transition temperature. [ABSTRACT FROM AUTHOR]

We propose a generalization of the stochastic resetting mechanism for a Brownian particle diffusing in a one-dimensional periodic potential: randomly in time, the particle gets reset at the bottom of the potential well it was in. Numerical simulations show that in mirror asymmetric potentials, stochastic resetting rectifies the particle's dynamics, with a maximum drift speed for an optimal average resetting time. Accordingly, an unbiased Brownian tracer diffusing on an asymmetric substrate can rectify its motion by adopting an adaptive stop-and-go strategy. Our proposed ratchet mechanism can model the directed autonomous motion of molecular motors and micro-organisms. [ABSTRACT FROM AUTHOR]

Stochastic differential equations (SDE) are a powerful tool to model biological regulatory processes with intrinsic and extrinsic noise. However, numerical simulations of SDE models may be problematic if the values of noise terms are negative and large, which is not realistic for biological systems since the molecular copy numbers or protein concentrations should be non-negative. To address this issue, we propose the composite Patankar-Euler methods to obtain positive simulations of SDE models. A SDE model is separated into three parts, namely, the positive-valued drift terms, negative-valued drift terms, and diffusion terms. We first propose the deterministic Patankar-Euler method to avoid negative solutions generated from the negative-valued drift terms. The stochastic Patankar-Euler method is designed to avoid negative solutions generated from both the negative-valued drift terms and diffusion terms. These Patankar-Euler methods have the strong convergence order of a half. The composite Patankar-Euler methods are the combinations of the explicit Euler method, deterministic Patankar-Euler method, and stochastic Patankar-Euler method. Three SDE system models are used to examine the effectiveness, accuracy, and convergence properties of the composite Patankar-Euler methods. Numerical results suggest that the composite Patankar-Euler methods are effective methods to ensure positive simulations when any appropriate stepsize is used. [ABSTRACT FROM AUTHOR]

In this paper, we devise a pentamode metamaterial plate exhibiting topological characteristics. By organizing pentamode metamaterial structural elements, topological boundary states are attained, effectively safeguarding propagation of elastic waves. Moreover, based on the numerical simulation model, we employ a polymer to fabricate a macro-scale specimen via additive manufacturing. Through assessing the vibrational response of the sample, we corroborate its topological attributes in governing elastic wave transmission. This discovery paves the way for a novel approach to manipulating acoustic/elastic waves employing pentamode metamaterials. [ABSTRACT FROM AUTHOR]

Asphaltenes represent a novel class of carbon nanofillers that are of potential interest for many applications, including polymer nanocomposites, solar cells, and domestic heat storage devices. In this work, we developed a realistic coarse-grained Martini model that was refined against the thermodynamic data extracted from atomistic simulations. This allowed us to explore the aggregation behavior of thousands of asphaltene molecules in liquid paraffin on a microsecond time scale. Our computational findings show that native asphaltenes with aliphatic side groups form small clusters that are uniformly distributed in paraffin. The chemical modification of asphaltenes via cutting off their aliphatic periphery changes their aggregation behavior: modified asphaltenes form extended stacks whose size increases with asphaltene concentration. At a certain large concentration (44 mol. %), the stacks of modified asphaltenes partly overlap, leading to the formation of large, disordered super-aggregates. Importantly, the size of such super-aggregates increases with the simulation box due to phase separation in the paraffin–asphaltene system. The mobility of native asphaltenes is systematically lower than that of their modified counterparts since the aliphatic side groups mix with paraffin chains, slowing down the diffusion of native asphaltenes. We also show that diffusion coefficients of asphaltenes are not very sensitive to the system size: enlarging the simulation box results in some increase in diffusion coefficients, with the effect being less pronounced at high asphaltene concentrations. Overall, our findings provide valuable insight into the aggregation behavior of asphaltenes on spatial and time scales that are normally beyond the scales accessible for atomistic simulations. [ABSTRACT FROM AUTHOR]

Forward flux sampling (FFS) is a path sampling technique widely used in computer simulations of crystal nucleation from the melt. In such studies, the order parameter underpinning the progress of the FFS algorithm is often the size of the largest crystalline nucleus. In this work, we investigate the effects of two computational aspects of FFS simulations, using the prototypical Lennard-Jones liquid as our computational test bed. First, we quantify the impact of the positioning of the liquid basin and first interface in the space of the order parameter. In particular, we demonstrate that these choices are key to ensuring the consistency of the FFS results. Second, we focus on the frequently encountered scenario where the population of crystalline nuclei is such that there are multiple clusters of size comparable to the largest one. We demonstrate the contribution of clusters other than the largest cluster to the initial flux; however, we also show that they can be safely ignored for the purposes of converging a full FFS calculation. We also investigate the impact of different clusters merging, a process that appears to be facilitated by substantial spatial correlations—at least at the supercooling considered here. Importantly, all of our results have been obtained as a function of system size, thus contributing to the ongoing discussion on the impact of finite size effects on simulations of crystal nucleation. Overall, this work either provides or justifies several practical guidelines for performing FFS simulations that can also be applied to more complex and/or computationally expensive models. [ABSTRACT FROM AUTHOR]

We explore the relationship between a machine-learned structural quantity (softness) and excess entropy in simulations of supercooled liquids. Excess entropy is known to scale well the dynamical properties of liquids, but this quasi-universal scaling is known to breakdown in supercooled and glassy regimes. Using numerical simulations, we test whether a local form of the excess entropy can lead to predictions similar to those made by softness, such as the strong correlation with particles' tendency to rearrange. In addition, we explore leveraging softness to compute excess entropy in the traditional fashion over softness groupings. Our results show that the excess entropy computed over softness-binned groupings is correlated with activation barriers to rearrangement. [ABSTRACT FROM AUTHOR]

Explicit and implicit size effects in computer simulations result from considering systems with a fixed number of particles and periodic boundary conditions, respectively. We investigate these effects in the relation D*(L) = A(L) exp(α(L)s2(L)) between reduced self-diffusion coefficient D*(L) and two-body excess entropy s2(L) for prototypical simple-liquid systems of linear size L. To this aim, we introduce and validate a finite-size two-body excess entropy integral equation. Our analytical arguments and simulation results show that s2(L) exhibits a linear scaling with 1/L. Since D*(L) displays a similar behavior, we show that the parameters A(L) and α(L) are also linearly proportional to 1/L. By extrapolating to the thermodynamic limit, we report the coefficients A∞ = 0.048 ± 0.001 and α∞ = 1.000 ± 0.013 that agree well with the universal values available in the literature [M. Dzugutov, Nature 381, 137–139 (1996)]. Finally, we find a power law relation between the scaling coefficients for D*(L) and s2(L), suggesting a constant viscosity-to-entropy ratio. [ABSTRACT FROM AUTHOR]

We investigate the effect of pressure on the carbon dioxide (CO2) hydrate–water interfacial free energy along its dissociation line using advanced computer simulation techniques. In previous works, we have determined the interfacial energy of the hydrate at 400 bars using the TIP4P/Ice and TraPPE molecular models for water and CO2, respectively, in combination with two different extensions of the Mold Integration technique [J. Colloid Interface Sci. 623, 354 (2022) and J. Chem. Phys. 157, 134709 (2022)]. Results obtained from computer simulation, 29(2) and 30(2) mJ/m2, are found to be in excellent agreement with the only two measurements that exist in the literature, 28(6) mJ/m2 determined by Uchida et al. [J. Phys. Chem. B 106, 8202 (2002)] and 30(3) mJ/m2 determined by Anderson et al. [J. Phys. Chem. B 107, 3507 (2002)]. Since the experiments do not allow to obtain the variation of the interfacial energy along the dissociation line of the hydrate, we extend our previous studies to quantify the effect of pressure on the interfacial energy at different pressures. Our results suggest that there exists a correlation between the interfacial free energy values and the pressure, i.e., it decreases with the pressure between 100 and 1000 bars. We expect that the combination of reliable molecular models and advanced simulation techniques could help to improve our knowledge of the thermodynamic parameters that control the interfacial free energy of hydrates from a molecular perspective. [ABSTRACT FROM AUTHOR]

When a shock wave impacts a roughened metal/gas interface, metal ejecta particles emit and transport in the gas. The exchanges of momentum and energy between ejecta particles and the gas occur. If active metal particles transport in the reactive gas, the heat released by a chemical reaction could change these exchanges. In this paper, we use numerical simulations to study solid cerium ejecta transporting in a vacuum, and in non-reactive and reactive gases. In vacuum, the emitted ejecta could self-similarly expand neglecting the particle interaction. In the non-reactive gas (He), ejecta particles slow down by the gas resistance and have the exchanges of momentum and energy with the gas. In the reactive gas ( D 2 ), the ejecta particles also slow down. The exothermic reaction could induce the temperature rise of the ejecta and the gas, which could induce changes in physical property values of the gas after the shock wave and the velocity of the shock wave. The numerical result shows that the maximum temperature of the ejecta may appear in the middle of the mixture zone, which may result from the ejecta temperature being controlled by two competitive effects. Furthermore, the maximum ejecta temperature increases rapidly in the beginning and then becomes steady. Finally, the ejecta with a different initial size distribution is investigated. The ejecta with a smaller maximum size has a larger maximum particle temperature, a larger gas temperature after the shock wave, and a larger chemical reaction function of the ejecta at the same moment. [ABSTRACT FROM AUTHOR]

The non-specular reflection scenario is considered important for many practical applications of gratings because this regime corresponds to the maximum efficiency of diffraction. Retroreflection is a particular case of a non-specular scenario when a grating returns a large portion of the incident light back to its source. We propose a detailed quasi-optic (microwave) experimental study of the retroreflection phenomenon in dielectric metasurfaces. Our study is supplemented by an analytical description and full-wave numerical simulation. The experimental sample of the metasurface is constructed as an array of disk-shaped low-loss ceramic resonators inserted in a host with air-like material properties. To ensure efficient reflection, the metasurface is coated on one side with a metallic foil. The conditions of retroreflection for any direction and polarization of an incident wave are demonstrated in both far-field and near-field experiments. The main contribution to the non-specular reflection of the Mie-type (HE 11) mode of the disk-shaped resonators forming the metasurface is revealed. The high efficiency of retroreflection in both TE (transverse electric) and TM (transverse magnetic) polarizations allows us to consider our metasurface as a prototype of planar grating rulers for high-precision displacement measurements. [ABSTRACT FROM AUTHOR]